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NATURE AT WORK: ONGOING SAGA OF EVOLUTION

Publication of The National Academy of Sciences, India

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CONTENTS Title

Page No.

Foreword Preface

v vii

Prof. Asis Datta, President, The National Academy of Sciences, India

Legacy Continuum 1.

The descent of humans and the Darwinian unification of all life P. Dayanandan

2.

Ida: A link to human evolution V.P. Sharma

21

3.

Darwin’s theory of evolution: Survival of nature’s fit! Veena Tandon and Gaurangi Maitra

33

4.

The life and research of JBS Haldane in India with special reference to Charles Darwin Krishna R. Dronamraju

5.

Charles Darwin: A driving force for humanity toward agnosticism Amit Sharma

1

51 59

Viruses, Microbes and Fungi 6.

Phylogeographic evolution of plant viruses Anupam Varma and Shelly Praveen

75

7.

Evolution of HIV-1 in India Pradeep Seth

93

8.

Darwin and microbial evolution T.K. Adhya and M. Patra

9.

Evolutionary relationships among cyanobacteria, algae and plants: Revisited in the light of Darwinism Radha Prasanna and B.D. Kaushik

10.

Biodiversity, phylogeny and evolution of fungi C. Manoharachari, I.K. Kunwar and S. Vishnuvardhan Reddy

103

119 141

Insects: Evolution in Action 11.

The origin of reproductive isolating mechanisms is an important event in the process of speciation: Evidences from Drosophila B.N. Singh

159

12.

Adaptive radiation and insects V.V. Ramamurthy and Asha Gaur

175

13.

Insights from mosquito evolution: Patterns, tempo and speciation Karamjit Singh Rai

197

14.

The saga of pollination biology Rajesh Tandon and H.Y. Mohan Ram

219

Genomics 15.

Darwinian evolution and post developments in genomics Arun Kumar Sharma

16.

Pathogen pressure and molecular evolutionary genetics of innate immunity genes in humans Partha P. Majumder

241

249

Unique Case Studies 17.

Macroevolution in relation to the drift models of the Indian plate Ashok Sahni and R.S. Loyal

18.

Testing the melanism-desiccation hypothesis: A case study in Darwinian evolution Ravi Parkash

279

Origin and evolution of human malaria parasite, P. falciparum and P. vivax Nidhi Datta and V.S. Chauhan

307

19.

267

20.

Evolutionary trends in soil-inhabiting Mahlaqa Choudhary and M. Shamim Jairajpuri

21.

Evolution of the cerebral cortex in amniotes: Anatomical consideration of neuronal types U.C. Srivastava and R.C. Maurya

329

Medicinal and aromatic plants: A case example of evolving secondary metabolome and biochemical pathway diversity Suman P.S. Khanuja, Tripta Jhang and Ajit Kumar Shasany

355

Conservation of Himalayan bioresources: An ecological, economical and evolutionary perspective Lok Man S. Palni and Ranbeer S. Rawal

369

22.

23.

Color Images Section

319

395

Foreword Charles Robert Darwin was born on 12th February, 1809 in Shrewsbury, England. Darwin shares his birthday with U.S. President Abraham Lincoln. Both were crusaders against slavery: Darwin disliked slavery and Lincoln abolished it. Darwin was a born naturalist and showed keen interest in nature from the very beginning. A breakthrough came when he was selected as a naturalist on the H.M.S. Beagle ship. His five year voyage on the Beagle started in 1931 and was completed in 1936. This was followed by publication of his research findings that challenged creationist views of the church. Darwin conducted a study of fossils and geological records and concluded rightly, that all life forms emerged over millions of years of evolution through the force of natural selection. In 1959 Darwin published his work on evolution in a book titled “On the Origin of Species by Means of Natural Selection or the Preservation of Favored Races”. The book was received as a scientific bomb shell and has since changed the human understanding of life forever. Today Darwin’s ideas on evolution provide foundation to modern biology. Darwin died of a heart attack on the 19th April 1882 and was buried in Westminster Abbey near the grave of Sir Isaac Newton. The scientific community is celebrating Darwin’s bicentenary worldwide in honor of his ingenuity, scientific thought, conviction and courage. Coinciding with the bicentenary celebrations are three major discoveries in paleontology, namely Darwinius masillae from Germany, skeleton of winged Dinosaur from China and fossilized Dinosaur eggs from India. The National Academy of Sciences, India (in short NASI) at Allahabad is paying tribute to British naturalist Charles Darwin by compilation of articles titled “Nature at Work: Ongoing Saga of Evolution”. Twenty three contributory articles bring out many facets of evolution and human understanding in this book. Articles begin with the Darwin’s legacy of the descent of man, ‘Ida’ the link to human evolution, theory of evolution, Haldane in India, and agnosticism. The second section describes the evolution of microbes, viruses and fungi affecting health and environment worldwide. Next section deals with the evolution of insects for understanding basic biology, adaptations, speciation, and interplaying with plants in pollination. The section on Genomics brings out the post-Darwinian developments in biology providing proof of unification at the molecular level and the discoveries of the cause of many genetic disorders. Finally there are seven unique case studies representing various facets of macro and micro Darwinian evolution taking examples from malaria, nematodes, amniotes, v

and implications for health and well being, hunger and food, bio-resources and conservation of biodiversity. In summary the book brings out the universality of Darwin’s concept of evolution ending in unification of life without exception from gross to molecular basis of the “Tree of Life”, a continuum. Many friends have been of great help in the preparation of this book. I wish to acknowledge the help and suggestions inter alia, 2009 Council of the NASI, Prof. M.G.K. Menon, Prof. H.Y. Mohan Ram, Prof. K.S. Rai, Prof. Anupam Varma, Dr. Amit Sharma, Prof. Veena Tandon, Prof. P. Dayanandan, Prof. R.C. Sobti, Dr. Mrs. Manju Sharma, and of course all the authors and co-authors for their excellent work on evolution. I am particularly grateful to the team of Springer India Pvt. Ltd. for their commitment and hard work that made it possible to bring out this excellent book on Darwin’s bicentenary. Finally, on my behalf and the NASI, I wish to thank Prof. Ananda Chakrabarty, distinguished Professor at the University of Illinois College of Medicine at Chicago, for the release of this book on 14th December 2009 during the 79th Annual Session of the Academy hosted by Calcutta University, Kolkata. Vinod P. Sharma CRDT, IIT, Delhi - 110016 Dated: 17th October, 2009

vi

Preface It is a pleasure that the National Academy of Sciences, India (NASI) Allahabad is bringing out a book titled “The Nature at Work: Ongoing Saga of Evolution” to celebrate bicentenary of Charles Robert Darwin. The book is edited by Dr. V.P. Sharma, former President, NASI. Charles Darwin was an English naturalist who realized and presented compelling evidences that all species of life have developed over time from common ancestors. Darwin’s scientific discoveries are the unifying theories of the life sciences. The theory of evolution really does explain everything in biology. The phenomena that Darwin understood in broad brush strokes can now be accounted for in the precise language of DNA. He established himself as an eminent geologist/biologist through his observations, theories and ideas and became famous as a popular author. This book is primarily for those who want to understand various theories of Charles Darwin. We have selected the most important parts of his writings and have added learned annotations. These annotations are highly precious and useful, especially for academics. This book is divided into five themes each clearly written by the eminent dignitaries/scientists of India. The text is well written and factual without being overwhelming. I found the information very interesting and well presented. We desire to express our gratitude to all the contributors who were kind enough to provide us relevant information on highly specialized areas of modern understanding of evolution and unification of life. I also believe that the book would provide an impression of his theories along with some new ideas which will serve as an inspiration and challenge for the professionals and enthusiast of science, young and old alike. A pressus book for personal possession, the libraries and an important item of gift of lasting value. Asis Datta President, NASI, New Delhi Dated: 14th October, 2009

vii

1 The descent of humans and the Darwinian unification of all life P. Dayanandan Department of Botany, Madras Christian College, 1/2 First Cross, MES Road, Tambaram, Chennai - 600 059 [email protected]

Abstract: The biological revolution that Darwin initiated has given us a view of an earth that was once devoid of life and where life originated and evolved from simpler pre-existing forms over immense periods of time. Darwin saw human beings as an integral part of this evolutionary history. How, when and where life originated remains an inscrutable challenge to science. However, discoveries in every branch of biology since the time of Darwin have affirmed the essential unity of life, including the 30 million or more extant species and more than 600 million extinct species. Darwin’s graphic representation of relationships between organisms is now employed to construct phylogenetic trees at all levels of biological organization. A Neanderthal fossil was the only hominin remain known at the time of Darwin. Today paleoanthropologists work with more than 20 species of hominins. The study of these fossil ancestors combined with the molecular dating techniques based on the analysis of mutations in mitochondrial and Y-chromosomal DNA have vindicated Darwin’s worldview of the origin of humans in Africa, as well as his suggestion that the great apes are the closest living ancestors of Homo sapiens. The discovery that all human beings on earth are descendants of one woman, the African ‘Eve’ who lived not more than 200,000 years ago has extended the Darwinian biological worldview into a unifying philosophical perspective. It is now possible to determine the mitochondrial and Y-chromosomal branch (haplogroup) of any human being with comparative ease. This helps in tracing the possible time and route of migration of our ancestors. The emerging consensus that our ancestors left Africa as recently as 70,000 years ago has profound implications for history, culture, linguistics, psychology and human predicament. The unification of all life, including human life is perhaps the most enduring contribution of Darwin’s evolutionary theory. Human beings are yet to fully comprehend the significance of this unification. Perhaps there is a lesson in Darwinism for how we humans should deal with each other and treat other life and nature with which we have an organic and primeval connection. Keywords: African ‘Eve’, Darwin, Evolution, Grand unification, Haplogroups, Human phylogeny, Mitochondrial DNA, Out of Africa, Tree of life, Y-chromosome

V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

2

Nature at work: Ongoing saga of evolution

Introduction One hundred and fifty years ago Darwin concluded the Origin of Species with his magnificent view of life on earth as one of organic relationship developed over immense time scales from one or a few forms of life: “There is grandeur in this view of life .... from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”1 Charles Wallace certainly shared an identical and independently developed evolutionary view of life. However, Wallace could not reconcile himself with Darwin’s views on the origin of human beings and how natural selection could account for the mental capacities and moral sensibilities of humans. Darwin formulated his theory based on extensive field work, meticulous observations and documentation and relentlessly pursued his views for nearly 50 years from the beginning of his exploration on the Beagle. Meanwhile the Origin of Species, first published in 1859, went through six editions. In the Origin of Species all that Darwin revealed about human evolution was this cryptic statement: “light will be thrown on the origin of man and his history.” Four years later in 1863, Thomas Huxley, who was a friend and ardent supporter of Darwin, applied the concept of evolution by natural selection to humans in his book Evidence as to Man’s Place in Nature.2 In his 1871 Descent of Man, the second most influential of his numerous publications, Darwin revealed that human beings too, were an unequivocal product of evolution.3 This in essence was a grand unification of all life. Implicit in the evolutionary theory is the still grander unification of life with nonliving matter. The origin of life was an abominable mystery then, and it continues to be no less a daunting challenge today in spite of the 1953 Miller-Urey experiment.3,4 During the past 150 years the best of biology has provided answers to the two fundamental questions that Darwin struggled with, namely the mechanism of inheritance and the process by which heritable variations occur. In turn biologists have come to assert with Dobzhansky that: “Nothing in biology makes sense, except in the light of evolution.”5 In this chapter we focus on how science has updated this extraordinary story of life on earth and the place and history of the human species; a story that was first narrated so eloquently by Darwin. In essence this updated story tells us that: life has a history measured in millions and billions of years; all species have descended in a branching pattern from common ancestors; populations can change over time and evolve into species; biodiversity is a product of evolution; all life, including the estimated 30 million living species and 600 million extinct species are related to each other; human beings who share some 500 genes with all living things are genetically related to all other life; modern humans evolved as recently as 250,000 to 200,000 years ago and all people living today share common descent from one woman, the ‘most recent maternal common ancestor’, who lived perhaps as recently as 200,000

The descent of humans and the Darwinian unification of all life

3

years ago. There is indeed grandeur in this view of life. Perhaps there can be no better tribute to Darwin in this bicentenary year than what paleoanthropologists and human evolutionary biologists and molecular geneticists are accomplishing to unravel human origins and their migratory routes by peering into fossil bones and DNA of chromosomes and mitochondria.

Darwin’s trees and unification of life Darwin made the first attempts at drawing ‘tree of life’ diagrams that initiated a powerful method of visualizing the very concept of evolution. As early as 1837/1838 Darwin drew trees (Figs.1–3) to clarify to himself the branching pattern of evolutionary divergence and extinction of species. Twenty years later another sketch of a ‘tree of life’ was the only illustration that appeared in the Origin of Species (Fig. 4). As the pre-Darwinian artificial systems of classification were replaced by classifications based on explicitly evolutionary principles, a variety of phylogenetic trees were constructed. As the available characters expanded from morphological and anatomical to biochemical and molecular data, sophisticated analytical tools such as computer assisted statistical methods of parsimony, maximum likelihood, least squares, neighbor-joining and Bayesian inference are now used in cladistics

Figures 1–3. Darwin drew these diagrams 20 years before the publication of the Origin of Species. In Figures 1 and 2 the branches represent living species and the dotted lines the extinct ancestors. Darwin noted that this tree of life should perhaps be “called the coral of life” with dead branches representing transitional forms that cannot be seen. Darwin’s comments for Figure 3 emphasized the importance of the extinction of species: “I think case must be that one generation then should be as many living as now. To do this and to have many species in same genus (as is) requires extinction. Thus between A and B immense gap of relation. C and B the finest gradation, B and D rather greater distinction” (From Darwin’s Notebook B: Transmutation of species, 1837–1838. http://darwin-online.org.uk/)

4

Nature at work: Ongoing saga of evolution

Figure 4. This diagram of the divergence of taxa is the only diagram that appeared in all six editions of the Origin of Species in the chapter on ‘Natural Selection’. The branching trees were used to explain how eleven species (A–L) of a genus can evolve and produce living lineages (A and I). Species F has remained unaltered as a living fossil. All other lineages have gone extinct. Darwin’s concept of evolutionary timescales was immense. He wrote: “The intervals between the horizontal lines in the diagram may represent each a thousand generations; but it would have been better if each had represented ten thousand generations”

and molecular systematics to construct evermore instructive trees. The legacy of Darwin’s “ever branching and beautiful ramifications” is all too evident in the new generation of trees of life such as the hyperbolic and cladogenetic trees and trees based on genome size.6 All modern phylogenetic trees of life, as the one shown in Figure 5, stand testimony to Darwin’s grand unification of all life. Trees such as this are now constructed as specialists working on various groups of organisms cooperate and pool their findings based on classical and molecular data. Darwin’s basic idea of branches diverging from common ancestors characterizes all such trees. In Figure 5 all life is shown to emerge from a common ancestor that first gave rise to Bacteria and the common ancestor of Archaea and Eucarya. The common ancestor of plants, protists, fungi and animals lived in the distant past. Plants share a more recent common ancestor with the characean green algae. Surprisingly, recent studies reveal that fungi and animals shared a common ancestor and hence fungi are more closely related to animals than plants.

The descent of humans and the Darwinian unification of all life

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Figure 5. Phylogeny of living organisms including major endosymbiotic events. (Courtesy: Dr. J. Peter Gogarten, Department of Molecular and Cell Biology, University of Connecticut)

Most biologists now consider that endosymbiosis7 was a powerful mechanism responsible for the evolution of some major groups during early periods. Darwin, of course, was not aware of this evolutionary force. The diversification of all eukaryotes became possible only after a common ancestor of Eucarya acquired a Proteobacterium-like cell as the mitochondrial symbiont. The acquisition of cyanobacterial photosynthetic endosymbionts was responsible for further evolution and diversification of protists and plants. Interestingly, green and red algal cells became secondary plastids in at least six different endosymbiotic episodes. We now have a view of life where Darwin’s unification is seen to be further fortified by endosymbiotic exchanges that unite many millions of species, including humans. In effect, all eukaryotes are chimeras. In a surprising historical twist, a billion years after our ancestral eukaryotes acquired mitochondria, scientists are now probing the DNA of these bacteria-turned-mitochondria to trace human origins and the routes of migration from the African homeland.

Africa and the great apes Darwin looked towards Africa for the progenitors of humans. In his 1871 Descent of Man Darwin reasoned: in any great region living species are closely related to extinct forms; chimpanzee and gorilla are the nearest allies of Homo sapiens;

6

Nature at work: Ongoing saga of evolution

Africa is where these great apes are living today; Africa must have been formerly inhabited by extinct apes related to the chimpanzee and gorilla; therefore “it is somewhat more probable that our early progenitors lived on the African continent than elsewhere.”8 The only human ancestral fossil known when Darwin published the Descent of Man was a Neanderthal skull discovered in 1856 in the Neander Valley, Germany. Some earlier finds from Belgium were later identified as Neanderthal fossils. Darwin died in 1882. Later discoveries confirmed that Neanderthals were indeed members of human lineage and they were once widespread in Europe. This prompted a search for fossil hominins leading to the discovery of Homo erectus in Java (1890) and China (1920s) and Australopithecus africanus in Zambia (1924). Since the 1960s when Louis and Mary Leakey made initial discoveries at Olduvai in Northern Tanzania, increasingly abundant fossils are being unearthed. Darwin would not be surprised if he were to see this array of fossils linking modern humans to ancestral forms in Africa. With more than 20 species of hominins already described and more that are likely to be unearthed, Darwin can have a hearty laugh at his caricature as a missing link! It is of interest to learn that recent molecular studies of hominoids (humans, gibbons, and the great apes - orangutan, chimpanzee and gorilla) have led to reassessment of affinities and proposals for new classification schemes.9 Indeed, some have argued for considering the chimp (Pan) as a member of the genus Homo. Studies on single nucleotide polymorphism reveal that human DNA is about 98.4% identical to that of chimpanzees. In traditional classification schemes only humans and their fossil ancestors are included in the family Hominidae and are referred to as hominids. The discovery of closer genetic affinity between humans and chimps has broadened the concept of hominids to include lineages of humans and the great apes (chimps, gorillas and orangutans) as members of the family Hominidae. The lineages of humans and the African great apes (but not orangutans) are all members of a subfamily Homininae. In this new classification scheme humans (Homo) and related bipedal fossil genera in human lineage such as Ardipithecus, Australopithecus, Paranthropus and Kenyanthropus, and possibly the early genera Sahelanthropus and Orrorin are members of the tribe Hominini, hence the common name hominins. Human beings are members of the primates group. In this bicentenary year of Darwin a 47 million-year-old fossil, Darwinius masillae, nicknamed Ida, is on display and reveals the deep ancestry of humans tracing all the way back to prosimians such as lemurs (See chapter 2 by Prof. V.P. Sharma in this volume). As shown in Figure 6 primate evolution began about 55 million years ago (mya), in early Eocene epoch. Humans and apes are tailless and share similar brain and body organization as well as complex social life. Several fossils collectively referred to as Proconsul that lived 27–17 mya in Africa and presumed to be early apes or their ancestors suggest that the Old World monkeys and the apes diverged from

The descent of humans and the Darwinian unification of all life

7

a common ancestor some 20-18 mya, in the early Miocene epoch. It was during the terminal Miocene epoch that the ape lineages separated from each other and the evolution of hominins accelerated. Molecular studies of hominoids suggest that the gibbons (Family Hylobatidae) and great apes (Family Hominidae) lineages diverged about 18–12 mya. The African great ape hominid lineage diverged from the orangutan hominid lineage about 12 mya. The Indian fossil Ramapithecus is considered to be an early genus in orangutan ancestry. Some believe that Pierolapithecus catalaunicus that lived about 13 mya might have been a common ancestor of the great apes and humans. The fossils Nakalipithecus from Kenya and Ouranopithecus from Greece appear to resemble the common ancestor of gorilla, chimpanzees and

Figure 6. A simplified family tree of primate evolution

humans. The human lineage emerged between 8 and 5 mya when first the gorilla and then the chimpanzee lineages separated from the hominin tribe. The earliest hominins might have been Sahelanthropus (7 mya) and Orrorin (6 mya). While chimpanzees and humans are closest living relatives, humans did not evolve from extant chimpanzees; both lineages had evolved independently over the past 6–7 million years. Further discussion in this chapter is devoted to a brief summary of evolution of the hominins leading to the emergence of modern humans Homo sapiens.

Descent of humans Although primates were present in Africa, Eurasia and the New World, the evolution of hominins was confined to Africa. The idea of a separate creation of human ‘races’ – known as polygeny – with its racist overtones is now discredited.

8

Nature at work: Ongoing saga of evolution

Some anthropologists still subscribe to a related concept of multiregionalism according to which speciation of different ‘races’ occurred after human-like species migrated out of Africa and settled in different regions of the world.10 We follow the emerging consensus views of ‘monogenesis’ and ‘Out of Africa’ according to which human evolution, including the emergence of anatomically modern humans (H. sapiens) occurred in Africa. During this period a few species of Homo (H. ergaster, H. erectus, H. antecessor and H. heidelbergensis) did move out of Africa within the last 2 million years but did not contribute to any further evolution of humans. The Out of Africa model is synonymous with the Recent Single-Origin Hypothesis, Replacement Hypothesis and Recent African Origin. Our own species evolved in Africa and a small group migrated out of Africa and colonized the rest of the world. The tree shown in Figure 7 is a graphic representation of the evolutionary relationship among the hominin fossils described so far. Paleoanthropology is one of the most active fields of research in biology, and specialists offer different interpretations of evolutionary relationships.11 Taxonomy of fossil hominins varies as some specialists tend to split and others to lump the different taxa. The 7 million-year-old Sahelanthropus tchadensis (Toumai), first described in 2001 from Chad, might have been a bipedal hominin. Some claim this to be a possible common ancestor of human and chimpanzee lineages. Our own genus, Homo, appeared about 5 million years later. Three other genera are known from Africa during the in-between period, namely Orrorin (6 mya) followed by Ardipithecus (5.5–4.4 mya) and Australopithecus (4–2 mya). A. afarensis, first described from Hadar, Ethiopia in 1973 might have been the ancestor of our genus Homo. Homo habilis, first discovered in 1962 in the Olduvai Gorge in Tanzania, lived from 2.4–1.4 mya in East and South Africa, and closely resembled Australopithecus. Nicknamed ‘handy man’, H. habilis was the first hominin to have made and used stone tools known as ‘choppers’ in the early Paleolithic period, more than 2 mya. Evolution of hominins continued in Africa eventually resulting in the emergence of anatomically modern H. sapiens, about 200,000 years ago. Yet H. sapiens was not the first hominin to leave Africa. H. ergaster (1.8 mya) closely followed by H. erectus and later H. antecessor and H. heidelbergensis (=H. rhodesiensis) left Africa bringing the Paleolithic technology to Eurasia. H. heidelbergensis and H. neanderthalensis with a thick skull, prominent brow ridges and non-prominent chin but with brain size (1200–1400 cc) similar to modern humans are sometimes referred to as “archaic H. sapiens”. Darwin’s insightful prediction that our earliest progenitors would be found in Africa turned out to be true. It might surprise us that in a matter of 4 million years the continent witnessed the rapid evolution of four genera (Australopithecus, Kenyanthropus, Paranthropus and Homo) and nearly 20 species of hominins; and

The descent of humans and the Darwinian unification of all life

9

Figure 7. An interpretative tree of relationship among hominins with time-scale. The connecting lines indicate well-supported relationship between the species

more will surely be discovered. Darwin also reasoned that the absence of any human remains in older fossil strata must indicate that the evolution of humans must have occurred recently and exceptionally rapidly. Several factors seem to have influenced human evolution. Climate change that resulted in the conversion of tropical forests into woodlands and savannah grasslands might have influenced the Miocene ancestral apes to descend from trees and become bipedal, thereby changing their foraging habits and freeing their forelimbs to make tools. Ice ages during the past 2 million years might have acted as selective agents in human physiological and physical adaptations and influenced the patterns of migration as hominins moved in search of food plants and animals. Brain development and the extraordinary ability to shape tools with hands and the mutual influence between brain development and the need to respond to the changing environment have all contributed to unique human qualities such as planning, innovation, abstract thinking and symbolic behavior. It appears that during the past 10,000 years humans have been evolving 100 times faster than in the past. The Neolithic revolution, which resulted in excessive consumption of starch and milk, urbanization, poor sanitation, epidemic diseases and changing food habits all seem to have operated and continue to operate as selective agents.12 Homo neanderthalensis lived until about 30,000 years ago in Europe while the small-sized H. floresiensis, discovered in 2004 in Indonesia, might have become extinct as recently as 15,000 years ago. Since the Neanderthals and modern humans

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Nature at work: Ongoing saga of evolution

were contemporaries in parts of Europe, researchers have wondered if there were gene exchanges between them. Recently the mitochondrial DNA (mtDNA) from fossil bones of H. neanderthalensis were extracted and compared with the DNA sequence of H. sapiens. It appears that the sequences are very different and the two remained as separate species ever since they evolved from a common ancestor, some 660,000 years ago until the Neanderthals went extinct about 30,000 years ago.13 The only genus and species of hominin that is living today and the only species that ever occupied all the continents is H. sapiens. During the past 20 years molecular geneticists have revealed a remarkable story of the origin and spread of humans, a story of unification of all human beings through a bacterial endosymbiont, the mitochondrion, and recluse Y-chromosome!

Humanity unified - the mitochondrial African mother Human beings, all 6.5 billion now living and the billions more that will be added, are remarkably like each other with 99.9% genetic similarity. A mere 0.1% difference is responsible for the diversity we observe. We are not a highly variable species. This similarity is due to our recent origin in Africa and the presumed small size of the population that left Africa and colonized the rest of the globe. Within the last 20 years a remarkable and unexpected story of our ancestry has emerged and is now profoundly affecting the way we think of ourselves. In an important paper published in 1987, Cann, Stoneking and Wilson reported their analysis of mtDNA samples of 147 people from five geographic populations. Using restriction mapping techniques to detect polymorphism and parsimony methods to infer a common ancestor they came to the conclusion: “All these mtDNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonized repeatedly.”14 This ancestral woman is now popularly known as ‘African Eve’ and ‘Mitochondrial Eve’. Subsequent studies15 have confirmed the findings of Cann et al. although the estimated age of this ‘mother’ is reported to be in the range of 150,000–250,000 years before present. Since the mtDNA now found in all human mitochondria do not undergo recombination, theoretically they all can be traced back to a single root, the so-called ‘coalescent point’. This point represents the Mitochondrial Eve. The implications of these studies are: modern humans evolved in Africa; about 200,000 years ago an ancestral woman in East Africa passed on her mitochondria to her offspring; transmitted to every generation only through the female line to both sons and daughters, her mtDNA is now present in all people on earth; this woman is the matrilineal most recent common ancestor (MRCA) of all people who ever lived since then, and the more than 6 billion people who are living today in all continents, including Africa. The matrilineal MRCA (= African Eve, Mitochondrial Eve) was not the only woman living at that time in Africa. For various reasons the

The descent of humans and the Darwinian unification of all life

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mtDNAs of other women were not passed on to subsequent generations; perhaps these other women did not beget daughters or their female lineages died out. It is likely that through their sons their genes still occur in the nuclear DNA of people living today. The mtDNA of our matrilineal MRCA is found in people outside of Africa also because it was carried by her female descendants when some people left Africa about 100,000 years later to colonize all other continents.

And a Y-chromosomal African father While a mitochondrion is inherited only through the mother, the Y-chromosome is passed on to the next generation only through the father. The difference between the two is that while both men and women receive mitochondria from their mothers, the Y-chromosome is passed on only to males. As with mtDNA it is possible to trace back the root – the coalescent point – of all Y-chromosomes found in males since most of Y-chromosomal DNA (YDNA) does not recombine during meiosis. A study16 of YDNA polymorphism in a worldwide sample of men using methods similar to the analysis of mtDNA revealed that the root of the human male family tree was placed in Africa, just like the female root. However, the date of the putative patrilineal MRCA, the ‘Y-chromosomal Adam’, was just 60,000 years. Again this does not imply that there were no other men around; only that the Y-chromosome of this male MRCA is now found in all men, in all continents. The more recent date (60,000–90,000 years) for the patrilineal MRCA is explained on the basis of human sexual behavior where the variance of reproductive success is higher for men. Unlike women, who all have more equal opportunities to have children, a few men can mate with more women and pass on their genes. The Y-chromosomal lineages of men who lived before the MRCA were lost. The mitochondria of one woman and the Y-chromosomes derived later from one man in Africa were passed on to people who spread throughout Africa, and through a group that migrated out of Africa to all other people in non-African continents. One would expect greatest genetic diversity in the DNA of mitochondria, Y-chromosomes, as well as other chromosomes in Africa, as indeed is shown by several studies.17

Wandering humans and their DNA trees and haplogroups The circular mtDNA inherited through mothers and the male-specific YDNA both carry mutations that are used for understanding human origins and for constructing trees from which the geographical origin and migration of human populations could be inferred.18 Since the mutations occur at a fairly regular rate it is possible to estimate the time when populations branched off using molecular dating techniques. mtDNA and most of YDNA do not recombine and hence genes are not shuffled as they are in autosomal chromosomes. mtDNA offers the advantage of small size of only 16,569 base pairs and 37 genes. These advantages are now widely

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exploited to discover an ever increasing number of polymorphic sites. Single nucleotide polymorphism (SNP) due to point mutations can be easily identified with restriction mapping. Contemporary human populations have accumulated a large number of mutations in mtDNA since the time of Mitochondrial Eve, the MRCA.19,20 Mitochondria also possess short Hyper Variable Regions (HVR1, 2 and 3) which have rates of mutation 100 times greater than that of the nuclear genome. The sequence of nucleotides in these regions (e.g. HVR1: 16,001–16,569) can be compared with a Cambridge Reference Sequence to determine specific markers that help assign individuals to unique mitochondrial haplogroups. Haplogroups are branches on the family tree of groups of people who share a set of genetic markers. All members of a haplogroup share a marker that first appeared in the MRCA of that group. Y-chromosome polymorphism is now increasingly used to understand the origin and migration of human populations. YDNA consists of many millions of nucleotides and provides scope for examining thousands of mutations. Besides SNPs the Y-chromosomes also carry non-coding microsatellites or Short Tandem Repeat (STR) regions consisting of repetitive DNA sequences. These repetitions lead to copying errors resulting in addition or subtraction of repeat units. Each STR is designated by a DYS number (DNA Y-chromosome Segment number). Analysis of markers on YDNA provides necessary information to assign individuals to Y-chromosomal haplogroups. Mitochondrial and Y-chromosomal haplogroups

Figure 8. A simplified tree of mitochondrial haplogroups. Haplogroups L4, L5, L6 and L7 are not shown. Haplogroups M, N and R can be considered as ‘Super haplogroups’ since they have many subclades. Some of the defining markers are shown. Marker mutations may occur as SNPs in coding regions or in HVR1 and HVR2 regions. The most ancient haplogroups L0–L3 are African; only during the colonial period people with these markers have been moved to non-African continents

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are now routinely analyzed in several laboratories around the world. A number of private testing companies also analyze DNA samples and provide information on genealogies and geographic origins. The Genographic Project21 is an ambitious worldwide project undertaken by the National Geographic Society with geneticist Spencer Wells to map the human family tree and trace the migratory routes of our ancestors.22 The Y-chromosome Consortium23 at the University of Arizona carries out collaborative studies on YDNA variations and nomenclature of Y haplogroups. Family trees constructed using mitochondrial markers provide a graphic picture of deep human matrilineal ancestry (Fig. 8). Three main groups, designated by letters L, M and N, and many subgroups are known. The earliest branching of the tree occurred in Africa about 200,000 years ago when the L0/L1 split occurred somewhere in East Africa. Today L0 is widespread among the San and Mbuti people in Africa. L1 and its branch L2 are also confined to Africa. Only after M and N macrohaplogroups branched off from L3 was there any major migration of the female ancestor out of Africa. Thus the woman in whose mtDNA a mutation first occurred, to found the L3 haplogroup branch, is known as the ‘Eurasian Eve’ since her descendants were the first to move out of Africa. Today the M group derived from L3 is found in East Africa, Asia, Melanesia, Australia and the Americas. The

Figure 9. Y-chromosomal haplogroups showing the defining markers. Haplogroups A and B are African branches with most diverse lineages dating back to 60,000–50,000 years. Major haplogroups C, F and K occur in India especially as exclusive subclusters of H, L and R

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N group, also born in Africa, later migrated out of Africa and moved northwards spreading to many parts of Asia, Europe, India and the Americas. Haplogroup R that branched off from N is now found in East and West Eurasian populations, accounting for nearly 75% of the lineages. The YDNA family tree also reveals ancient splits that occurred in our male lineage in Africa (Fig. 9). Haplogroup A defined by the marker M91 is perhaps the deepest of our branches, now confined to Africa and prevalent among the Khoisan, Ethiopians and Nilotes. Haplogroup B with marker M60 is also confined to Africa mostly among the Pygmies and Hadzabe. Descendants of B with a marker M168 (‘Eurasian Adam’) were perhaps the first males to leave Africa more than 60,000 years ago. A man born to this migrant group had the marker M130 defining the haplogroup C. His descendants are considered to have moved along the coast into India, and moved beyond to Southeast Asia and finally into Australia. M130 is now found in <5% of the Indian population mostly along the coastal belt in Maharashtra, Tamil Nadu, Andhra Pradesh, Orissa and West Bengal. Thus both mtDNA and YDNA polymorphism provide information useful for tracing human migratory patterns.24

Out of Africa and into India The Indian Subcontinent was a decisive juncture in the early migration of hominins. Long before the entry of modern humans, other species of Homo had left Africa and spread to many parts of Eurasia, as attested by fossil remains and early Paleolithic stone tools. The Indian subcontinent too, had its share of early hominin migrants dating back to 2 million years.25 Oldowan tools have been found at Riwat in Soan valley in Western Punjab and in the Siwalik rocks of Himachal Pradesh. Early Acheulean stone tools in Hungsi valley in Karnataka are dated to be 350,000-years-old. Similar stone tools are also known from Attirampakkam near Chennai. Fossil remains of early hominins are rare in India; a few remains found in the Central Narmada valley are believed to be at least 500,000-year- old.26 These remains may belong to either H. erectus or H. heidelbergensis. Earliest fossil remains of modern humans are found in Africa, Middle East and Australia. The ‘Omo skull’ from Ethiopia is dated to be about 195,000-yearsold. Human remains found in Eastern Mediterranean regions and in the Qafzeh and Skuhl caves of modern Israel suggest that modern humans moved into this extended area of the African continent as early as 110,000 years ago. However, the descendants of these early settlers disappeared about 50,000 years ago. The area was then colonized by the Neanderthals and only much later by another wave of modern humans. Paleoanthropologists believe that the first wave of modern humans left Africa only about 66,000–70,000 years ago.27 The genetic diversity now found in all non-African countries is a legacy of this early group of H. sapiens

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who left Africa. After 2,000 generations the descendants have multiplied to more than 5 billion people now living in non-African countries. The Y-haplogroup C, defined by the marker M130 was the earliest clan to migrate through India into Sri Lanka, Southeast Asia and eventually Australia.28 mtDNA studies also show that the people of New Guinea and Australia belong to the M and N haplogroups that left Africa through the ‘southern coastal route’ more than 50,000 years ago.29 Although early migrants traveled through India, the oldest fossils of modern humans have been discovered so far only in Australia (50,000 years), Thailand (37,000 years) and Sri Lanka (30,000 years). The mtDNA haplogroup M that branched off from L3 about 60,000 years ago and its variants occur in nearly 30% of the Indian population. (The author of this chapter belongs to an East Eurasian subgroup M* carrying markers that first appeared some 50,000 years ago in his maternal ancestor; M* constitutes 30–50% of the gene pool in Pakistan and Northwest India.) It is well established that Africa is genetically the most diverse continent in the world, which is a reflection of nearly 250,000 to 200,000 years of accumulation of polymorphism in mtDNA as well as in nuclear genome. While no other continent can match this diversity, India appears to be the second richest region in genetic diversity. The reasons for this diversity appear to be: a) early settlement of people who first left Africa, b) subsequent entry of people at various periods from the Northeast and Northwest, c) a process of stratification of the society, and d) a countervailing process of exogamy and intermixture of various groups. Sexual selection might also have played a role in the diversity we observe. Singh, who identified 4,693 major communities and more than 50,000 small endogamous groups, described a typical Indian as a “migrant par excellence”.30 The Anthropological Survey of India recognized 418 tribal communities in India who belong to Andamanese, Austro-Asiatic, Dravidian, or Tibeto-Burman language families.31 Seventy-five of these indigenous communities have been identified by the government and described using the unfortunate label, “Primitive Tribal Groups”. Others have described them as ‘relic’ tribes implying that they were the earliest settlers. Indeed the Onges and Jarawas of the Andaman Islands share many characteristics with the Khoisan and Pygmies of Africa suggesting that they were among the earliest groups, if not the earliest, to leave Africa, traverse Indian mainland and settle in the Islands.32 Besides the tribal communities, hundreds of different caste, outcaste and religious communities live in India. During the past 10 years this rich diversity has been under intense investigation by human geneticists. Sophisticated molecular and statistical techniques are used to detect new markers and to assign people to various haplogroups, determine gene flows, and trace relationships between various communities and their past migratory history and linguistic affinities.33

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The Y-haplogroups common in India include: C with marker 130; H with the ‘Indian marker’ M69; the ‘Indian Clan’ L (M20) found in 50% of South Indian men, and different subgroups of haplogroup R. The R group defined by the marker M207 descended from the central Asian clan marker M45. Descendants of M45 populated most of Europe and North America. R1A1 (M17) that occurs in 35% of Hindi-speaking men and 10% of Dravidian-speaking men is considered as the Indo-European marker associated with the migration into India of IndoEuropean language speakers, about 10,000 years ago. Haplogroups H, L and R2 are exclusive to the Indian Subcontinent, with F* nearly so. Subgroup O3e is associated with Tibeto-Burman speakers and O2a lineage is found among AustroAsiatic speakers. The focus of this chapter is on Darwin and his unification of life. The rapidly growing field of phylogeography of mtDNA and YDNA haplogroups cannot be covered in any detail here. The brief reference to phylogeography is made in order to highlight the exciting potential it has to unify people by reminding them of their shared common ancestry. (The author belongs to haplogroup H with the marker M69 which first appeared as a mutation in his male ancestors more than 30,000 years ago, somewhere in the Middle East!) Investigation of more than 200 Indian populations34 is now shedding light on the genetic basis for ethnic diversity in India. As additional markers are added and techniques for the study and statistical analysis of polymorphism of autosomal chromosomes are developed, many questions that have puzzled classical anthropologists, historians, sociologists and linguists about the peopling of India, the biological and cultural diversity, stratification of the society, and susceptibility and resistance to diseases will be answered. The dialog between human molecular geneticists and classical scholars is likely to result in new insights and revision of cherished concepts in anthropology and history.35 A recent study has suggested that most Indians are descendants of two genetically divergent ancestral populations, the ‘Ancestral South Indians’ (ASI) and ‘Ancestral North Indians’ (ANI). The latter is genetically close to Middle Easterners, Central Asians and Europeans while the ASI lineage has no close affinity to any outside group except the ancient isolate of indigenous Andaman Islanders.36

“Light will be thrown on the origin...” Darwin answered his own visionary statement of throwing light on the origin and history of humans by writing his second famous book, Descent of Man. This completed his grand unification of the biological world, genetically and temporally. Darwin also suggested another category of unification in the human family. He was keenly interested in the origin of language and its relation to human intellect. He also explained the process of biological evolution using the evolution of language

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as a metaphor. His observation on human evolution and language was farsighted: “If we possessed a perfect pedigree of mankind, a genealogical arrangement of the races of man would afford the best classification of the various languages now spoken throughout the world”. Statistical methods that help construct human family trees are also used to construct trees of major language families, tracing historical linguistic structural relations in some cases to 20,000 years ago.37 Since the “Out of Africa” date is <100,000 years perhaps all languages, too, will be traced to their roots in Africa someday. Darwin scrupulously adhered to methods of scientific enquiry and would not entertain any place for supernatural powers in the process that led to the evolution of humans endowed with amazing “powers of observation, memory, curiosity, imagination, and reason”.38 The human species may have developed through a cold and purposeless process of evolution but Darwin was not amused by the racism and discrimination that tore apart the unity and dignity of the human species; he attributed ignorance and self-interest to such divisive attitudes.39 Darwin loathed slavery as much as his abolitionist grandparents Erasmus Darwin and Josiah Wedgwood did, almost a 100 years before him. For Darwin, abolition of slavery was the ‘highest good’ even if it entailed a war that might result in ‘a million horrid deaths’. In this bicentenary year of Darwin, two well-known Darwin scholars and editors of his book and authors of his biography – Adrian Desmond and James Moore – have suggested40 that Darwin might have found encouragement in the common descent of humans from apes as proof in support of the essential unity of all human groups and as a challenge to racist ideologies. Theodosius Dobzhansky in his book on evolution41 quoted Einstein: “The most incomprehensible thing about the world is that it is comprehensible.” The majesty of Darwin’s theory is that we now comprehend a certain unity in a world that still is mysterious in many other ways. For Darwin the unified biodiversity had a certain splendor and dignity. In concluding the Origin of Species he wrote: “When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Silurian system was deposited, they seem to me to become ennobled”.42 Darwin was acutely aware of past extinctions as a natural process. He also visualized life on earth as “an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes with various insects flirting about....and dependent on each other in so complex a manner”.42 Darwin was the great unifier of all life. Today he would be appalled to see how the human species is now the cause of the sixth major extinction of the diversity life. Perhaps he might have some insight into the puzzling predicament of a living earth now endangered by one of its own manifestations, human beings with extraordinary intellect and reasoning power. Darwin also shaped the course of science by secularizing it. Mayr pointed out that Darwin “presented 50 or 60 biological phenomena easily explained by

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Nature at work: Ongoing saga of evolution

natural selection but quite impervious to any explanation under special creation, and equally inexplicable to so-called intelligent design.43 Free from dogmas, modern science has made impressive progress in many fields since Darwin. One such achievement is the illumination of immense time scales that we are helped to comprehend. This time scale for life on earth extends to nearly 4 billion years, close to the time of the formation of the earth. Someday when scientists discover how life originated from non-living matter, Darwin’s grand biological unification will merge with the unification that physicists seek of the fundamental forces of the universe. Acknowledgements: I am grateful to Dr. V.P. Sharma for inviting to me to contribute this chapter for a book that commemorates Charles Darwin. I thank Mr. Leslie Lawrence for his patient help with creating the Figures. Thanks to Dr. J. Peter Gogarten for kind permission to use his instructive phylogenetic tree of living organisms. As always, my wife Anne, encouraged, supported and helped me in many ways during the short time I had to write this chapter.

References 1.

Darwin C (1999) In: The Origin of Species by Means of Natural Selection or The Preservation of Favoured Races in the Struggle for Life. London: Murray; 1859. Reprint New York, Bantam Books

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Glendorff N, Xu Y, Labeden B (2008) The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner, Origin and early evolution of life Edited by Dr Eugene V Koonin. Biology Direct 3:29

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Glansdorff N (2000) About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol Microbiol 38(2):177–85

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Dobzhansky TH (1973) Nothing in biology makes sense except in the light of evolution. Am Biol Teacher 35:125–129

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Wood BA, Richmond BG (2000) Human evolution: taxonomy and paleobiology. J Anat 197:19–60

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Ward P (2008) What will become of Homo sapiens? Sci Am India 4:44–49

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Serre D, Langaney A, Chech M, et al. (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2(3):E57

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Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36

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Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713

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Underhill PA, Shen P, et al. (2000) Y chromosome sequence variation and the history of human populations. Nature Genetics 26:358–361

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Tishkoff SA, et al. (2009) The genetic structure and history of Africans and African Americans. Science 324:1035–1044

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Stoneking M (2008) Human origins. The molecular perspective. EMBO Rep 9:546–550

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Behar DM, Villems R, et al. (2008) The Dawn of Human Matrilineal Diversity. Am J Hum Gen 82:1130–1140 (http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=2427203#app2)

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Gonder MK, Mortensen HM, Reed FA, de Sousa, Tishkoff SA (2006) Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages (http://mbe.oxfordjournals.org/ cgi/content/full/24/3/757)

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The National Genographic Project. (www.nationalgeographic.com/genographic)

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Wells S (2007) Deep Ancestry: Inside the Genographic Project. National Geographic Society, Washington DC; Wells S (2002) The Journey of Man: A Genetic Odyssey, Penguin Books India (P) Ltd., Delhi

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The Y-chromosome Consortium. (http://ycc.biosci.arizona.edu/)

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Oppenheimer S (2004) In: The Real Eve: Modern Man’s Journey Out of Africa. Carrol and Graff, New York

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Habib I (2001) In: Prehistor. Tulika Books, New Delhi

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Sankhayan AR (2005) New fossils of Early Stone Age man from Central Narmada Valley. Curr Sci 88:274–707

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Stanyon R, Sazzini M, Luiselli D (2009) Timing the first human migration into eastern Asia. J Biol 8:18

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Wells S: The Journey of Man, A Genetic Odyssey by Spencer. p 123–125, http://www. google.com/search?hl=en&q=Wells+S%3A+The+Journey+of+Man%2C+A+Genetic+O dyssey.+p+123%E2%80%93125&btnG=Search&aq=f&oq=&aqi=

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Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P (2007) Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA 104:8726–8730

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Singh KS (2002) In: People of India: an introduction. OUP, New Delhi

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Mandal H, Mukherjee S, Datta A (2002) India: An Illustrated Atlas of Tribal World. Anthropological Survey of India, Kolkata

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Thangaraj K, Singh L, Reddy A, Rao V, Sehgal S, Underhill P, Pierson M, Frame I, Hagelberg E (2003) Genetic Affinities of the Andaman Islanders, a vanishing human population. Curr Biol 13:86–93

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Majumder PP (2008) Genomic inferences on peopling of South Asia. Curr Opin Genet Develop 18:280–284. Krithika S, Maji S, Vasulu TS (2007) For a good review of previous publications see Molecular Genetic Perspective of Indian Populations: A Y-Chromosome Scenario. In: Anthropology Today: Trends, Scope and Applications. BhasinV, Bhasin MK (Eds.), Anthropologist Special, Kolkatta 3:385–392

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34.

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Pitchappan RM, Kavitha VJ, Wells SR (2008) Genomic Implications of Dravidian Cultural Evolution. (www.firstgreatmigrations.org/.../DR-Pitchappan-19%20JUNE%202008.doc)

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Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494

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Mindell DP (2009) Evolution in the Everyday World. Sci Am India 4:58–65

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Howard J (2006) Darwin - A Very Short Introduction. OUP, New Delhi

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Desmond AJ, Moore JR (2009) Darwin’s Sacred Cause: How a Hatred of Slavery Shaped Darwin’s Views on Human Evolution. Allen Lane, London

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2 Ida: A link to human evolution V.P. Sharma Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, New Delhi - 110016 [email protected]

Abstract: Year 2009 is being celebrated as the bicentenary of British naturalist Charles Robert Darwin’s birth as well as 150 years of his book “On the Origin of Species by Means of Natural Selection, or The Preservation of Favored Races in the Struggle for Life” in short “On the Origin of Species”. Darwin is hailed as one of the greatest scientist who put forth the theory of gradual evolution and branching of all life forms. Unfortunately, then fossil records were incomplete to produce evidence of human evolution. For 200 years paleobiologists were looking for any evidence of a transitional fossil to showcase the evolution of monkeys, apes and human. The story of Ida began in 1983 when she was collected from Messel pit in Germany by an unknown collector, and displayed in his home for 20 years before deciding to sell. The fossil Ida was preserved in nature for ages in the Germany’s Messel pit, a crater rich in Eocene Epoch fossils. Ida lived when major changes were taking place on earth, the dinosaurs had become extinct, the Himalayas were forming and a range of mammals thrived in vast jungles all over the world. Prof. Jørn Hurum of the Natural History Museum, University of Oslo, Norway bought the fossil for 1 million USD, assembled top international team of experts, studied the fossil secretly for 2 years, and satisfied themselves as to the genuineness of the fossil. Finally Prof. Jørn Hurum announced the discovery of 47 million years old fossil - a link in the evolution of monkeys, apes and man. He named the fossil “Ida” and her scientific name is Darwinius masillae (named in honor of Charles Darwin’s bicentenary). Ida will remain for long a subject of intense research and discussion almost throughout the world. The fact that all life forms have common ancestors at some point of time is a well established universal reality as unfolded by research on DNA. Keywords: Darwin, Evolution, Darwinius masillae (Ida), Paleobiology, Primate, Religion

Introduction Prof. Jørn Hurum of the Natural History Museum, University of Oslo, Norway announced the discovery of Ida - the missing link that led to the evolution of monkeys, apes and man (Ida, pronounced “ee-dah”). This breakthrough V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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announcement was well timed coinciding with the bicentenary celebrations of English naturalist Charles Darwin. It is noteworthy to mention that Darwin for the first time gathered evidence of evolution by natural selection, and said “that species change over time through the selective retention of beneficial traits, gradually evolving into new species. In this way, all species alive today are descended from common ancestors”. In November 1859 Darwin published his ground breaking theory “On the Origin of Species by Means of Natural Selection, or The Preservation of Favored Races in the Struggle for Life” in short “On the Origin of Species”.1 At that time there were major gaps in the fossil records. Darwin acknowledged that the lack of fossil evidence of the intermediate transitional fossils is a serious problem between species posed a problem, and “this was the most obvious and gravest objection which can be urged against my theory”.1 Two years later in 1861 the first transitional fossil Archaeopteryx2, 3 was discovered. Thereafter, evidence has been collected that unambiguously brings out the intermediate form in major animal groups. For example, the finding of Archaeopteryx has supported the intermediate forms between dinosaurs and birds. As Prof. Jørn Hurum explains, Darwin said a lot about transitional species and how they were missing from the geological record. Quoting Darwin he said “that if a transitional species is never found, his whole theory will be wrong”. Explaining the importance of Ida, Prof. Hurum said that “for the last 50 years we’ve gained a deeper and deeper understanding of species that show transitions between large groups of mammals. Ida is very comparable to some of the most significant fossils that have been described like Lucy,4 the Neanderthals,5 Tyrannosaurus rex6 and Archaeopteryx.3 It’s a really important specimen that will become an icon of evolution. So I think Darwin would be really happy about this specimen”.

The discovery of “Ida” Fossil Ida was unearthed in 1983 by a private fossil hunter from Grube Messel pit near Frankfurt, Germany (Fig. 1). The village Messel is located about 35 km south-east of Frankfurt and the word masilla is the name of a 9th century monastery where the fossil was found. The Messel site has yielded hundreds of superbly preserved fossils including eight species of crocodile, 20 or so snakes, more than 60 specimens of pygmy horse, more than 1,000 bats, insects with colored pigments on their wings still visible, the largest ant ever to crawl the planet, and eight fragmentary primate specimens. Messel is now UNESCOs world heritage site. At the time of Ida’s finding, the German collector (anonymous) had no idea of how valuable the fossil is. The fossil was preserved in a polyster resin and hung for 20 years in his home, and admired like the painting of Vincent Willem van Gogh. The fossil was split and sold in two parts separately; a lesser part was purchased for the private museum in Wyoming, USA. Prof. Jørn Hurum, was the first to recognize the significance of the fossil. The fossil was reassembled in 2007

Ida: A link to human evolution

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Figure 1. Left: An artist’s reconstruction of the Eocene period ecosystem shown on left side. Credit: Christopher Klein and Mark Hallett. At the upper left corner is an adapoid primate, Europolemur, a close relative of Darwinius. Right: Messel pit site in Germany-UNESCOs world heritage site. Credit: Atlantic Productions http://blogs.ngm.com/blog_central/2009/05/darwiniusand-the-real-missing-link.html

and now belongs to the Natural History Museum, University of Oslo, Norway.7 In 2006 Thomas Perner, a private collector facilitated the deal of Ida. He showed the fossil to Prof. Hurum at the annual Hamburg Fossil and Mineral Fair in Germany. Prof. Hurum was amazed at the “most beautiful fossil worldwide”. This to him looked like a blue print of human evolution. The asking price was more than $1 million (£660,000), almost 10 times the normal value of such a fossil. After 6 months of negotiations Thomas Perner brokered a $1 million (£629,000) deal of the 47 million years old fossil in a vodka bar in Hamburg. An international team of scientists headed by Prof. Hurum at the Natural History Museum have studied this fossil for 2 years before making an announcement. The fossil is named “Ida” after Prof. Jørn Hurum’s daughter who in maturity is equivalent to his 6-year-old daughter Ida. Ida’s scientific name is Darwinius masillae given in honor of English naturalist Charles Darwin. The discovery of the 95% complete ‘lemur monkey’ Ida is described by experts in detail, and their final conclusion was that Ida is completely genuine and authentic (Fig. 2). The fossil was amazing and awesome. Such a well preserved specimen has never been encountered anywhere in the world. The fossil belongs to Eocene era and Ida (she) lived in semi-tropical forest 47 million years ago. Ida was preserved in the oil shale. This shale consists of soft finely stratified rock of mud or clay and easily splits. The fossil is 95% complete and perfectly preserved. In contrast “Lucy” which was thus far the most reliable fossil evidence for direct descendent of man. Lucy was found in Ethiopia, is 3.18 million years old and only 40% complete. Ida’s fossil shows soft body outline as well as the preserved gut contents of seeds, fruits and leaf but no insects. Ida when died was a juvenile female, 6–9 months in age, 58 cm (23 inch) overall length of the body and about 24 cm (9.4 inch) tail. Ida as an adult would have weighed about 1 kg, but she was probably 60% of her adult body weight. Ida was perhaps a nocturnal with large eye holes in the skull.

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Figure 2. (Left) Dr Jens Franzen and Dr Jørn Hurum studying Ida the fossil. Photograph: Sam Peach/Atlantic Productions, and (Right) Fossil Ida: Photo credit: Atlantic Productions Ltd.

She is female as she does not have a penis bone. She has talus foot bone present in the humans. She has nails rather than the claws. Her teeth are similar to those of monkeys. Her forward facing eyes are similar to humans. This allows her 3D vision and ability to judge distances. Ida has five fingers on hands, short arms and legs. It lacks a grooming claw and fused row of teeth known as a toothcomb a characteristic feature of Lemur. It is notable to mention that Ida fossil is 20 times older than other fossils used as evidence of human evolution. Prof. Hurum said that the impact of Ida on the world of paleontology will be “somewhat like an asteroid falling down to earth”. Because Ida fossil was so complete, it was also described as a “Rosetta stone”.8 “This fossil “promised to change everything that we thought we understood about the origins of human life”.9–11 The discovery of fossil Ida ends 200 years search of the evidence of evolutionary history of Homo sapiens. The team headed by Prof. Hurum announced the discovery of Ida on May 19, 2009 at the American Natural History Museum, New York. Announcing the discovery Hurum said “It is something about owning a part of history, that you know when you show it to people it will change things ... It is a powerful feeling to have something ... nobody knows about.” Prof. Hurum declared that Ida was “the most complete fossil before human burial”. Hurum showed pictures of the Mona Lisa and the Rosetta stone, making a point about the importance of “Ida”, and he called it the Holy Grail and the lost ark of paleontology.12 Sir David Attenborough said, while narrating the documentary on “Ida” at BBC. “This little creature is going to show us our connection with the rest of all the mammals - with cows and sheep, and elephants and anteaters.” “The more you look at Ida, the more you can see, as it were, the primate in embryo.13” Because she is so complete, the scientists who have studied Ida describe her as a “Rosetta stone” for making sense of early primate evolution. “[She is] the eighth wonder of the world14” said Jens Franzen,9 at the Senckenberg, who is another co-author of the paper, describing the fossil in the journal PLoS ONE. Further Hurum said: “This is the first link in human evolution. A find like this is something for all humankind. It tells a part of our evolution that’s been hidden so far”. “This

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is our Mona Lisa and it will be ... for the next 100 years.13,15” “This little creature is going to show us our connection with all the rest of the mammals. The link they would have said until now is missing ... it is no longer missing.” Renowned broadcaster and naturalist Sir David Attenborough. The day after the Ida launch UK-based Guardian newspaper featured a front-page article under Sir David Attenborough’s personal by-line which is reproduced below.16 “Humanity is very egocentric. We are fascinated with ourselves. I’m not sure that it is a particularly nice characteristic but we are. When we look round at the natural world, there is often an ulterior motive. We desperately want to know where we came from...” ...and later continued, as part of the layout of a special two-page spread about the discovery. “...The more you look at Ida the more you can picture, as it were, the primate in embryo. She represents the seed from which the diversity of monkeys, apes and ultimately every person on the planet came...”

Importance of Ida The fossil Ida or Darwinius, was officially revealed on May 19, 2009 at New York’s American Museum of Natural History. On May 20, 2009 a day after the announcement in New York, Google’s search page featured “Ida”, and on clicking the logo, one automatically reaches at the “missing link” (Fig. 3). Simultaneously a book, a movie, a press release, news reports, TV special and an interactive web site were all launched to tell the world that in Ida the “missing link” of the man’s evolution has been found.17

Figure 3. Darwinius masillae, the fossil known as “Ida” was displayed on Google’s search page

The Ida fossil is more similar to anthropoids, the group that includes apes, monkeys and humans. Ida lived around the time when primates split in to prosimians or the non-human branch who have survived as the modern lemurs; and the monkeys, apes and humans evolved from the other branch known as anthropoids. Ida has anthropoid features placed within the primate family tree. Prof. Jørn Hurum said she is perhaps a transitional fossil between primitive lemur-like primates and the monkeys, including the human lineage. “This is the first link to all humans – truly a fossil that links world heritage,17 ” he said: “This fossil rewrites our understanding of the evolution of primates... It will probably be pictured in all textbooks for the next 100 years”.15 As a primate, Ida is part of our own order, and able to throw light on our own ancestry. She comes from

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Figure 4. Sketch of Ida are published by the research team on the Public Library of Science website. Creative Commons Attribution License Franzen et al.9

a highly significant age—the time when the anthropoids, our own subgroup of primates, were branching off from the prosimians” (Fig. 4). Darwin was ridiculed for his thesis on evolution. On the November 17, 1877, Charles Darwin was awarded an honorary doctorate by Oxford University. As he headed towards the podium, unruly undergraduates unfurled a giant banner of half-man half-monkey titled “Missing Link”. Such was the feeling against his monumental contribution to science. The notion that humans were connected to other animals was causing hurt in the Christian society (Fig. 5). When Darwin told the Bishop of Worcester’s wife about his theory of evolution, she remarked: “Descended from the apes! My dear, let us hope that it is not true, but if it is, let us pray that it will not become generally known”. On the bicentenary of Darwin “Pope has now argued that man descended from apes, and natural selection was the means by which some species prospered while others failed”. In 2009 Rev Dr Malcolm Brown, Director Church of England issued this statement “Charles Darwin: 200 years from your birth, the Church of England owes you an apology for misunderstanding you and, by getting our first reaction wrong, encouraging others to misunderstand you still. We try to practice the old virtues of ‘faith seeking understanding’ and hope that makes some amends.”18

Discussion The theory of evolution by natural selection as outlined by Charles Darwin is now widely accepted. During Darwin’s period, fossil records were few and that was the biggest obstacle in convincing skeptics. In the last 150 years fossil records have unambiguously proved Darwinian evolution. But during his period Darwin had to face the wrath of the Church of England for his theory of evolution as it was considered against the divine creation. Today as we celebrate the bicentenary of

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Figure 5. Caricature of Charles Darwin as an ape published in The Hornet, a satirical magazine 22 March 1871. University College London Digital Collections, Author unknown. This caricature shows Darwin with the body of an ape. As “Darwinism” became widely accepted in the 1870s, caricatures of Charles Darwin with an ape or monkey body symbolized evolution19

this great man his views on religion stand vindicated by the Church of England.18 There are still missing specimens in the chain of evolution of various animals and plants. The search for more fossil evidence would profoundly affect the young minds. Even for atheists it may be recalled that Genesis 1 states, “And God said, let the earth bring forth the living creature” and “Let the waters bring forth abundantly.” This allows the teaching that God let the earth and waters do its thing and create life, which would not contradict Darwinism or religion. As Editor in Chief, National Geographic magazine Bill Allen states in his letter from the Editor “National Geographic aims to explore the world, often by highlighting scientific concepts such as evolution. Is this approach necessarily at odds with faith, which lies beyond the possibility of scientific proof? No. Just as religion did not disappear after Galileo demonstrated that the earth is not at the center of the solar system, evolution does not exclude God from our origins, the ‘mystery of mysteries’—a 19th century astronomer’s description borrowed by Darwin himself”.19 Jørn Hurum explains evolution for all life forms, “When we say that Ida is related to all the monkeys and apes that live today, at the same time we’re saying that they all have separate lines of evolution. Chimpanzees, gorillas, orangutans and lemurs all have the same amount of evolution as humans do. We just evolved in different directions. The beauty about the theory of evolution is that we all have a starting point somewhere, and then the ancestors go in different directions (Fig. 6). What we see with specimens like Ida is something about the

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Figure 6. Showing the place of Ida Drawinius masillae in the primate family. Humans first walked on earth 190,000 years ago in the 4.5-billion-year history of earth. http://image.guardian.co.uk/ sys-files/Guardian/documents/2009/05/20/Primate_tree.pdf

deep evolution of all primates - we have a common ancestor somewhere down the timeline. All of us.” Primates have evolved 55 million years ago and between 40 and 50 million years ago a branching took place splitting apes, monkeys and humans from the second group that includes lories and lemurs. Ida lived during the Eocene period. This period began about 55 million years ago and by this time 10 million years had lapsed since the dinosaurs had become extinct. Darwinius masillae “Ida” lived some 47 million years ago in the middle Eocene (in Greek “New Dawn”) period, and dinosaurs disappeared some 18 million years ago before Eocene. It was in the Eocene period that the first large land mammals appeared on the earth. This was the period when warm-blooded animals continued their evolutionary transition to the biodiversity in animal life we see today. Decent of man continued selecting for favorable mutations resulting in modern man (Fig. 7).20 Ida may belong to our own primate ancestry that led to monkeys, apes and man, but the announcement of “Ida - the missing link” has become controversial. It may be noted that evolution proceeds via incremental changes. The fossil record of each change is incomplete. Skeptics are still cautious in accepting this

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Figure 7. Evolution of monkeys, ape and Man20

as the missing link.21 Primatologists interested in evolution were conspicuously absent at the news conference and most of them believe that Ida was the ancestor of lemurs, not humans. John Fleagle Professor at Stony Brook University, New York who reviewed the manuscript before publication state “that the fossil is not a lemur but a link in the evolution of man”. Ida’s full significance would emerge only after it has been debated extensively among the paleontologists in the coming years. While final verdict will take time, it is safe to avoid the word “missing link”. Ida will remain an important discovery of great importance as there are very few fossil records from this Eocene (in Greek “New Dawn”) period. Finally as we go to press, debate on the “Ida’s” place in evolution is becoming murkier. A group of paleontologists writing in Nature (Lond.) claim that 47 million years old fossil Darwinius masillae belongs to lemurs and lorises. Nonetheless we believe that not in too distant a future such an undisputed fossil in the lineage of monkey, ape and man would be found;22,23 and until such time DNA story24 has already clinched the issue. Darwin’s theory of evolution has stood test of time, and has proved to be of invaluable help in explaining the various new pathogens causing pandemics. Work of Watson and Crick24 that every organism carries a 4-letter code of DNA25 common to all life, vindicated Darwin’s theory of evolution. For example, chimpanzee and human genomes are highly related. Such similarities based on genome analysis of various animals and plants have proved to be a boon in understanding common descent. Further advanced genetic research is marching ahead to solve the problem of hunger and health in man and animals. The evolution of various microbes is causing serious human health problems world over. In the last decade or two about 30 new microbes or their malignant forms have appeared and caused high morbidity and mortality, and heavy economic losses. The examples are plague, AIDS, Ebola virus, SARS, H1N1 viral influenza, tuberculosis, malaria, West Nile virus, Japanese encephalitis et al. By the process of mutations and natural selection they acquire resistance to chemicals that were initially very useful.

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These organisms change to new and more dangerous forms, and some also jump from animals to man. To watch the entire panorama of plant and animal life, consequences of biodiversity loss, and emergence of lethal organism is mind boggling. Darwin would have been thrilled to see “the nature at work”.

References 1.

Darwin C (1859) In: On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life. 1st edition, John Murray, London. http://darwin-online.org.uk/content/frameset?itemID= F373&viewtype=text&pageseq=1, retrieved 2009–01–09

2.

Ostrom JH (1976) Archaeopteryx and the origin of birds. Biologic J Linnean Soc 8: 91–182

3.

Nedin C (1999) All About Archaeoptery. http://www.talkorigins.org/faqs/archaeopteryx/ info.htmlx

4.

They Didn’t Love Lucy. New York Times, March 13, 2009. http://www.nytimes. com/2009/03/19/arts/artsspecial/ 19bust.html?_r=2&pagewanted=all

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Tattersal I, Jeffrey H, Schwartz (1999) Hominids and hybrids: The place of Neanderthals in human evolution. PNAS 96(13):7117–711

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Erickson GM, Makovicky PJ, Currie PJ, Norell MA, Yerby SA, Brochu CA (2004) Gigantism and comparative life-history parameters of tyrannosaurid dinosaurs. Nature 430(7001):772–775

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Andrew L (2009) Celebrity fossil primate: missing link or weak link? Science 324: 1124–1125

8.

“It’s really a kind of Rosetta Stone,” commented study co-author Professor Philip Gingerich, of the Museum of Paleontology at the University of Michigan, Science Daily, May 19, 2009. http://www.sciencedaily.com/releases/ 2009/05/090519104643.htm

9.

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5):e5723.

10.

World Heritage Fossil: Science Daily, May 19, 2009. http://www.sciencedaily.com/ releases/2009/05/ 090519104643.htm

11.

The Guardian [UK] “To get a glimpse of the Ida fossil, the media make monkeys of themselves”. http://www.guardian.co.uk/science/2009/may/19/ida-fossil-primatemedia-us

12.

Ida: The Holy Grail of Missing Links? http://www.arn.org/blogs/index.php/2/2009/05/20/ ida_the_holy_grail_of_evolutionary_specu_1

13.

National Geographic Magazine. September, 2009

14.

Randerson J. Ed Pilkington in New York Deal in Hamburg bar led scientist to Ida fossil, the ‘eighth wonder of the world’ guardian.co.uk, Tuesday 19 May 2009. http://www.guardian. co.uk/science/2009/may/19/fossil-ida-missing-link-discovery

15.

“Backgrounder to Ida Fossil.” The Hindu, May 20, 2009. http://www.hindu.com/ holnus/008200905201041.htm

16.

http://www.age-of-the-age.org/evolution/darwinius_masillae.html#ida_darwinius_masillae_ study_background_story

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17.

World heritage fossil. Science Daily, May 19, 2009. http://www.sciencedaily.com/ releases/2009/05/ 090519104643.htm

18.

Church of England. http://www.telegraph.co.uk/news/newstopics/religion/2910447/CharlesDarwin-to-receive-apology-from-the-Church-of-England-for-rejecting-evolution.html

19.

Janet BE (2002) The Power of Place. Vol. 2, Jonathan Cape, Charles Darwin, London

20.

www.edb.utexas.edu/.../socialcognitive.htm

21.

O’Leary. Scientific American quietly disowns Ida “missing link” fossil. 21 July 2009. http://www.uncommondescent.com/intelligent-design/scientific-american-quietly-disownsida-missing-link-fossil/

22.

Rex D (2009) Fossil primate challenges Ida’s place. Nature 46:1040

23.

Seiffert ER, Perry MGJ, Simons EL, Boyer DM (2009) Conversant evolution of arthropoidlike adaptations in Eocene adapiform primates. Nature 461:1118–1121

24.

Watson JD, Crick FHC (1953) Molecular structure of nucleic acid-a structure for deoxyribose nucleic acid. Nature 171(4356):737–738

25.

Watson JD, Crick FHC (2003) Molecular structure of nucleic acids A Structure for deoxyribose nucleic acid. Am J Psychiatry 160:623–624

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3 Darwin’s theory of evolution: Survival of nature’s fit! Veena Tandon* and Gaurangi Maitra** *Department of Zoology, North-Eastern Hill University, Shillong - 793022, Meghalaya, India [email protected], [email protected] **Assam Rifles Public School, Laitkor, Shillong - 793022, Meghalaya, India [email protected]

Abstract: Even after 200 years after his birth, Charles Robert Darwin and his work are still central to any discussion on evolution. What is the relevance of evolution as Darwin perceived it? What were the pre-Darwinian, Darwinian and post-Darwinian pictures? Among the ancient pre-Darwinian theories Aristotle’s ‘Scala Naturale’ and the ‘Special Creation’ theory are perhaps the most important, whereas Lamark’s theory of ‘Evolution’ and Lyell’s theory of ‘Uniformitarianism’ are perhaps the most important modern ones, before Darwin’s work. His voyage of circumnavigation on the Beagle lead to pertinent observations: the similarities of structures between fossils and living forms in the same area; the presence of related but different species in adjacent areas of the same continent; the resemblance of species on isolated islands to those of the nearest continent and differences between species on closely adjacent islands of the Galapagos Archipelago in relation to their modes of life and feeding ; natural selection and survival of the fittest. The conclusions arising out of these and other observations were published as “The Origin of Species by means of natural selection or the preservation of Favored Races in the Struggle for Life”. But Darwin’s theory could not explain how the variations favored by natural selection initially arose or were inherited; the lack of intermediate forms and the long time frame needed for the changes to occur were two further objections to it. However, in the post-Darwinian era beginning with the rediscovery of Mendelism to modern day molecular biology, and the inputs from radioactive dating, these and other queries have not only been answered but they also strongly vindicate Darwin’s theory that has indeed stood the test of time and has emerged as the most convincing and fittest of all! Man has always wondered where he came from, wondered what his origins were and wondered spellbound at the wonderful variety of life around him! Was he a demigod, a spectator or participant in the natural scheme of things? May be on a star studded night, when man looked up at the sky and wondered, he became mankind. It is probably this single quality of wonder, more than anything else that made Charles Darwin synonymous with evolution in particular and biology in general. Even two hundred years after his birth, Charles Robert Darwin and his work are still central to any discussion on evolution. Darwin was an ‘evolutionary’, with a M.A. degree in theology and with an unquenchable V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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thirst for natural history! Darwin carefully marshaled his facts for more than two decades after his return from the famous Beagle voyage before publishing his magnum opus in 1859. Through this book, he set out to provide evidences that all life is interrelated and life forms are mutable; that they evolve from the simple to complex forms directed by nondeterministic natural selection; and the changes that make the organism suited to its environment and are passed onto the progeny result in descent with modification. The theory made change in organisms an irrevocable part of life. It created a controversy, because to accept this change would be going against certain religious dogma. But change is an inescapable fact of life. Is it therefore true that “nothing in biology makes sense except in the light of evolution”?1 In the century and half since publication of this book, the rapid advances in Biology have lead to investigating the very molecules that make up life! From the first detailed description of the nucleus in 1830 to the elucidation of the human genome is a mere 170 years! In this quickly progressing scenario, what is the relevance of evolution as Darwin perceived it? What were the pre-Darwinian, Darwinian and post-Darwinian pictures? And, how are they relevant today? Keywords: Darwin, Evolutionary theory, Natural selection, Variation, Neo-Darwinism, Origin of Species, Evidences from molecular biology

Evolution in the pre-Darwinian times Every human society had and continues to have its personal story of origin. Some of these are codified into written religious texts. Unlike a scientific theory whose strength lies in the fact that it should be falsifiable, religious theories suffer from the burden that to falsify is sacrilege! Added to this is the immutability of creation preached by most Semitic religions. Thus the traditional Judeo-Christian maintained that there was a special and independent creation of every species and life forms do not change through time from generation to generation. These creationists’ views were widely held, even by scientists, right into the early nineteenth century. On the other hand, the non-Semitic, especially Vedic religions, are closer to natural reality in their cyclical view of life. Thus immutability did not become an issue with them. Born in 384 BCE, Plato’s student Aristotle in his ‘History of Animals’ classified organisms in relation to a hierarchical ‘Ladder of Life’, placing them according to complexity of structure and function.2 Aristotle’s philosophy would thrive for centuries before being challenged. In AD 164, Galen, personal physician to the Roman Emperor, Marcus Aurelius, developed the belief that everything in the universe was created by God. The divine design was revealed in the form and organization of the human body.3 The struggle for existence was apparently first described by Al-Jahiz in the ninth century.4

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In his book ‘The Wisdom of God’ John Ray, the seventeenth century naturalist, who defined the species and genus, cited innumerable examples of the perfection of organic mechanism. Many examples of useful adaptations and design in nature were suggested by him, such as the structure of the eye, the hollowness of the bones, the camel’s stomach and the hedgehog’s armor.5 John Ray’s work influenced the leading biological scientist of the mid 18th century, Carolus Linnaeus. The latter’s most important contribution to science was his logical classification system for all living things which he proposed in his book ‘Systema Naturae’, first published in 1735. He apparently believed that he was just revealing the unchanging order of life created by God. Late in his life, however, he was troubled by the fact that plant hybrids could be created by cross pollination. These were varieties that had not existed before. Linnaeus stopped short of concluding that these plants had evolved.6 Buffon, in his ‘Historie Naturelle’, a 44 volume encyclopedia describing everything known about the natural world, wrestled with the similarities of humans and apes and even talked about common ancestry of Man and apes. Although Buffon believed in organic change, he did not provide a coherent mechanism for such changes. He thought that the environment acted directly on organisms through what he called ‘organic particles’. In his publication ‘Les Epoques de la Nature’ he openly suggested that the planet was much older than the 6,000 years against what was proclaimed by the church,7 and discussed concepts very similar to those in Charles Lyell’s ‘uniformitarianism’, which were formulated 40 years later.8 Erasmus Darwin, the paternal grandfather of Charles Darwin and an eminent speculative biologist, believed that evolution has occurred in living things including humans, in his poem Zoonomia. But his mechanisms of change were unclear; he also suggested that the earth and life on it must have been evolving for millions of ages before the commencement of the history of humankind.9 The first evolutionist who confidently and very publicly stated his ideas about the processes leading to biological change was a French protégé of the Comte de Buffon. He was Jean-Baptiste Chevalier de Lamarck who believed that microscopic organisms appeared spontaneously from inanimate materials and then transmuted, or evolved, gradually and progressively into more complex forms through a constant striving for perfection. The ultimate product of this goal-oriented evolution was thought by Lamarck to be humans. He believed that evolution was mostly due to the inheritance of acquired characteristics as creatures adapted to their environments and that creatures could develop new organs or change the structure and function of old ones as a result of their use or disuse. This idea was clearly put forward publicly in ‘Philosophie Zoologique’, published in 1809.10 Georges Curvier, the famous French comparative anatomist and paleontologist had identified skeletons of the extinct mammoths, pterosaurs and the giant lizard

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Mosasaurus. The proof of change lay before his eyes! Yet this undoubtedly great paleontologist rejected evolution on the grounds that he knew of no fossil forms between existing species and the 5,000 year old mummies! Cuvier had travelled to Egypt with Napoleon and seen mummified animals. He attributed sudden catastrophic changes (or Catastrophism) to account for changes in the Earth’s surface and extinction of animals.11 Cuvier’s theory would be superseded by the theory of Uniformitarianism with the publication of the first of the three volumes of Charles Lyell’s ‘The Principles of Geology: Being an Attempt to Explain the Former Changes of the Earth’s Surface, by Reference to Causes now in Operation’ in 1831. Uniformitarianism used the uniformity of nature as a basis for investigation with the present being a key to the past. In Lyell’s own words, “the animate and inanimate world, of which we find memorials in the Earth’s crust, may be similar both in kind and degree to those which are now in progress”.12

Inferences from the voyage Darwin joined the second survey expedition of the ship HMS Beagle that sailed from England on December 27, 1831. He carried the first volume of Lyell’s publication with him on this voyage. Originally planned to last two years, the journey lasted almost five– the Beagle did not return until October 2, 1836. Darwin spent most of this time exploring on land as the ship proceeded with its survey work. Darwin’s notes made during the voyage illustrate observations on Biology, Geology and Paleontology. These lead to the main inferences drawn from the voyage. Among the fossil haul in the region Punta Alta, Argentina was a large piece of the tessellated covering like that of the armadillo, but of gigantic size,13 which Darwin immediately realized must belong to an enormous Armadillo, living species of which genus were so abundant there. This first real pointer to evolution came from the Pampean formations of South America indicating the similarities of structures between fossil and living forms in the same area! Darwin noted how the rhea (a flightless ostrich-like bird), despite their similarity, hardly overlapped in their geographic distribution within the same continent. Instead, they seemed to replace each other as one travelled north to south; whereas the larger Rhea americana (also known as the greater or American rhea) was found beyond the Rio Negro in the Northern Patagonian Pampas, on the southern plains this was replaced by a related but smaller and distinct species (now called Rhea pennata or the lesser rhea or Darwin’s rhea).14 Thus, there was the presence of related but different species in adjacent areas of the same continent (Figs. 1 and 2). The islands that Darwin visited added a wealth of information. He found that 23 of the 26 species of land birds in the Galapagos had a close affinity with the South American mainland.15 European land shells were common to

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Figure 1. Rhea americana range. Source: Wiki- Figure 2. Rhea pennata range. Source: Wikimedia Commons media Commons

the Madeira Islands and its adjoining islet of Porto Santro. These observations made Darwin write, “such colonists would be liable to modification– the principle of inheritance still betraying their original birthplace”. 14 Indicating that the species of the isolated islands showed resemblance to those of the nearest continent. Darwin found the finches of Galapagos Archipelago, agreeing on many points – a peculiar structure of their bill, short tails and general form and in their plumage (Fig. 3). All species, excepting two, fed in flocks on the ground, and had very similar habits.13 Darwin found it very remarkable that this group showed a near perfect gradation in beak structure. The original beak was any hardly different from that of a warbler pointing clearly to the fact that all the finches had a common ancestor. It illustrates how natural selection has led to the evolution of a common ancestral species into a variety of forms adapted to different ecological niches.

1. Geospiza magnirostris 2. Geospiza fortis 3. Geospiza panrula 4. Geospiza olivacea Finches from Galapagos Archipelago

Figure 3. Darwin’s Finches. Source: Wikimedia Commons

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Formulation and publication of the theory Darwin returned from his voyage in 1836. The findings of the voyage were summed up in his Journal of Researches, published in 1839. The facts supporting the notion that species change were inescapable. He began the first of his notebooks on transmutation within a year of his return, in 1837. Darwin admitted ‘descent with modification’ and concluded that nature was in an open continuous process of ‘becoming’. Having accepted Lyell’s theory of uniformitarianism, it seemed logical to Darwin that change in land forms should be echoed in the flora and fauna, otherwise they would be doomed to perish. The multitude of living forms around him was a testimony to their ability to change with the environment. But how was this change directed? In October 1838, Darwin read Malthus’s famous treatise,’ An Essay on the Principle of Population’.15 It at once struck him that under natural circumstances favorable variations would tend to be preserved, and unfavorable ones to be destroyed. The result of this would be the formation of new species! With this insight Darwin had the frame work of his theory in place. He combined the forces of blind competition and random variation to explain development of design in living organisms. This neatly cut out the need for a designer or God. Knowing how controversial this matter was, he perhaps feared to rush into publication, where men like Buffon and Cuvier had feared to tread. In 1858, sick with malaria in the jungles of Malaysia, Alfred Russell Wallace posted Darwin a theory of evolution that he called “On the Tendency of Varieties to depart indefinitely from the Original Type”! This essay contained exactly the same theory as Darwin’s.15 Shocked as he was at having his life’s work preempted, Darwin did not dare to tear up a letter from a sick man and deny its existence. This joint paper entitled, ‘On the Tendency of Species to form Varieties and on the Perpetuation of Varieties and Species by Natural Means of Selection’ was read out on 1st July 1958, in the Linnaean Society! There was no significant reaction from the audience. The first edition of ‘The Origin of Species by Means of Natural Selection or The Preservation of Favored Races in the Struggle for Life’ was published on November 24, 1859. ‘The Origin’ in its opening chapters introduces variation under domestication and in nature and provides evidence to show how the constant intra and inter specific competition lead to the struggle for existence leading to natural selection or the survival of the fittest. Darwin also showed how species of the same genus vary in an analogous manner. Hybridism, the geological record, geographical distribution and their effect on variation is supported by a wealth of data. The finale is magnificent “There is a grandeur in this view of life, with its several powers, having being originally by the Creator into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been and are being evolved”.14 ‘The Origin’ did not seem to negate the role of a creator at this point, but did negate a single act of uniform creation.

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Reaction to ‘The Origin of Species’ The public reception to the book was very mixed. The Church of England scientific establishment went against the book, while the Anglicans supported Darwin’s natural selection as an instrument of God’s design. The Revd. John Stevens Henslow, the botany professor whose natural history course Charles had joined thirty years earlier, gave faint praise to ‘The Origin’ as ‘a stumble in the right direction’ but distanced himself from its conclusions.16 The most famous confrontation took place at the public 1860 Oxford Evolution debate during a meeting of the British Association for the Advancement of Science, when the Bishop of Oxford, Samuel Wilberforce argued against Darwin’s explanation. In the debate that followed Joseph Hooker argued strongly for Darwin and Thomas Huxley established himself as ‘Darwin’s bulldog’– the fiercest defender of evolutionary theory on the Victorian stage.17 Two famous nineteenth century comparative anatomists, Louis Agassiz at Harvard University and Richard Owen in England, surprisingly did not support the theory. Revd. Adam Sedgwick, geologist at the University of Cambridge who had taken Darwin on his first geology field trip, could not see the point in a world without God. The famous traveller in Africa and missionary David Livingstone could see no struggle for existence on the African plains.16 Many scientists of the day welcomed Darwin’s theory enthusiastically. Hewett Cottrell Watson, a famous nineteenth century English botanist, plant ecologist and evolutionist hailed Darwin as the “greatest revolutionist in natural history of this century”. Professor Robert Edmund Grant, who had shown him the study of invertebrates when Darwin was a student at the University of Edinburgh and who was still teaching Lamarckian evolution at University College London dedicated a book to Darwin. Asa Gray, the famous American botanist arranged the first US Edition of ‘On the Origin of Species’. Gray was a staunch supporter of Darwin in America, and collected together a number of his own writings to produce an influential book, ‘Darwiniania’.16 Sir Charles Lyell, the leader of the Uniformitarianism Theory in geology took almost a decade to completely accept Darwin’s theory.

Objections to the theory But whatever the reception, certain valid questions remained. Natural selection could account for the success of well developed adaptations but had no explanation for the initial stages of these developments, the development of the eye and the peacock’s feather were the most glaring examples of this lack of explanation. The absence of intermediate forms and the gaps in the fossil records being the other valid objections. The theory also demanded an extremely long time for small variations to accumulate. This was incompatible with the then estimated age of the earth. The most serious flaw was perhaps that Darwin had no satisfactory mechanism to show how variations were passed on to further generations.18

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Objections overruled! Initially the publication ‘The Mutation Theory’ (1900–1903) by Hugo De Vries gave rise to the proposition that mutation and not natural selection was responsible for evolution. De Vries’ theory that evolution, especially the origin of species, might occur more frequently with such large-scale changes than via Darwinian gradualism, basically suggesting a form of saltation became one of the chief contenders for the explanation of how evolution worked. At the same time Gregor Mendel’s trailblazing work in 1900, demonstrated in pea plants that inheritance follows definite rules. Each organism has two genes per trait, which segregate when the organism makes male and female gametes. Each gene in a pair is distributed independently during the formation of gametes and this clearly indicated as to how variations could be passed on and therefore supported Darwin’s theory and provided an answer to one of the main objections against it, i.e., how variations could be passed on! During 1910–1915, T.H. Morgan’s team from the fly room in Columbia University deduced the existence of genes, linked them to inheritance and mapped their location on chromosomes. This further strengthened the notion that natural selection was less important than mutations. Fisher, Haldane and Wright developed models to show that mutations only provide raw materials on which natural selection must work to produce speciation. Work on radiometric analysis that began in the early 1900s finally put the accepted age of Earth of 4.55 billion.19 This data helped to further the cause of Darwin’s theory by providing enough time for variations or mutations to accumulate. Darwinism was thus beginning to reemerge as neo-Darwinism. Darwinism only gained from the tremendous surge in Biology, especially in the work leading up to the proof that DNA was the genetic material. This opened the doors to the ‘Secret of Life’! 1953: The Double Helix structure of DNA was revealed by Francis Crick, James Watson and Maurice Wilkins, based on X-rays taken by Rosalind Franklin. Francis Crick’s suggested mode of DNA replication and Central Dogma of Biology solved the puzzle how variation are inherited. The new field of Molecular Biology was born and it proved Darwin was right! The decades following DNA structure elucidation gave us the vital genetic code, restriction enzymes, reverse transcriptase and DNA fingerprinting. It culminated in complete sequencing of the human genome.

Support to Darwinian postulates from modern biology Variation under domestication The effect of a Mendelian factor/or present day gene could be slight or powerful. Maize, the new world gift to humankind, has an almost unrecognizable ancestral,

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Figure 4. Teosinte vs. Maize. Source: teaandscones.wordpress.com/../page/3

wild form called toesinte. This bushy plant evolved into the Maize with its single stalk, due to mutations in the regulatory area of the one gene controlling cell division pattern during stem development. The change from the hard unappetizing small kernels to the soft, exposed kernels we are used to biting into is again due to change in a second developmental gene (Fig. 4). Mesoamericans bred the maize from toesinte by artificial hybridization with no access to all this special knowledge and in relatively few steps.20 Differences between ancestral and modern day forms have always been good support for the fact that species do and can change. Another South American plant that shows great variation under domestication is the tomato. In two thousand years of domestication, the original variety (Fig. 5) has given rise to 7500 varieties, with a whole spectrum of taste, color, texture and size. It is also interesting that in moving from its home in Peru, its pollinator, a species of halictid bee, did not move with them. Modern day cultivars have therefore been selected for self pollination. The frequent problem of blossom drop in domestic cultivars of tomato shows that attempted self pollination is not a great success. This could be due to a natural mechanism for preventing self pollination. In the flower the stigma extends well beyond the anthers, and it grows into that position a couple days before the anthers begin pollen shedding. Wild halictid bees, the best wild pollinators in field situations, are very sensitive to pesticides and cannot be introduced in crop fields. With the native pollinator absent, the other bees that might possibly serve are in short supply. Bumblebees are the second best, with honeybees a distant third, when they work the tomato blossoms.21 Darwin wrote in ‘The Origins’ “When we compare the individuals of the same variety or subvariety of our older plants and animals, one of the first points which strikes us is, they generally do not differ more from each other than do the individuals of any one species or variety in the state of nature”.14

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Convergent evolution The Moray eels (Muraena retifera) can eat prey, very much larger than their body. At the University of California, Davis (USA) Rita Mehta, an expert on snakes’feeding behavior, teamed up with fish biomechanist Peter Wainwright. Having worked on snakes, they looked for a similar mechanism in this eel. And surely enough, they found the moray eel using a second set of jaws to both restrain and transport prey! The eel’s pharyngeal jaws reach up from behind the skull to grasp prey in the oral jaws – mechanically similar to the ratcheting mechanisms used in snakes (Fig. 6). Similar adaptations found in animals widely separated phylogenetially, is a classical case of convergent evolution. It allows a fish and snake to be part of striking similar morphological, behavioral and ecological convergence!22 Darwin wrote in ‘The Origin’ “That mere physiological importance of an organ does not determine its classificatory value, is almost proved by the fact that in allied groups, in which the same organ, as we have every reason to suppose, has nearly the same physiological value, its classificatory value is widely different”.14

Figure 5. Wild tomato from Chile. www.usda. gov/is/pr/2005/051230,tomatoes. photo credit to Carl M Jones, University of California, Davis

Figure 6. Eel ratcheting jaws. blog.ngm.com/ blogcentral/2009/03/jaws-two.html

Adaptive radiation The works of twentieth century evolutionary biologists have shown beak and body size to change with climatic changes and they record possible examples emerging new species.29 In this era of molecular genetics, the various genes that are switched on in the developing beaks of finch chicks have been checked out. The gene for calmodulin (a molecule involved in calcium signaling that is vital in many aspects of craniofacial development and metabolism) is expressed more strongly in the long and pointed beaks of cactus finches than in the beaks of other species. An elongation of the upper beak, similar to that seen in cactus

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finches is seen when the levels of calmodulin were boosted artificially.24 The bone morphogenetic protein gene 4 [BMP4] induces cartilage and bone formation and also acts in mesoderm induction, tooth development, limb formation and fracture repair in humans. BMP4 is expressed at the putative site of fusion in the mid facial region. Its malfunction leads to the most common craniofacial birth defect (i.e., clefts of the lip and/or palate) in humans. BMP4 also plays a critical role during early embryonic development in the craniofacial region of chicks. In cichlid fish of Lake Victoria, the algae scrapping jaws have been modified into thick powerful jaws capable of crushing open snail shells.25 The BMP4 gene has been found responsible for this development. This same gene is found most strongly expressed in the large ground finch (Geospiza magnirostris) in the Galapagos Islands. The finch uses this robust beak to crack open large seeds and nuts (Fig. 7).24 The BMP4 gene provides an excellent example of the same gene responsible for the same function in different classes of vertebrates, thus strongly vindicating Darwin’s theory that all species have a common origin. Struggle for existence Human fossils indicate that tuberculosis (TB) has been around for more than half a million years. Today it claims two million lives annually and affects two billion people. This is due its resistance to antibiotics and mutlidrug regimes (MDR). This MDR-TB form has changed into the extensively drug resistant type XDRTB. This new form, first found in the 2006 KwaZulu, Natal outbreak has spread to 49 countries by 2008. New antibiotics to treat both types are being produced and undergoing clinical trials; SQ109 inhibits cell wall synthesis and PA-842 slows its cell division. But in vitro and in vivo result correlation have never been promising for TB. Like a bacterium worth its salt, Mycobacterium always finds a way out through evolution! With its genome sequenced in 1998, the new field of chemical genomics is being used to combat its evolutionary wizardry. Using bioinformatics as a tool the final goal is to replicate the bacterium in silico and thereby study its complete dynamics in a computerized cell free system and nullify its disease causing potential.26 Is it not also showcasing evolution of human ability? Necessity is surely the mother of invention in both the bacterium and human being. The real problem lies in not knowing the complete human - Mycobacterium interaction story. Darwin wrote in ‘The Origin’ “It is therefore good to give any one species advantage over another. Probably in no single instance should we know what to do. This ought to convince us of our ignorance on the mutual relations of all organic beings; a conviction as necessary, as it is difficult to acquire”.14

The descent of man In 1974, anthropologists working in a maze of ravines at Hadar in northern Ethiopia

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Figure 7. BMP4 at work: scienceblogs.com/.../06/nytimes_on_evodevo.php

followed a small clue on a slope. They found nearly 40% skeletal remains of a hominid, or humanlike creature that lived around 3.2 million years ago. Based on its small size, and pelvic shape, they concluded that it was female.27 It was later identified as Australopithecus afarensis and it is an ape closely related to human beings (Fig. 8). Here was an intermediate form in the story of human evolution! Something both Cuvier and Darwin missed seeing! Katherine S. Pollard provides significant insights into chimp-human dissimilarity despite 99% similarity. Using the huge computer cluster at the

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University of California, Santa Cruz and a self designed computer programme, Pollard highlights some sequences that are uniquely human. Human accelerated region 1 (HAR1) is a group of 118 bases in that part of our genome that is dissimilar from that of the apes. This region has hardly changed in vertebrates whose genomes are available to us. Between the chimp and chicken, which diverged some 300 million years ago, there is a two base difference in this sequence; whereas between the human and chimp, which diverged only 6 million years ago, there is a difference of 18 bases! HAR1 is required for the formation of a healthy cerebral cortex (Fig. 9). That HAR1 is not a protein encoding region but encodes RNA was proved by experimental work from a UC group at Santa Cruz. Thus, it is also the first documented example of a RNA-encoding sequence that seems to have been positively selected, showing that natural selection, Darwin’s bedrock for mechanism of evolution, can occur at the nucleotide level. To a Hindu mind, the letters HAR1 look uncannily like the word hari (meaning the preserver) an allusion not very far off the mark, considering the fact it controls the development of the vital cerebral cortex! Its malfunction is linked to congenital lissencephaly (smooth brain) and adult schizophrenia.28 Similarly, HAR2 has an ancestral version in the ape that does not promote the same level of wrist and thumb development as its modern version does in humans. It seems to be responsible for the uniquely

Figure 8. Female homonid skeleton. Source: Wikimedia commons

Nature at work: Ongoing saga of evolution

Figure 9. HAR1 makes us human?

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human dexterity that leads to tool making and technology.28 This only underscores Darwin’s postulates of common descent and shows diversity and adaptation arise from natural selection. Therefore, in 1860, TH Huxley was right to end the famous Oxford debate against Darwinism by apparently saying that he was not ashamed to have a monkey for his ancestor, but he would be ashamed to be connected with a man who obscured the truth. This was in reply to Bishop Samuel Wilberforce’s question as to whether it was through his grandmother or his grandfather that Huxley considered himself descended from a monkey.17

Beyond Darwin Darwinian medicine applies evolutionary data to our understanding of health problems and health promotion. Matching disease to genotype can result in customized medicine. Darwinian medicine tells us inconveniences like fever, diarrhea, vomiting, actually help in cleansing out microbial infections! Vaccines against human papilloma virus and improved hepatitis C vaccines have been developed by a process called directed evolution. Mixing segments of 20 different human interferons has given us a jigsaw that is 250,000 times more effective against viral replication than the normal interferon. Uniquely human complex problems like air traffic control, stock portfolio options, electronic circuits, optimum combinations of medicines, orbits of communication satellites for minimizing signal loss are finding answers from evolutionary or genetic algorithms that are often less symmetrical than conventional designs but far more effective! Critical areas like ecosystem services on which the life and livelihood of this planet depends could benefit tremendously from evolutionary methods and knowledge.29

Conclusion Religious dogma held center stage till Charles Darwin did a Copernicus act for biology and rewrote the script for the play of life. In retrospect it seems that only a blind person would be incapable of learning from the billions of years of nature’s experiments revealed on the voyage. The real reward from the Beagle voyage was the huge data base on which generations continue to work. It gave Darwin the raw material, with which he synthesized his theory of Organic Evolution, set out in the ‘Origin of Species’. The theory of evolution propounded in this volume has not only survived but has vigorously prevailed in the century and half since its publication. No small tribute to its ‘fitness’! Darwin’s theory is a foundational pillar of modern science at par with relativity and quantum theory. Darwin, like all original thinkers, marched to his own drumbeat. He rejected ‘Scala Naturale’ for branching evolution, accounted for design without designer via natural selection and embraced uniformitarianism. Today natural selection has basic relevance

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from basic science to practical pursuits, from biotechnology to forensic science. We still have questions to answerHow common is natural selection? How far does it occur at the molecular level? What is the origin of genetic variation on which natural selection works? Nature’s open book and evolution only underline the philosophy - the only permanent thing in life is change. Therefore, when evolution and change are synonymous, we must acknowledge that “Nothing in biology makes sense except in the light of evolution”.1

References 1.

Dobshansky T. Theory of evolution. http:// bio.classes.ucsc.edu/bio20c/evolution/Lecture1. Html

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Bynum WF (1975) The great chain of being after forty years: an appraisal. In: History of Science.

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Spanenburg R, Moser DK (1999) From the ancient greeks scientific revolution. In: The History of Science. Universities Press (India) Limited

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Bayrakdar M (1983) Al-Jahiz and the Rise of Biological Evolutionism. (Third Quarter) The Islamic Quarterly, London

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Ray J. The Wisdom of God Manifested in the Works of the Creation. http://www.jri.org. uk/ray/wisdom_links.html.

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Linnaeus Carolus. http://www.biodiversitylibrary.org/bibliography/542. 10th Edition (2 volumes) online at the Biodiversity Heritage Library

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James Barr (1987) Biblical Chronology: Legend or Science. The Ethel M. Wood Lecture 1987. Delivered at the Senate House, University of London on 4 March 1987. London: University of London, 1987. Pbk. ISBN: 7187088644. pp 1

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Leclerc, Georges-Louis, Comte de Buffon. http://www.eoearth.org/article/Leclerc,_GeorgesLouis,_Comte_de_Buffon

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Darwin E. Zoonomia; or the Laws of Organic Life. http://www.gutenberg.org/ etext/15707

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Jay GS (2002) The Structure of Evolutionary Theory. Belknap Harvard, Harvard

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Martin JS, Rudwick (1997) In: Georges Cuvier, Fossil Bones, and Geological Catastrophes. The University of Chicago Press

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Uniformitarianism (1982) In: Encyclopedia Britannica Macropedia Volume, 15th edition, University of Chicago

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Darwin CR (1989) In: Voyage of the Beagle. Browne J, Neve M (Eds.), Penguin Books

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Darwin CR (1989) In: The Origin of Species. Modern Library Paperback Edition

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Darwin CR: In: The Autobiography of Charles Darwin With the Original Omissions Restored. Edited and with appendix and notes by his grand-daughter Nora Barlow. London: Collins. pp 118, 1809–1882

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Reaction to Darwin’s theory. http://en.wikipedia.org/wiki/Reaction to Darwin’s theory

17.

Lucas JR (1979) Wilberforce and Huxley: A Legendary Encounter. Historical J 22(2): 313–330

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18.

Miller J (1986) In: Darwin for Beginners. Writers and Readers Cooperative in association with Unwin Paperbacks

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Claire P (1956) Age of meteorites and the earth. Geochimica et osmochimica Acta 10(4):230–237

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Kingsley DM (2009) From atoms to traits. Scient Am 4(1):33

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Tomato: [ http://en.wikipedia.org/wiki/Tomato]

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Mehta RS, Wainright PC: Raptorial Jaws in the throat help moray eels swallow large prey. [http://www.nature.com/nature/journal/v449/n7158/abs/nature06062.html]

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Stix G (2009) Darwin’s Living Legacy. Scient Am 4(1):14

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Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ (2006) The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches. Nature 44: 563–567

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Terai Y, Morikawa N, Okada N (2002) The Evolution of the Pro-Domain of Bone Morphogenetic Protein 4 (BMP4) in an Explosively Speciated Lineage of East African Cichlid Fishes. Mole Biol Evol 19:1628–1632

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Barry CE, Cheung MS (2009) New tactics against tuberculosis. Scient Am 4(3):52–57

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Johanson D, Maitland E (1981) In: Lucy: The Beginnings of Huhumankind. Simon and Schuster, New York

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Pollard KS (2009) What Makes Us Human? Scient Am 4(5):34–37

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Mindell DP (2009) Evolution in the Living World. Scient Am 4(1):58–65

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4 The life and research of JBS Haldane in India with special reference to Charles Darwin Krishna R. Dronamraju Foundation for Genetic Research, P.O. Box 27701-0, Houston, Texas, USA 77227 [email protected]

Abstract: JBS Haldane (1892–1964) was a polymath, a great scientist who made important contributions to multiple sciences such as Physiology, Genetics, Biochemistry, Statistics, Biometry, Cosmology and philosophy, even though he did not possess an academic degree in any science. His most important contribution to science was the mathematical theory of evolution which combined the evolutionary process defined by Darwin and the science of genetics founded by Mendel. Haldane moved from London to live and work in India in 1957. As a Research Professor at the Indian Statistical Institute in Calcutta, Haldane directed research on local fauna and flora, which followed the Darwinian tradition. In 1962, he moved to head the Genetics and Biometry Laboratory in Bhubaneswar but died in 1964 because of cancer. Haldane’s research and teaching in India benefited many young scientists, partly because of his great knowledge, but also because of the encouragement he provided by emphasizing the dignity and value of scientists to society. Haldane was a fierce critic of science administration and science policy. Haldane advised the Defense research organization in India in problems related to deep sea diving, and adaptation to extremes of cold temperatures and atmospheric pressures, while breathing toxic mixtures of various gases, based on knowledge gained by painfully experimenting upon himself. We were very proud that Haldane who chose to spend his last years in India. Both Haldane and his wife (scientist Dr Helen Spurway) applied for Indian citizenship which was granted in 1961. Thus, he fulfilled the promise he made to his friends in London that he would die as an Indian. Keywords: Darwin, Mendel, Biometry, Animal behavior, Human genetics, Statistics, Paleontology, Epidemiology, Speciation, Population genetics, Natural selection

Introduction JBS Haldane (1892–1964) was born on 5th November 1892, in Oxford, England. He was a distinguished British scientist who migrated to live and work in India in 1957. Haldane was invited by Prof. Prasanta Chandra Mahalanobis, Director V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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of the Indian Statistical Institute in Calcutta, to be a Research Professor at the institute. He was known as a polymath, an individual who possessed great intelligence and knowledge of multiple disciplines. In 1962, Haldane moved to Bhubaneswar to direct the Genetics and Biometry Laboratory which was set up especially for him by the Chief Minister of Orissa Mr. Biju Patnaik. Unfortunately, he was diagnosed with cancer in 1963 and was operated in London, but the cancer recurred and Haldane died on 1st December, 1964.1 Haldane directed my PhD in genetics from the Indian Statistical Institute. Mrs. Haldane (Dr Helen Spurway) was also a scientist who specialized in genetics and animal behavior. I worked closely with the Haldanes at Calcutta and Bhubaneswar. We traveled together to attend several scientific meetings, for instance, to Sri Lanka, Israel, UK, France and Italy, etc.

Background Haldane was a great popularizer of science and contributed numerous articles to newspapers and popular magazines in several countries including India. Some of these essays were recently published in a book which I have edited.2 Many of his essays were written while traveling on trains and planes. Haldane always carried a pad and pen and started writing as soon as he had a few minutes to spare. He never possessed a degree in any branch of science, yet he became one of the great and influential scientists of the 20th century. Haldane, who was popularly known as ‘JBS’ or ‘Prof’ or simply ‘Haldane’ was a polymath, that is to say, a genius who possessed almost universal knowledge. He made important contributions to several sciences as well as to philosophy, religion, logic, popular writing, and ethics. In science, Haldane’s contributions covered physiology, genetics, biochemistry, statistics, biometry, cosmology and history and philosophy of science. As a popular writer of science, Haldane covered even more subjects, including zoology, physics, chemistry, mathematics, geology, geography, astronomy, meteorology, politics, psychology, non-violence, military affairs, theology and literature. He was a marxist and supporter of Soviet science from about 1937 to 1950 but abandoned that position when the science of genetics was suppressed in the Soviet Union under the pseudo-scientist Lysenko who was supported by Stalin. Haldane’s distinguished relatives include his father John Scott Haldane, physiologist at Oxford University, his uncle Viscount Haldane who was Minister for war and Chancellor of the Exchequer in Prime Minister Asquith’s cabinet, his great uncle Burdon Sanderson, first Waynflete Professor of Physiology at Oxford University, his sister (Lady) Naomi Mitchison, prolific writer of numerous books in fiction, non-fiction, travel, history, politics and other subjects. His three nephews are distinguished scientists in the life sciences. Haldane’s scientific reputation is based on his extensive series of papers on the mathematical theory of Darwinian natural selection (evolution). The independent contributions of Haldane and

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R.A. Fisher in England and Sewall Wright in the United States led to the establishment of the branch of genetics called ‘population genetics’. Haldane’s classic work, The Causes of Evolution3 was a founding document of this process. However, Haldane’s scientific work was much broader than that of his colleagues. In addition to his monumental work in genetics, Haldane made important contributions to enzyme kinetics in biochemistry. In physiology, Haldane is best remembered for his daring experiments in testing the effects of poisonous gas mixtures, cold temperatures and higher atmospheric pressures in which he employed himself as the ‘guinea pig’. They were often painful experiments, causing convulsions and injuries. He also conducted many diving experiments to investigate a submarine accident for the British Navy, once again employing himself as his own ‘guinea pig’. He suffered permanent injury because of rapid decompression during the experiments and the back pain haunted him rest of his life.4

Science in India Haldane’s research in India was primarily influenced by the Darwinian tradition. His major contribution to science was his mathematical theory of evolution (natural selection) which was an interpretation of Darwin’s theory of evolution in the context of Mendelian genetics. During the years: 1924–1934, Haldane’s series of mathematical papers on this subject became a foundation for the new scientific discipline called ‘population genetics’. However, after his arrival in India, Haldane saw Darwin from a new perspective.5 Much of our early research was concerned with a detailed analysis of ‘meristic variation’ in ‘Bateson’s6 terminology. As Haldane explained to our visitors, all our research projects followed the Darwinian tradition. They were summarized in my book: Haldane: The Life and Work of JBS Haldane with special reference to India.1

Animals have rights and duties Haldane5 stated that Christian theologians drew a sharp distinction between humans and other species. Hence, Darwin’s declaration that human beings have descended from animals created a furor among Europeans. Whereas many eastern religions such as Hinduism, Buddhism and Jainism have long recognized that animals have rights and duties. Indian art and religion have depicted divinity in various animal forms and kindness towards other species has long been an accepted tradition, at least in theory if not in practice always, in India. There are no parallels in Europe and North America. There is still some opposition to teaching evolution in some Christian communities, especially in the southern United States. Not only did

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Haldane interpret Darwinism from the Indian philosophical and religious point of view, but he also developed several research projects on Indian species of plants and animals which are in the Darwinian tradition. As his students, we were all encouraged to conduct research on different projects in that tradition. There were certain characteristics which are common to all these projects: (a) Much of our research involved measuring biological variation, especially ‘meristic’ variation, that is to say, variation in like parts such as petal numbers in flowers, venation in leaves, number of teeth, or bilateral spotting in caterpillars, etc. (b) research involved local resources as much as possible, (c) the projects did not require much financial support, (d) the methods employed were simple but the results had scientifically profound consequences, (e) the observations must be quantified wherever possible, (f) the project should be flexible enough to facilitate the incorporation of any new and unexpected results and the resulting change in direction or methods, (g) it is necessary to have several ongoing projects simultaneously to achieve quick results as there will always be some lines of pursuit which may not bear fruit, and (h) the results should be published immediately. Some of the projects were an imitation of Darwin’s experiments. One such example is the estimation of the volume of soil brought to the surface by earthworms per acre per year. It is a sound research project in ecology and agriculture. S.K. Roy conducted experiments with mixtures of rice varieties planted in plots which gave increased yields of seeds in some cases.6 Another project, which was my research interest, is the investigation of color preferences of Lepidoptera among different colored flowers and their impact on speciation.7 By their preferential visits to different varieties of a plant species differing in flower color, insect pollinators can create reproductive isolation within a species. By means of increasing such isolation (for instance, it could happen if there is a new flower color mutant appearing in the plant population) further divergence can follow, ultimately leading to complete isolation and speciation. Such speciation has been called ‘sympatric speciation’, as opposed to ‘geographic speciation’ where such geographic factors as floods, earthquakes and climate change can result in reproductive barriers within a species. Haldane believed that such research projects are following the Darwinian tradition and would have interested Darwin greatly. Another colleague T.A. Davis8 pursued research on coconut palms, and discovered that palms with left-handed coiling in their crowns produce more nuts than those with right-handed spiraled crowns. Haldane stated that they were what Darwin called ‘fools’ experiments. S.D. Jayakar and Mrs. Haldane (Dr. Helen Spurway) collaborated with me to conduct biometrical investigations of the nest-building activity of the solitary wasp, Sceliphron.9 Anthropologist A.K. Ray10 conducted population studies of toe anomalies and their possible genetic basis. Haldane commented that such studies are easier to follow in India because many people have bare feet or wear sandals, unlike western countries where shoes and boots are worn by many.

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Consequences of Darwinism Haldane regarded Darwin’s work in botany as his most original and important contribution to science. That work includes books on insectivorous plants, climbing plants, sexuality in plants, and inbreeding in plants. Charles Darwin is best known for his work on evolution; however, that subject was also discussed by many others including his grandfather, long before Darwin. His experiments on plants, although not so well known, are original. Haldane encouraged us to follow Darwin’s research in botany. But, Haldane wondered what Darwin’s attitude which led to his discoveries was. Darwin was most open minded in his attitude towards all living beings. Haldane wrote: “Darwin did not draw a sharp line between earthworms and the old gentlemen who had failed to interest him in mathematics at Cambridge. From the biographical account of his son Francis, we know that Darwin was totally immersed in his experiments and observations. Indeed, he was so dedicated that he used human attributes when describing his experimental animals and plants. Haldane5 explained that such dedication is characteristic of saints in ancient India. He stated that a saintly attitude with total dedication results in excellent science and it is needed today in India. Haldane5 drew attention to Aristotle’s logic and his difficulties in classifying animals which he based on similarities. Darwin, on the other hand, foreshadowed a logic based on differences. In the Origin of Species, Darwin11 wrote: “Systematists will have only to decide (not that this will be easy) whether any form be sufficiently constant and distinct from other forms, to be capable of definition, and if definable whether the difference be sufficiently important to deserve a specific name... Hence, without rejecting the consideration of the present existence of intermediate gradations between any two forms, we shall be led to weigh more carefully and to value higher the actual amount of difference between them.” Haldane regarded Darwin’s statement as the starting point for a whole new program in statistics.

Figure 1. JBS Haldane before his death

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There are ethical consequences of Darwinism which have not always been desirable. Darwin was led to the theory of natural selection by reading Malthus on population growth. Although Darwin pointed out the importance of physiological adaptation, he left the erroneous impression that the struggle for life was analogous to war and economic competition in the human species. Consequently, Darwinism was used to justify wars and persecution. Social Darwinism is an undesirable and unwanted consequence of Darwinism. On the other hand, Darwinism has reminded us of our responsibility towards other species. It opened up a whole new aspect of our social behavior, the attitude we should adopt towards other species which are related to us, although distantly. Haldane believed that an Indian perspective of Darwin offers a corrective to the ‘western’ point of view. Additional information can be found in my book: Selected Genetic Papers of JBS Haldane.12 Science and ethics are discussed in Haldane’s Daedalus Revisited.13

Impact on Indian science The foremost impact of Haldane’s activities in India was to raise the social awareness of scientists and their value to society. As an outspoken scientist of great importance, Haldane utilized his position to express publicly what he thought about the state of science in India. He was a fierce critic of the science administration in India and pointed out many of its deficiencies. He fought for greater independence for younger scientists, lesser beaurocratic complications in science administration, increased support for scientific research by the Central Government, and greater dignity and respect for the scientific workers in society. He pointed out the need to raise the quality of research and the teaching standards. Haldane’s efforts were applauded by the younger generation. Many of them believed that he was voicing their grievances fearlessly when they could not do so themselves. Haldane’s emphasis on the utilization of local resources for research opened a new tradition in the 1960s when many Indian scientists returning from Europe and North America were complaining of lack of facilities in India. Haldane, on the other hand, suggested several research projects which could be followed in India without utilizing expensive equipment or great expense. All our research projects met these criteria which were defined by Haldane1. Yet, the results were of profound importance and interest. They followed the Darwinian tradition. India had produced great scientists of its own; some examples are J.C. Bose, C.V. Raman, P.C. Mahalanobis and Homi Bhabha among others. Haldane’s migration to India added another dimension. We were fortunate that he chose to live and work in India during his last years. He saw the resources of India — the fauna and flora, from a fresh perspective. Consequently, many younger scientists who listened to his pronouncements with an open mind continued to follow the traditions started by Haldane long after his death in 1964. Today, his impact can

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be seen in several sciences, such as ecology, population genetics, animal behavior, human genetics, biometry, statistics, paleontology, epidemiology and several other biological and medical sciences. One branch of research which benefited India’s Defense Department was Haldane’s contributions to human physiology which was concerned with adaptation to cold temperatures and higher atmospheric pressures, as well as his great work in diving physiology and inhalation of various toxic gases. Haldane’s advice is of great interest to both underwater research of the Navy and also to the physiological problems encountered in space flight.14 The fundamental physiological principles enunciated by Haldane and his father are still important today in many fields and are followed by scientists all over the world. Two such examples are the use of heart-lung machines in surgery and the development of a cure of tetany. To conclude, the impact of Haldane’s great genius will be felt in India and the rest of the world for many years to come.

References 1.

Dronamraju KR (1986) Haldane: The Life and Work of JBS Haldane with Special Reference to India. Aberdeen (UK): Aberdeen University Press (1985). (A summary was published in my review: “On some aspects of the life and work of John Burdon Sanderson Haldane, FRS in India. Notes and Records of the Royal Society of London) 41:211–237

2.

Dronamraju KR (Ed.) (2009) What I Require from Life: Writings on Science and Life from JBS Haldane (with a Foreword by Sir Arthur C Clarke), Oxford University Press, Oxford

3.

Haldane JBS (Ed.) (1932) In: The Causes of Evolution. Longmans. Green, London

4.

Dronamraju KR (Ed.) (1968) In: Haldane and Modern Biology. Johns Hopkins University Press, Baltimore

5.

Haldane JBS (1959) In: An Indian Perspective of Darwin. Centennial Review, Michigan State University,

6.

Roy SK (1960) Interaction between rice varieties. 57:137–152

7.

Dronamraju KR (1960) Selective visits of butterflies to flowers, a possible factor in sympatric speciation. Nature 186:178–179

8.

Davis TA (1963) The dependence of yield on asymmetry in coconut palms. J Genet 58:186–215

9.

Spurway H, Dronamraju KR, Jayakar SD (1964) One nest of Sceliphron madraspatanum. J Bombay Nat Hist Soc 61:1–26

10.

Ray AK, Haldane JBS (1965) The genetics of a common Indian digital abnormality. Proc Nat Acad Sci 53:1050–1053

11.

Darwin C (Ed.) (1859) In: On the Origin of Species. John Murray, London

12.

Dronamraju KR (Ed.) (1990) In: Selected Genetic Papers of JBS Haldane. Garland Publishing Inc., New York

13.

Dronamraju KR (Ed.) (1995) In: Haldane’s Daedalus Revisited. With a Foreword by Nobel laureate Joshua Lederberg. Oxford University Press, Oxford

14.

Haldane JBS (1960) Physiological problems at high pressure. Aero Medical Society J 1–10

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5 Charles Darwin: A driving force for humanity toward agnosticism Amit Sharma Structural and Computational Biology Group, ICGEB, New Delhi - 110067, India [email protected]

Abstract: Charles Darwin’s insights into evolution of biological life are perhaps the most significant contributions in the realm of human existence. There have been many other startling scientific discoveries, and indeed many are yet to come, but arguably none have caused such intense, visceral reactions in mankind like Darwinian ideas. Nearly a century and a half after the unbiblical Origin of Species appeared, the fact of biological evolution as a step-wise, slow, blind, non-religious phenomenon continues to awe many, while riling the religious bigots. More significantly, Darwinian forays into evolution of life have laid the foundation for modern scientific investigations, and have profoundly guided and influenced all spheres of biological research. The role of ‘evidence’ to back up human ideas has become a mainstay in evolved thought. A direct result of this quest for ‘evidence’ is the devaluation of religious claims. Rejection of all religious neurosis is however insufficient now, and its possibly time to adopt ‘evidence-based existence’. The short essay here deals with some such issues. Keywords: Atheism, Darwin, Dogmas, Evolution, Religion All great truths begin as blasphemies. —Bernard Shaw

When interviewed,1 an African prostitute revealed that although she had had on average ~10 clients a day over the past 25 years (many of whom had been HIV positive and had subsequently died), she had miraculously remained HIV free. The interview ended with her final statement where she felt “thankful to god for saving her from HIV”. The irony here may be lost on the devout but genetic evidence has shown that it was not the divine this lady should have thanked, but rather a rare mutation in her genome that probably arose ~700 years ago1. This mutation makes human cells resistant to infection by HIV, and may have evolved to resist bubonic plague or smallpox at the time. Poignantly, this genetic roulette makes it likely that her genes, which can withstand the HIV rampage in Africa, V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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may spread over the next generations in the population and save many from HIV. I hope this story illustrates two points – (a) the power of modern biology in light of evolutionary processes, (b) the ludicrous nature of religious belief to explain such biological oddities (wonders). This essay deals with the implications of Darwin’s evolutionary discoveries for understanding our existence.1–3 Accounts of Darwin’s biographical life may be found elsewhere in this book, or indeed on various websites dedicated to Charles Darwin. In particular, this essay deals with the dichotomy between our new understanding of biological life (derived from Darwin’s works) and the alternative explanations for life’s origins (derived from the axis of monotheistic and older religious systems). Revolutions in science over the past many centuries, including Copernican and Darwinian discoveries, have provided unambiguous, testable, rational and unbiased answers to understandable human inquiries about emergence of both our universe and life in it. However, the sway of dogmatic beliefs on humanity continues to rise – and despite more than 150 years of Darwinian revolution his insights remain topics of debate. An excellent example of the continuous nature of debate on Darwinian insights is the launch of this very book. Clearly, a lot remains to be learnt and accepted about Darwin, evolutionary biology and the inherent contradictions between Darwinian ideas and varied versions of religious stories. Note in contrast that Copernican and Galilean scientific revolutions have been more widely accepted and there are, hopefully, no books commissioned that still debate whether earth is at the centre of our universe (although again, there must be a band of zealots who think differently). In part, lack of general acceptance of Darwinian insights into the origins of biological life stem from deep seated hubris humans have had – fueled further by religious delusions. Most dogmatic belief systems remain essentially in complete denial of scientific discoveries, perhaps because the latter directly threaten or overthrow the schizophrenias that religions like to perpetuate. I have at least, as I hope, done good service in aiding to overthrow the dogma of separate creations. —Charles Darwin

Part I: On Darwin – the master iconoclast Charles Lyle, father of geology, profoundly influenced Charles Darwin. Charles Lyle had proposed (correctly) that the earthly landscapes were not formed over a few thousand years (as has been wrongly advocated by dominant religious systems) but instead over millions of years by gradual change and as a result of natural (physical) forces.1 Darwin read up on Charles Lyle’s geological insights while on Beagle, and there is little doubt that this must have influenced Darwin tremendously. To dwell on the vastness of time since earth formed and life

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~4.5 billion years

Cyanobacteria

Earth birth

Eukaryotes

Single celled

Scale

Multicellular

Mammals Vertebrate

Time

500 million years 50 million years 5 million years

= represents time required for continuous re-incarnation of a 100 year old human more than 50,000 times Figure 1. A linear perspective on the length of time (horizontal bar) since earth originated and since various forms of life evolved. Note that for the first ~2000 million years there was only bacterial life. The vertical bars represent times when respective life forms appeared. The scale bars represent time periods and the smallest speck equates ~5 million years. If a human lived for 100 years then this smallest speck will contain more than 50,000 reincarnations, back to back. The scale of time since life originated on earth and started to evolve is almost unfathomable by everyday human markers of time

evolved is challenging to say the least (Fig. 1). In a way, Darwin’s insights may be considered very similar to Lyle’s – the difference essentially lies in the resolution of objects studied. Just like in Lyle’s (geological) universe, in the Darwinian world also there is the (biological) landscape, the eons of slow change and the natural force (natural selection) that orders objects (life). Many a long dispute among divines may be thus abridged: It is so; It is not so. It is so; it is not so. —Benjamin Franklin

Darwin’s discoveries on the evolution of life and mechanisms therein have influenced most if not all scientists. Fundamental research in biology during the last 150 years has developed within the framework of evolutionary biology – and has led to revelation of the genetic (DNA) basis of life. The key tenets of Darwinian1–3 and modern evolutionary biology4–6 are: (1) Random mutations are the central players that drive evolution, (2) Harmful mutants are deleted and beneficial variations tolerated by force of natural selection, (3) Evolution moves

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forward by collecting small, useful variations in a gradual manner over a vast length of time, (4) Process of evolution has remained the same over time, and (5) All biological life (extinct and extant) may be drawn as a ‘tree of life’ – as depicted by Darwin in the Origin of Species. The first two points are the mainstay of Darwinian ideas. Satan hasn’t a single salaried helper; the Opposition employs a million. —Mark Twain

Mutations are considered to be random occurrences but only in the sense that there is no foresight (i.e. the system is unaware of beneficial mutations a priori). The key insight into the random mutations that have driven evolution is that these alterations are not ‘directed’ or ‘guided’. Mutations are in general random and occur rarely.4–6 But most importantly, mutations are blind to whether they will end up benefiting the organism or not. The next step - natural selection - is far from ‘random’. These twin processes of ‘change’ and then ‘fixation’ iterate and thereby underpin evolution of life. Many organisms have existed for billions of years without any significant (genomic) change. Others may evolve rapidly under various biological or environmental stresses. In either case, natural selection watches over and approves those best adapted. In humans, juggling of parental genes during sexual reproduction provides enough fuel for natural selection to keep working on the resulting progeny. However, the saga of variation (mutations) versus fixation (natural selection) does not play out evenly. Once organisms have ‘adjusted/adapted’ to their environmental stresses, they may still incur random mutations but these variations will not be policed by natural selection unless a new selective pressure is applied on the system. An example of this is the genetic discovery of resistance amongst some humans to infection by HIV.7 This genetic background in ‘select’ humans has probably existed for ~700 years but it is only the recent appearance of HIV infection in humans that these ‘mutant’ genetic profiles may start to play a role in natural selection. Therefore, stochastic variation, without direction or purpose, fuels evolution. Herein, chance begins to surface as a key ingredient in evolutionary processes, but not without natural selection watching over it.8–11 The introduction of ‘chance’ in matters of life is unsettling for creationists, who like to believe that humans or even animals are “engineered” biological specimens. But as science has shown over and over again, chance and chance alone is responsible for the diversity in the living and in the dead. Evolution is driven forth by genetic randomness which is followed by determinism via natural selection. Mechanistically, all biological diversity has therefore been generated by force of natural selection which works upon random genetic tinkering. These evolutionary processes are terrifically creative and powerful, as evidenced by the wonders of flora and fauna. The Darwinian idea of evolution by natural selection constitutes a fundamental law of nature which governs life. This Darwinian revelation has thankfully obviated any requirement

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for solace in whimsical and mythical stories of life’s origins as divine gifts. But natural selection is also blind, emotionless, directionless and in itself aimless and perpetual. By the development of vaccines, drugs, surgeries and health care systems, modern medicine aims to fight back the ruthless and stoic force of natural selection. With our new understanding of natural selection as a power that both creates and destroys, aimlessly, we have and must continue to protect those who are genetically or otherwise weak and will be therefore the first victims of natural selection. No amount or effort spent on religious intercourses will rescue children and the frail from opportunistic viruses, bacteria and parasites (which altogether are only doing what their genomes drive them to do). Only man’s ingenuity and rigorous commitment to reason, rationally and science can protect all of us from the blind force of natural selection. We can allow satellites, planets, suns, universe, nay whole systems of universes to be governed by laws, but the smallest insect, we wish to be created at once by special act. —Charles Darwin

Natural selection cannot anticipate future environments on earth. Therefore, the set of existing organisms can never be fully prepared for environmental catastrophes that await life. An outcome of this is the extinction of those species which cannot overcome environmental adversity. This failure to survive, in modern terms, can be attributed to the genomes which are unable to withstand geological vagaries or biological mishaps (infections, diseases and so on). In biological evolution on earth, extinction of species has been a major feature. Earth may presently have up to 10 million species, yet more than 90% of species that have ever lived on earth are now extinct.8–11 Once again, the creationist doctrines fail to satisfactorily address why a divine creator will firstly bother to create millions of species and then allow them to perish. The Darwinian explanation for extinct life is once again simple, elegant and at once convincing – biological life goes extinct as a function of environmental or biological assaults for which their inheritance deems them ill-equipped. Therefore, the so-called Darwinian theory of evolution is not a theory at all. Evolution happens – this is a fact. The mechanism of evolution (Darwin proposed natural selection) is also amply supported by scientific data. Indeed, to date no single zoological, botanical, geological, paleontological, genetic or physical evidence has refuted either of the central two main Darwinian ideas. To those free of religious bigotry, Darwinian laws are acceptable just like the laws proposed by Copernicus, Galileo, Newton and Einstein – sets of natural laws that explain natural phenomenon in the universe. The spectacle of what is called religion, or at any rate organized religion, in India and elsewhere, has filled us with horror, and I have frequently condemned it and wished to make a clean sweep of it. —Jawaharlal Nehru

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Darwin’s original tree of life, which can be viewed in other chapters of this book, remains a stunning depiction of extinct and extant life. Creatures who ‘made it’ through the lines are present today and those where lines ceased did not (extinction). The other striking implications of this tree of life include (1) questioning the idea of progress in evolution, and (2) wondering whether there is a single route to the biological present. All modern day biological life is equally evolved, and most organisms have been evolving for a lot longer than humans. All that natural selection has ensured is the passing over of genetic contents from one organism to its subsequent generations. Darwin’s original tree of life has been verified by genomic studies in the past two decades.12 None of the modern scientific genomic discoveries have refuted the core of Darwinian ideas. From the tree of life discussion, it follows naturally that all organisms can be traced back, most probably, to one ancestor in whom life originated billions of years ago. A man has no reason to be ashamed of having an ape for his grandfather. If there were an ancestor whom I should feel shame in recalling, it would be a man of restless and versatile intellect, who, not content with success in his own sphere of activity, plunges into scientific questions with which he has no real acquaintance, only to obscure them by an aimless rhetoric, and distract the attention of his hearers from the point at issue by eloquent digressions and skilled appeals to religious prejudice. —Charles Darwin

A key question in evolutionary biology has been regarding complexity – either organizational and/or genomic.8–11 Will it be fair to understand that life has been getting more complex since its inception ~3.5 billion years ago? The likely answer here is no. It has been shown that many ancestral genomes were comparable in genomic content to the modern ones. It even seems that some organisms may have undergone gene loss and genome shrinking as possible modes of evolution. Therefore, excessive genomic cargo does not correlate with biological complexity (compare the number of genes between humans, mice and rice). Again, it was Darwin’s genius to tie together the most complex and the simplest of organisms into one interconnected thread of life. Darwin provided the idea that the apparent grandeur of life in nature, regardless of its biological size and complexity, had a natural basis and did not require any metaphysical justifications. Devout believers are safeguarded in a high degree against the risk of certain neurotic illnesses; their acceptance of the universal neurosis spares them the task of constructing a personal one. —Sigmund Freud

Chimpanzees are the closest living relatives of humans and our common ancestor probably lived ~6–8 million years ago (Fig. 2). Humans and chimps belong to the hominid group which also has other charming members (some

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Figure 2. Top panel - shows the striking structural parallels between hands of humans and his cousins. Structural features like these are in abundance when one compares anatomies in related (and at times unrelated) biological creatures. Genomic studies of the underlying genetic basis (DNA) for these similarities confirm the anatomical observations. Lower panel – a family album of humans with closest cousins. Gorilla and chimpanzee genomes are ~99% identical to the human genome – a fact that seals the debate on human evolution from ape-like ancestors

extinct) like gorillas and orangutans. There is no single evolutionary line that leads to humans, rather there are branches and more branches and furthermore more branches.8–11 This kind of speciation requires thousands of years making it difficult to observe. In another sobering thought, it seems that there were up to five different hominin species that existed previously – now only homo sapiens sapiens does. All people today are classified as Homo sapiens sapiens and these likely arose ~200,000 years ago from earlier species (Fig. 3). Data from fossils indicate that modern humans likely evolved from archaic humans in East Africa. Modern human fossils from Asia suggest that the present species may have been in

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Asia around 60,000 years ago. It seems that human population started to grow fast ~40,000–60,000 years ago. This growth was concomitant with migration into new areas on earth and other developments. Incredibly, the present world population has reached close to 6.6 billion people, although it is abundantly clear that earth with its finite natural resources cannot support so many. Migration levels, gene flow and genetic intermixing today are probably the highest they have ever been in history – best examples are populations of cosmopolitan cities worldwide. Clearly, the drama of Darwinian evolution is very much on-going, both in terms of genetic variations and forces of natural selection. There are several examples of this already, and include development of genetic resistance to infectious agents like malaria parasites and HIV. The growing and potent field of comparative genomics is revealing features of the physical principle (i.e. DNA) that drives evolutionary processes at an ever increasing pace.12 In time, we shall know how different the present human race already is from those humans who existed 10,000–30,000 years ago. Millions of humans of varied genetic stocks and ancestries co-exist in modern cities the world over. On one hand, this pool represents an exciting DNA cauldron which may ensure appearance of enough mutations that may come in handy for humans. However, these DNA broths also provide fertile ground for contagious diseases – potentially adding new selective pressures. DNA neither knows nor cares. DNA just is. And we dance to its music. —Richard Dawkins

~Millions of years

Human ancestors

5–4

Ardipithicus ramidus

4

Australopithecus anamensis

4–2.7

Australopithecus afarensis

3–2

Australopithecus africanus

2.2–1.6

Australopithecus robustus

2.2–1.6

Homo habilis

2.0–0.4

Homo erectus

0.4–0.2

Homo sapiens archaic

0.2–0.03

Homo sapiens neandertalensis

0.2–present

Homo sapiens sapiens

Figure 3. Shown here is immediate human ancestry after breaking away from the apes many millions of years ago. Note the time required for a new species to arise. The past ~half a million years represents a gradual evolution of modern humans from homo sapiens arachaic

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Figure 4. Web of life based on genome sequencing of numerous biological specimens. These diagrams place all organisms whose DNA has been sequenced on a relatedness map. The three kingdoms of life – namely, bacteria, archaea and eukaryotes are shown along with representative organisms from each. Revelation of encoded DNA information from 1000s of organisms now supports the tree of life view that Darwin had proposed. These data suggest that all biological life is related and likely originated from a common ancestor via transfer of DNA through eons. The dot indicates position of humans on this genetic web along with the number of genes present in humans

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The physical basis for transmission of evolutionary processes was still not discovered at the time of Darwin. We now know it to be DNA, and it binds all life together (Fig. 4). Our ancestors have passed on, in an immaculately unbroken fashion, their DNA to subsequent generations. Past humans who could not procreate before their death failed this Darwinian odyssey, and their DNA is no more amongst us. One of the last experiments that Charles Darwin conducted was on cockles. In 1882, Walter Crick (a shoe maker keen on molluscks) contacted Darwin about a cockle he had found hitchhiking on a water beetle. This find invoked Darwin’s curiosity and eventually resulted in a study published in Nature in 1882 titled along the lines of “On the dispersal of freshwater bivalves”. A few days later Darwin died, and a few years later (in 1903) Walter Crick also died.13–15 However, exactly 50 years hence, not too far from where Darwin had written the Origin of Species, Walter Crick’s grandson and avowed atheist Francis H.C. Crick discovered the structure of DNA – the very physical principle that has enacted evolution of life over billions of years. If revealed religions have revealed anything it is that they are usually wrong. —Francis Crick

Part II: On sadistic prescriptions Not only is there no God, but try getting a plumber on weekends. —Woody Allen

The two Charles’s - Lyle and Darwin - had made it perfectly feasible for humans to exist without recourse to any divine dogmas, to wonder about life and the universe without seeking flimsy, prejudiced and contradictory explanations for existence of our universe and its life. However, religious beliefs have continued to enslave humankind the world over. In a sense, religious beliefs aim to overrule the essence of ‘nature’ in us, to control the encoded DNA that propels us, in favor of ‘nurturing’. The latter provides not only flexibility and but also a window of opportunity to propagate just about any dogmatic system. It may be considered that almost all religious dogmas are essentially un-Darwinian – their effort is to abolish natural diversity in humans and to replace it with a sterile uniformity. But uniformity in biological life is contradictory to Darwinian facts. Life is in constant dynamism both as a result of environmental vagaries and underlying genetic differences. The worst vice of the fanatic is his sincerity. —Oscar Wilde

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Figure 5. A linear view of the past 80,000 years of existence of homo sapiens sapiens. The start of the arrival of various religious dogmas is indicated (~4000 years ago). Recent 500 years have witnessed evolution of the most significant scientific ideas to date. This period has provided the deepest and greatest discoveries regarding our place in the universe. These scientific discoveries have debunked prevalent dogmatic beliefs and nullified any role of the divine in physical or biological evolution of our universe. Lower panel - note the average life expectancy of humans in the past 10,000 years. It is evident that growth of religious ideas and practices had no impact on increased life expectancy (or quality) in humans. The significant jump in human life span (and in quality) has happened directly as a result of developments in science (more specifically, of evidence-based medicine)

Creationist ideas take away the beauty of discoveries that bright human minds make in the realm of science. The effort of creationists is to provide a divine explanation for existence and evolution of the physical and the biological universe. But this effort is constantly, almost daily, being thwarted by scientific discoveries (Fig. 5). When sufficiently challenged on scientific grounds, the devout seek

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refuge in illusionary dichotomies like ‘science and religion are separate spheres of life’. In fact, there is nothing intellectual, cerebral, scientific, or intelligent in any of the religious movements about either the evolution of biological life or about the physical universe. The religious existence that is idealized by many devout is suffocating, revengeful, painful, and full of vacuous religious practices not to mention prohibitions, orders, sermons, restrictions and regulations. Worst of all, many a religious lifestyles are justified on the schizophrenic concept of heaven and hell. Religious prescriptions have included (and still do in many societies) incarceration, starvation, laceration, mutilation, strangulation, suffocation, crushing, choking, burning, garroting, stoning, flogging, amputation, and crucifixion. A quick survey of modern times shows that the most troubled, backward, violence-ridden, illiterate, undemocratic, misogynistic, non-egalitarian and scientifically backward nations also happen to be very religious. This is not a simple coincidence, and the underlying message is clear – people still adhere to religious explanations for origins of physical and biological life no matter how contradictory these are to facts. A quick preview of sociological facts on the extent of human suffering on earth is sufficient to put even the most religious of human minds into a contemplative mode about the creator. The divine creation and its subjects seem to be replete with misery, starvation, violence, rape, child torture, genocides, massacres, droughts, famines and disease epidemics. The ‘cure’ for apostasy may be death. Yet, religions are followed blindly, and their fictitious tales about development of the universe are actively propagated. Contrast this scenario with the elegant, beautiful, consistent, cogent, testable and evidence-based understanding of biological and geological life on earth provided by Darwin and Lyle. We can make a lot more sense of human travails in light of evolution of both the physical and the biological universe. Darwin’s discoveries allow us to reject the religious and spiritual basis for human misery and to confront earthly realities by accepting our place in this evolutionary tussle. Incurably religious, that is the best way to describe the mental condition of so many people. —Thomas Edison

In a recent survey of the Indian scientific workforce (from most if not all top Indian institutes), it was revealed that ~88% were convinced about the theory of evolution.16 But the good news ends here. It appears that only ~25% of the polled declared themselves as either agnostic or atheistic. Many of the polled seem to value religious myths and/or are open to various beliefs. In the same study, it was discovered that ~50% of the surveyed scientists feel there is efficacy in homeopathy and also in praying (perhaps both will be even better). More than 10% of the polled believed in palmistry, horoscopes, vaastu, astrology and faith healing. Close to 40% of the interviewees felt it was acceptable to seek divine blessings before

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launch of rockets. Finally, ~24% and 38% of the scientific workforce believed that holy people and god can perform miracles, respectively of course. Such blinding adherence is likely a direct function of religious conditioning from childhood. In India in general, besides participation in religious systems, there is wide public acceptance of additional ‘belief systems’ including crystal healing, stone healing, reiki, distance healing, faith healing, magnetic therapy, numerology etcetera. Such brazen acceptance of systems which lack evidence reflects a sad albeit sound conditioning. The mechanism of propagation of such conditionings is rather clever however. Religious doctrines and other belief systems victimize children (and the naïve) first and foremost as part of a grand conditioning program. This routine is clearly meant to offset the genetic programming in children, which probably tends to question rather than obey initially. Religious brain-washing and conditioning in the irrational also aims at neutralizing the inherent genetic differences in humans. In order for this religious indoctrination to work, it is essential that the nascent minds of children are addressed (or overpowered) – time lost at this stage may result in transition of children’s minds into young thinking adults and possible rejection of the suffocating religious myths thus fed. It is due to this that one finds that although many parents are happy for their children to decide on their ‘lives’ (careers, spouses, etc.) once children have attained adulthood and maturity, the same parents will not wait that long for religious subjugation of their children. The precious, impressionable, malleable, flexible minds of young children are the easiest targets for intellectual asphyxiation by rigorous religious conditioning with the ulterior motive of propagating myths about divinity. It is feasible that if indoctrination of children into belief systems ceased from hereon, religions will likely dwindle to insignificance within a few human generations. One is often told that it is a very wrong thing to attack religion, because religion makes men virtuous. So I am told; I have not noticed it. —Bertrand Russell

Contrary to religious beliefs in man’s perfection (or perfection in the work of the imaginary creator), there are numerous imperfections evident in humans as a result of Darwinian evolution. Cleary, most organisms are not perfectly adapted to their environments, and struggle for survival continues on a daily basis on earth. Rudimentary organs showcase the dynamic nature of natural selection, as these organs are essentially of little or no value to the biological individual at present. From a creationist perspective, these vestigial flesh and bones smack either of incompetence of the creator, or at best of wastefulness and poor design. Humans exemplify some of these ‘design faults’. A list of potential defunct organs in humans include appendix, paranasal sinuses, vomeronasal organ, coccyx, extrinsic ear muscles, toes, neck rib, Darwin’s point, third eyelid, palmaris muscle, subclavius muscle, male nipples, wisdom teeth, erector pili, thirteenth rib, male

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uterus and female Vas Deferens. Evolution by natural selection on the other hand provides very satisfactory answers for these ‘extra’ organs, as these organs were probably of value to our ape-like ancestors or even earlier. Far from being the ultimate specimen of divine’s creativity, the reality of homo sapiens sapiens reflects ‘manufacturing’ on an ‘off’ day. Furthermore, humans seem to have no special status on earth (1) arguably in terms of being the most complex, (2) or of continued existence for the longest period, or (3) as most efficient biological machines, or (4) as the best ‘designed’ creature. Except human brain, every other human organ most likely has a superior homolog in another animal species on earth. Therefore, humans are not the pinnacle of evolution. We are far from perfect. We are also increasingly susceptible to new diseases and infections. Modern molecular biology has provided ample evidence for clear genetic linkages for numerous human ailments including heart disease, diabetes, infections, cancer, obesity, stroke and neurodegenerative disorders. These may be justified as divine retribution for agnostics or atheists but only flippantly. Darwinian insights into human evolution warn us that in the absence of medical science, modern humans will likely have a very precarious existence – left at the mercy of natural selection. Darwinian principles have shown us that divine miracles do not create life, do not nurture life and do not destroy life. Indeed, the object of life is uncomfortably balanced between environmental pressures and genetic wherewithal. Most of evolved creatures remain imperfect as all that natural selection cares about are the differential selective advantages that arise as a result of random mutations. Never mind perfect, even a fraction of normal vision or hearing or extra running prowess may be sufficient to tide a creature over its rivals. This daily, endless and directionless struggle is being closely watched and monitored by the force of natural selection and not by an imaginary, benevolent albeit inept ‘engineer’. At a molecular level, our DNA reflects that we are not much more than vehicles for its transfer to subsequent generations. Our DNA today is a collection of ‘noise’ made in passage over eons past – aberrations that despite their blindness allowed DNA propagation in those environmental conditions. A most striking and at once humbling depiction of biological life is presented by the so-called tree of life which places all biological beings on an evolutionary network – here man rests in peace amongst and between his biological relations and without a damn stamp of ‘miracle’ about him (Fig. 4). All extinct and extant life can trace its origins to one or few original organisms. It is the genetic cargo in those ancient organisms that has resulted in us of today. These linkage ideas have been verified by the description of genomic web of life based on DNA sequencing of numerous biological agents.12 Which is it: is man one of God’s blunders, or is God one of man’s blunders? —Friedrich Wilhelm Nietzsche

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Expectedly, after the death of Charles Darwin stories began to float about his so-called death-bed conversion to theism and even retraction of his theory.13–15 Darwin’s daughter Henrietta and son Francis both refuted such ludicrous claims – although I shall argue that even in the event that Darwin had a fit of undeserving sympathy for religion and possibly some trepidation toward the end of his life - even then we need not fall prey to the same. We don’t need know conversions. Darwin’s achievements and his genius helped man realize his material nature. Since Darwin, his ideas have also provided a backbone for all theoretical life sciences and also for modern medicine. Darwinian laws of mutation and natural selection reign over our deepest insights into modern biology. Ironically, those in denial of Darwinian principles seldom fail to utilize the benefits of modern medicine or for that matter any scientific advancement. The urge to cling to empty faiths is strong in many, despite the fact that only science rescues mankind. Darwin provided a materialistic basis for biological life, taking away its pretensions of links with divinity. Since Darwin, it is clear that biological life has no guiding forces, no accountability, no forgiver, no heavenly monitoring system, no loving overseer, no voyeuristic interferer, no spatial benefactor, no (moral) hero and no sympathetic angel. Darwin’s insights provide a driving force for humanity to withdraw from time-warped, non-scientific, irrational and poor attempts at explaining human life via divinity. With and after Darwin we can embrace science, reason, rationality and evidence-based existence without recourse to religious distortions. Darwinian discoveries have obviated the need for bogus explanations for origin of life once and for all. Darwin has made agnosticism or even atheism a human necessity. So, let’s revel and let our DNA rebel.

A short list of some facts relevant to this essay ● ● ● ● ● ● ● ● ● ● ●

Earth and proximal stars are ~4.6 billions years old. Earth was shaped by geological and physical forces during this time. Liquid water on earth is ~3.6 billion years old. Life originated in simple forms close to ~3 billion years ago. Organized, multicellular life is ~800 million years old. There were no birds or mammals 250 million years ago. Dinosaurus and humans could not have co-existed as 60 million years separate them. Major life forms of the past are no longer living. All present forms of life arose from ancestral forms that were different. Humans and modern apes have common ancestors. All biological life is related and shares a common genetic basis.

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● Religious dogmas appeared in the most recent 2–5% of the time since homo sapiens sapiens have been around. ● Clearly, the ‘creator’ needed evolution of language before ‘appearing’. ● Human life expectancy has increased as a function of modern medicine. Clearly, the ‘creator’ engineered low life span and unhealthy humans to start with. ● There is no evidence for better ‘upkeep’ of the devout over agnostics and atheists. ● To date, there is no evidence for any miracle.

References 1.

Richard Dawkins Series – ‘Genius of Charles Darwin’ and ‘Dawkins on Darwin’

2.

Darwin C (Ed.) (1871) In: The Descent of Man, and Selection in Relation to Sex. John Murray

3.

Darwin F (Ed.) (1887) Charles Darwin’s Autobiography. Basic Books, New York

4.

Koonin EV (2009). Nucleic Acids Res 37(4):1011–1034

5.

Haldane JBS (1932) In: The Causes of Evolution. Longmans, Green & Co., London

6.

Huxley JS (1942) In: Evolution: The Modern Synthesis. Allen and Unwin, London

7.

Zolopa AR, Cllavel F, Soriano V. “HIV infection and antiretroviral resistance”.

8.

Avise JC (2006) In: Evolutionary Pathways in Nature: A Phylogenetic Approach. Cambridge University Press, Cambridge, UK

9.

Dawkins R (1976) In: The Selfish Gene. Oxford University Press, Oxford

10.

Dawkins R (2004) The Ancestor ’s Tale: A Pilgrimage to the Dawn of Life Houghton Mifflin

11.

Dawkins R (1986) The Blind Watchmaker. Longman

12.

Interactive Tree of Life can be viewed at http://itol.embl.de/

13.

Barlow N (1958) In: The Autobiography of Charles Darwin Collins. London

14.

L. Eiseley (1958) In: Darwin’s Century: Evolution and the Men Who Discovered It, Doubleday. New York

15.

Hodge MJS, Radick G (Eds.) (2003) In: The Cambridge Companion to Darwin. Cambridge University Press, Cambridge

16.

International Survey Worldviews and Opinions of Scientists India (2007–08) by Ariela Keysar, Barry A Kosmin and Dr N Innaiah. For information on Institute for the Study of Secularism in Society and Culture see www.trincoll.edu/secularisminstitute.

6 Phylogeographic evolution of plant viruses Anupam Varma* and Shelly Praveen** Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi - 110012, India *[email protected], **[email protected]

Abstract: Viruses, discovered about four decades after the publication Darwin’s treatise ‘The Origin of Species’, are important tools to address the questions related to the evolution of species. Viruses are unlikely to have existed in the pre-cellular environment, as they require the complex host cell system to replicate and are inert outside such cells. Viruses might have coevolved with their natural hosts. Some of the present day viruses could be escaped host genes, as the genome of some of such viruses is found to be integrated with host genome. However, there is no reason to believe similar origin of all viruses. The viruses that might have originated in one group of organism may occur in another group. Some viruses replicate both in plants and insects as their hosts, leaving the question open about their origin. Whatever the origin, biologically, morphologically and molecularly similar viruses seem to have evolved in diverse pathosystems suggesting convergent evolution. High rates of mutations, genomic recombination, intensification of agricultural practices, exchange of germplasm, and human intervention in inadvertently introducing exotic viruses to new environments and host genes for susceptibility have played key roles in the evolution of present day viruses. In this article, we briefly discuss phylogeographic evolution of some of the important plant viruses like badna-, begomo-, poty- and tospoviruses, which have emerged as a severe constraint in improving crop productivity in the tropics and sub-tropics. Keywords: Phylogeographic, Evolution, Plant viruses

Introduction Viruses, discovered about four decades after the publication of the treatise “The Origin of Species by Means of Natural Selection or Preservation of Favoured Races in the Struggle for Life” by Charles Darwin in in 1859, are emerging as important tools to address the questions related to the evolution of species raised by Darwin. Viruses and the viroids, the simplest known replicating systems, have been an attractive subject of speculation about their origin for long. Although V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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the viruses are unlikely to have existed in primitive forms in the pre-cellular environment, as they require the complex host cell system to replicate and are inert outside such cells, the possibility of their pre-cellular origin cannot be ruled out. Origin of viruses by degeneration of cells of obligate cellular parasites seems improbable as the viruses use the host protein synthesizing machinery, generally lack membranes and do not multiply by binary fission. It is logical to assume that the present day viruses might have originated in their natural hosts and may have found niche in a diverse host system. Some of them could be host genes that escaped, as the genome of some viruses is integrated with host genome. However, there is no reason to believe similar origin of all viruses, and the viruses that might have originated in one group of organism may occur in other group. Some viruses replicate both in plants and insects as their hosts, leaving the question open about their origin. Whatever the origin, biologically, morphologically and molecularly similar viruses seem to have evolved in diverse pathosystems suggesting convergent evolution. The size of the genome of plant viruses varies from 250 nt for viroids, the smallest known pathogens to about 30 kbp for the largest plant infecting reoviruses. The viruses appear to have co-evolved with their hosts. Therefore, chances are that the viruses infecting insects might have evolved along with insects about 400 millions year ago, plant viruses around 200 to 40 million years ago, and mammalian viruses about 80 million years ago. However, so far, there is no evidence of the occurrence of viruses in the fossils. The advent of efficient detection techniques may soon unravel the possible fossilized viruses. Bunya-, Reo- and Rhabdoviruses, which infect vertebrates, invertebrates and insects, may have had a common origin in insects. Interestingly, some insect viruses like Nilaparvata lugens reovirus and Rhopalosiphum padi virus, which do not infect plants, can be acquired by healthy insects from plants on which infected insects have fed. Insect viruses could have moved to plants and animals about 135 million years ago during the cretaceous period. Some of the viruses like the Tymoviruses might have moved across the contingent as a result of continental drift 138–80 million years ago. Co-evolution of plant viruses with their hosts is testified by the evolution of potato viruses like Potato virus X and Andean potato mottle virus in the Andean region of South Peru and Northern Bolivia, which are the centres of origin of potato.

Underlying factors for the evolution of viruses Many of the plant infecting viruses, like Tobacco mosaic virus, Cucumber mosaic virus and potato viruses, have been known for a long time and continue to cause serious disease problems in various parts of the world. Gradually many ‘new’ viruses have been discovered with the help of improved and efficient diagnostic techniques (Fig. 1). A large number of new viruses have been identified during the last two decades mainly due to the development of advanced molecular diagnostic

Phylogeographic evolution of plant viruses

Figure 1. Development of diagnostic techniques for plant viruses

Box 1: Underlying factors leading to emergence of new variants of viruses  Genotypic changes  Mutations  Recombinants  Pseudo recombinants  de novo gene acquisition  Host factors  Introduction of new crops or their genotypes susceptible to endemic viruses  Changes in the cropping system  Movement of viruses to new ecosystem  Vector factors  Environmental factors

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Figure 2. Emergence of viruses in tomato

techniques. This is amply illustrated by the sharp increase in the number of viruses infecting tomato in various parts of the world in the last decade (Fig. 2). With the expected development of diagnostic DNA Chips, the number may swell many folds. All the ‘new’ viruses may not be new but detected as a result of increased efforts and application of molecular diagnostics. Yet, many new strains and truly new viruses seem to have evolved due to various underlying factors (Box 1). Among these, high rates of mutation and frequent genomic recombination have played important roles in the evolution of viruses. Intensification of agricultural practices, exchange of germplasm, and human intervention in inadvertent introduction of viruses to new environments and introduction of genes for susceptibility in efforts to improve crop productivity have also been critical. These factors have resulted in wide geographical distribution of viruses and emergence of serious virus disease problems across the world. Here we examine phylogeographic evolution of some plant viruses which have emerged as major constraint in crop production particularly in the Indian sub-continent.

Badnaviruses Badnaviruses, bacilliform DNA viruses, belong to family Caulimoviridae. The importance of these viruses has been realized relatively recently, although the diseases caused by them have been in prominence for a long time. Emergence of Cacao swollen shoot virus (CSSV), the first Badnavirus described in 1947 is an excellent example of an inconsequential virus assuming a serious proportion due to the introduction of exotic plants in a new environment. In the first half of

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the last century cacao was introduced in West Africa from South America. Soon, CSSV, which occurs in indigenous wild plants, was transmitted by several species of mealy bugs in a semi-persistent manner to cacao causing devastating swollen shoot disease. To check the spread of CSSV, it is estimated that since 1945 over 100 million cacao trees have been cut down in Ghana alone. Several badnaviruses affecting banana, citrus and sugarcane in India have been characterized recently. Phylogenetic analysis of nucleotide sequences of their genomes and the genomes other badnaviruses shows their clustering according to their hosts rather than their geographic origin (Fig. 3). Citrus yellow mosaic virus (CMBV) was first detected in 1992 in Karnataka in Pomello plants, since then it has spread to Andhra Pradesh and Maharashtra apparently due to the distribution of infected plants. The viruses affecting citrus are subject of extensive research in all citrus growing regions of the world, but, CMBV has not been found in

Figure 3. Phylogeographic analysis of badnaviruses based on full length genome sequences: Banana streak Acuminata virus (BSAuV) DQ092436; Banana streak virus (BSV) NC008018; Banana streak Trichy virus (BSTrV) DQ859899; Banana streak GD virus (BSGDV) DQ451009; Banana streak golden finger virus (BSGFV) NC 007002; Banana streak Mysore virus (BSMysV) AF 214005; Banana streak OL virus (BSOLV) NC003381; Cacao swollen shoot virus (CSSV) NC001547; Citrus yellow mosaic virus – Acid Lime (CMBV-AL) EU489744; Citrus yellow mosaic virus - Pummelo (CMBV-PM) EU489745; Citrus yellow mosaic virus Rangpur Lime (CMBV-RL) DQ875213; Citrus mosaic virus Sweet Orange (CMBV-SO) AF347695; Commelina yellow mottle virus (ComYMV) X52938; Dioscorea bacilliform virus (DaBV) DQ822074; Dracaena mottle virus (DrMV) DQ473478; Kalanchoe top-spotting virus (KTSV) NC004540; Sugarcane bacilliform virus (SCBV) NC003031; Taro bacilliform virus (TaBV) AF357836; The isolates from India are shown by dark pink circles; these group with an isolate from China (BSGDV)

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any other country indicating its possible origin in India. Interestingly CMBV is phylogenetically closely related to CSSV. The two viruses could have a common progenitor. Experimental transmission of CMBV to cacao has not been tried, but so far there is no report of the occurrence of cacao swollen shoot disease in India, although cacao is grown in the region where CMBV is spreading, indicating biological differences between the two viruses. Banana streak virus (BSV), unlike CMBV , the viruses causing streak disease of banana are widespread, but all the isolates occurring in India and other countries, sequenced so far, cluster together. Kalanchoe top spotting virus (KTSV) also clustered with BSV isolates suggesting a possible common origin of these viruses, although they do not cross infect their natural hosts. Banana could have been the host of the ancestor of BSV and KTSV, and that independent host shifts could have occurred subsequently during the evolution of these viral species. Extensive spread of BSVs is facilitated by the global trade in planting material, and micropropagated from infected but apparently symptomless plants. Banana streak disease was first observed in 1958 in West Africa and subsequently in many banana growing countries. Significance of banana streak disease in the evolution of viruses was realized a decade ago when the molecular and cytogenic evidence showed integration of viral genome with the host genome.1 The integrated complete Banana streak OL virus (BSOLV) sequences found in banana cv. Obina l’Ewai (Musa AAB group) may have arisen by recombination between the host and viral DNA during their co-evolution. Such integrated sequences could cause episomal infection under certain conditions like the micro-propagation or development of inter-specific hybrids by crossing Musa acuminata (A genome) and M. balbisiana (B genome). Musa B genome seems to be the main source of BSV.2 In India, the genome sequences of commonly occurring Banana streak Mysore virus (BSMysV), have been found integrated with the genome of banana cv. Poovan (Musa AAB group), which is grown throughout the country. Integration of BSMysV genome with the genome of other cultivars is also expected as the entire germplasm of M. balbisiana seems to contain sequences of BSMysV. Similar integration of Badnavirus sequences could also occur in other hosts. Further work is required to understand the significance of integration of viral sequences with the host sequences and their role in the evolution of these viruses.

Begomoviruses Begomoviruses, belong to family Geminiviridae. The genome of begomoviruses consists of circular ssDNA encapsulated in twinned icosahedral particles, which are transmitted efficiently by whitefly Bemisia tabaci. The genome of some begomoviruses is monopartite consisting of single circular molecules of about 2.8 kb, known as DNA A, some have bipartite genome consisting of DNA A and another molecule of similar size known as DNA B. All the monopartite

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begomoviruses and some bipartite begomoviruses also have a betasatellite DNA of about 1.4 kb, which code for a single 13 kDa protein and depend on viral DNA A for replication. Some monopartite begomoviruses also have a self-replicating alphasatellite molecules coding for 36 kDa protein. Both types of satellite molecules depend on the helper virus for encapsulation and transmission. The significance of alpha-satellites is not known, but beta-satellites are shown to increase the virulence of the helper viruses. Interplay of these molecules with plant hosts and the vector whitefly has resulted in evolution of a large number of Begomovirus species. Begomoviruses have been broadly grouped as New World (NW) begomoviruses occurring in the Americas and Old World (OW) begomoviruses occurring in other parts of the world. The genome organization NW and OW begomoviruses is similar except that the latter also have an additional ORF AV2. NW begomoviruses need both DNA A and DNA B for infection whereas DNA A alone of OW begomoviruses can cause infection. Greatest diversity in begomoviruses and their satellites occurs in South-East Asia, indicating a possible centre of origin for these viruses.3 Phylogenetically, the begomoviruses originating in different continents like Africa, Asia and Americas form distinct clades. Amongst the Asian begomoviruses, those originating in India cluster separately indicating that begomoviruses have originated in different regions and are mainly evolving intra-regionally. A major reason for their geographical restriction is the absence of transmission of these viruses through true seeds, although some have spread through the intercontinental movement of vegetative propagules of plants and infected transplants.4 Begomoviruses have been a major constraint in Indian agriculture for a long time, but during the last two decades they have emerged as devastating pathogens of crops. Major contributory factors in the emergence of begomoviruses are the evolution of variants through mutation, recombination and pseudo-recombination. In addition, intensification of agricultural practices, introduction of susceptible genotypes for crop improvement, climate change and increase in vector population have also contributed to the emergence of begomoviruses in India and other countries.4 Begomoviruses associated with cotton leaf curl disease Cotton leaf curl disease (CLCuD) has been endemic in Africa for a long time, but in the Indian sub-continent, it was first observed in a small pocket in the Multan area in Pakistan about fifty years ago. It remained confined to that area, and first emerged in a serious proportion in 1988 in a newly released susceptible cotton var. S12 and by 1993, the disease affected 0.2 million ha in Pakistan. In India, it was first noticed in 1989 in a few plants of Gossypium barbadense in an experimental field at New Delhi (Fig. 4), where it was contained by rouging of symptomatic plants and avoidance of cultivation of G. barbadense. However, in 1994 and 1995, CLCuD appeared in epidemic proportion in commercial

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G. hirsutum fields in Punjab and Rajasthan along the border with Pakistan. The incidence of the disease formed a gradient, gradually declining in fields further away from the border. Emergence of CLCuD in epidemic proportion in those years was apparently caused by the viruliferous whiteflies blown in by dust storms from the adjoining CLCuD affected fields in Pakistan. The spread of CLCuD was restricted in the subsequent years by (a) cultivating G. arboeum, which is not affected by CLCuD and resistant varieties of G. hirsutum, (b) avoidance of cultivation of G. barbadense and its hybrids, which have been found to be most susceptible, (c) avoidance of cultivation of Okra in the CLCuD prone areas, as it can help in the buildup of inoculums, and (d) integrated management of weeds and vector Bemisia tabaci. Five Begomovirus species, Cotton leaf curl Alabad virus (CLCuD), Cotton leaf curl Gezira virus (CLCuGV), Cotton leaf curl Kokhran virus (CLCuKV), Cotton leaf curl Multan virus (CLCuMV), and Cotton leaf curl Rajasthan virus (CLCuRV), and their satellite DNA molecules are associated with CLCuD5. In India, CLCuD is caused by Cotton leaf curl Bangalore virus (CLCuBV), CLCuKV and CLCuRV. In Sudan, it is caused by CLCuGV and in Pakistan by CLCuAV, CLCuKV and CLCuMV. CLCuD also occurs in the backyard gardens in Karnataka. A new Begomoviruses species, tentatively named as CLCuBV, is associated with the disease in Karnataka. Fortunately, it has not spread to the commercial crops of cotton in Southern India. The CLCuD associated begomoviruses in India and Pakistan are highly divergent and form two distinct phylogenetic clusters. These viruses appear to have originated independently of CLCuGV, with which they share <75% sequence identify. Moreover, the isolates from the north-western parts of Indian sub-continent could have emerged as recombinants of endemic begomoviruses. Yellow mosaic disease of grain legumes Yellow mosaic disease (YMD) was first observed in the late 1940s in Lima bean

Figure 4. Cotton leaf curl caused by CLCuV

Figure 5. Golden mosaic disease of cowpea caused by MYMIV

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(Phaseolus lunatus) in Western India and in the late 1950s in mungbean in Northern India. Since then YMD has spread to all parts of the Indian Sub-continent affecting a variety of grain legumes.4 Cowpea is one of the important grain legumes in India. The cowpea varieties grown in India were immune to the begomoviruses causing YMD in other grain legumes, except a variant causing minor yellow fleck disease, but in 1978 a golden mosaic disease (Fig. 5) appeared in some germplasm lines introduced from West Africa and by 1984, it emerged as serious disease problem throughout Northern India. Like CLCuD, YMD in cowpea also emerged with the introduction of susceptible exotic germplasm.6 Two distinct bipartite begomoviruses have been identified to cause YMD of grain legumes in the Indian Sub-continent. In Northern India, YMD epidemic is caused by Mungbean yellow mosaic India virus (MYMIV) and in Southern India and Thailand by Mungbean yellow mosaic virus (MYMV). Several variants of MYMIV occur in different regions and crops in Northern India. The variant(s) of MYMIV causing golden mosaic disease in cowpea (CpGMD) must have evolved in the late 1970s when susceptible genotypes were introduced from West Africa. In western India CpGMD seems to be caused by pseudorecombination of genomic components, as the disease was shown to be caused by MYMIV DNA A in association with DNA B of MYMV, which was closely related to DNA B of an isolate MYMV from southern India.7 In 2004, a severe leaf distortion disease appeared in cowpea in Northern India. The infected plants developed yellow mosaic, downward leaf curling and enations. This disease was also caused by another variant of MYMIV in association with a betasatellite molecule.8 Analysis of sequences of DNA A and DNA B of a larger number of cowpea infecting isolates of MYMIV is required to identify the mutations, rcombinations and pseudorecombinations leading to increase in the host range of MYMIV. The begomoviruses causing yellow mosaic disease of grain legumes in India form a distinct group of begomoviruses, with MYMIV spreading in northern India and MYMV in southern India. YMDs have been mainly managed by the use of resistant varieties, but the life span of resistant varieties is limited due to fast emergence of resistant breaking viral variants.6 Begomoviruses affecting tomato Tomato is the natural host of largest number of begomoviruses, and the number is increasing at a fast rate; 52 begomoviruses were reported to cause diseases of tomato until 2003, and by 2006, the number swelled to >70 (Fig. 2). The diseases known by their generic names “tomato leaf curl” and “tomato yellow leaf curl” are most common. In India, tomato leaf curl disease (ToLCD) – known to occur for over sixty years – is widespread. Four distinct begomoviruses have been identified to cause ToLCD in India. Two, Tomato leaf curl Bangalore virus (TolCBV) and Tomato leaf curl Karnataka virus (ToLCKV) are monopartite and the other two, Tomato leaf curl Gujarat virus (ToLCGV) and Tomato leaf curl New Delhi

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virus (ToLCNDV) are bipartite begomoviruses. The distribution of these viruses suggests diverse origin of the begomoviruses causing ToLCD in India. ToLCGV and ToLCNDV have also been detected in weed hosts like, Datura metel, Solanum nigrum and wild sunflower, but not the other two viruses (ToLCBV and ToLCKV) in north-western India. Nearly 1000-fold increase in whitefly population and appearance of biotype-B of B. tabaci resulted in a severe epidemic of ToLCD in southern India in 1999. Limited surveys indicate that ToLCBV is distributed in Southern India, ToLCNDV in Northern India, whereas ToLCGV and ToLCKV have a wider distribution. Mixed infection with these viruses also occurs, including with ToLCKV, which is prone to recombination. Variability in tomato infecting begomoviruses seems to be arising due to genomic recombination. Several isolates of begomoviruses affecting tomato in India have been sequenced. Tomato infecting begomoviruses form two distinct branches.9 One branch is represented by the monopartite viruses isolated from southern India and another by the bipartite viruses isolated from northern India. Phylogenetically

Figure 6. Phylogeographic analysis of Tomato leaf curl viruses based on DNA-A genome: Tomato leaf curl Bangalore virus (ToLCBV) - keral I DQ852623; ToLCBV-keral II NC003891; Tomato leaf curl Gujarat virus ( ToLCGV) -AF449999; Tomato leaf curl New Delhi virus (ToLCNDV) - Himachal AM850115; ToLCNDV-India-Mild (ToLCNDV-Ind-m) U15016; ToLCNDV-IndiaSevere ToLCNDV-Ind-s U15015; Tomato leaf curl Iran virus (ToLCIV-I) NC005842; ToLCIV-II AY297924; Tomato leaf curl Karnataka virus (ToLCKV) BanII AF295401; ToLCNDV - Pakistan:Punjab AM258977; Tomato leaf curl Philippines virus (ToLCPhV ) NC005032; ToLCV-Puerto Rico AY134494; Tomato leaf curl Seychelles virus (ToLCSV-Sey) AM 491778; Tomato leaf curl Taiwan virus (ToLCTwV) NC003898; ToLCNDV Thai AB330079; Tomato leaf curl Vietnam virus (ToLCVV) NC004153

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these viruses differ from those occurring in South-East Asia, Australia, and South Africa. However, one branch of South and West Indian isolates represented by ToLKV is phylogenetically close to the Iranian isolates. The phylogenetic analysis, thus, showed emergence of distinct tomato infecting begomoviruses in different geographical regions (Fig. 6). The southern isolate TOLKV appears to be recombinant of viruses occurring in western and southern India. Interestingly in Northern India only ToLCNDV has been found. This virus seems to be most wide spread among the tomato infecting viruses from India, as it not only occurs in Pakistan but also in Thailand. Betasatellites are shown to be an important factor determining the virulence and evolution of begomoviruses. Considerable diversity has been found in betasatellites associated with tomato begomoviruses. India is a major producer of chilli (Capsicum annuum). The crop is susceptible to several viruses in various parts of the world. In 2004, a severe epidemic of chilli leaf curl disease (ChiLCD) destroyed the chilli crop in Jodhpur district of Rajasthan in India. The affected plants developed upward leaf curling, puckering, and leaf size reduction, stunting and produced no fruits. The epidemic was caused by the emergence of a variant of Chilli leaf curl virus (ChiLCuV), which shared 96.5% sequence identity with the ChiLCuV – [Pak:Mul] and is distantly related (59–68% sequence identity) to Cotton leaf curl Multan virus, Pepper yellow leaf curl Indonesia virus and Tomato leaf curl New Delhi virus.10 The virus must be endemic in the chilli growing areas of Rajasthan, but emerged in epidemic proportions due to weather conditions favouring build up of whitefly population.

Okra leaf curl disease Bhindi (Okra) Yellow vein mosaic disease (BYVMD) is endemic in India, but the crop was free of leaf curl disease (BLCuD), which commonly occurs in West Africa, until the late 1980s when it emerged after the introduction of okra genotypes from West Africa for crop improvement, particularly for breeding for resistance to BYVMD. Mixed infection by the viruses causing BYVMD and BLCuD is common in northern India. The plants infected by both the viruses are not productive. Such infections increase the chances of evolution of recombinants. Potyviruses Potyviruses, belong to family Potyviridae. They form the largest group of filamentous viruses. Many of the potyviruses are economically important and cause serious diseases throughout the world. Several potyviruses occur in India, causing serious diseases in a variety of crops like cucurbits, grain legumes, papaya, potato and sugarcane. Here we examine the phylogeographic evolution of Papaya ring spot virus (PRSV). PRSV is a serious constraint in the production of papaya in various parts of the world. In India, it was first found to occur in Pune region and

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Figure 7. Phylogeographic distribution of PRSV in India. (Source: Jyoti Sharma and A. Varma)

subsequently in various parts of Northern India. Gradually, it also spread to other parts of the country. Until 1972, PRSV was not found in regions south of Pune, but in mid 1970’s, the virus appeared in Karnataka. Papaya plantations in Tamil Nadu were free from this virus until 2001. During this period, popular papaya varieties like CO-2 and CO-7 were grown in the region. However, a couple of years later, the virus appeared in Tamil Nadu as well, in a very serious form, so much so that the experimental plantation of variety CO-7 of papaya at Coimbatore Agriculture University had to be completely uprooted. The virus also appeared in commercial plantations of papaya var. CO-2. The isolates which have been characterized from India11 show clustering according to geographical origin, except that an isolate phylogenetically related to a southern isolate was also found to occur in northern

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Figure 8. Phylogeographic analysis of Papaya ring spot viruses (PRSV) based on coat protein gene: PRSV – Australia (PRSV-Aus) U14736; PRSV – Bangladesh AY 423557; PRSV – Bangalore AF120270; ; PRSV – Brazil AF344640; PRSV – China AF243496; PRSV – Coimbatore AY687386; PRSV – Delhi AF063220; PRSV – Hyderabad AY238880; PRSV – Japan AB044339;PRSV Lucknow AY458620; PRSV – Philippines AF506894; PRSV Pune (mild) AF063221; PRSV Pune (severe) AY238881; PRSV – Raipur AY491011; PRSV – Ranchi AY458619; PRSV – Solan AF238883; PRSV – Thailand U14743; PRSV – USA D00595; PRSV – Varanasi AY238882; PRSV – Vietnam U14742; PRSV – West Bangal (PRSV-WB) AY238885

India. This could be due to the possible movement of infected transplants from southern to northern region. Similar spread also seems to have occurred for an isolate occurring in the western region (Fig. 7). The phylogenetic analysis also shows clustering of the isolates of Indian origin according to their geographical distribution (Fig. 8), except the clustering of PRSV-severe isolate originating from Pune with that the isolates originating in northern India. Interestingly PRSVmild isolate formed an independent branch; this isolate has been found useful in providing cross protection against the severe isolates. The isolates occurring in northern India group with the isolates from Australia, Brazil and USA, whereas, the isolate from Bangladesh seems to have separated from this cluster (Fig. 8). Similar relationship was also reflected in the comparison of full length sequences. Full length sequences of PRSV isolates from Delhi indicate genetic recombination of the Indian isolates with the American isolates.12 Based on the phylogeographic evidence it has been suggested that PRSV

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might have originated in India and spread through South-East Asia to eastern pacific region and also separately to the Americas, and from there to Australia, and Taiwan.13 PRSV is not transmitted through seeds, although there is a preliminary report from South-Asia of its seed transmission in papaya. Also, so far, there is no evidence of seed transmission of cucurbit infecting PRSV in cucurbit hosts. However, the movement of virus through transplants taken by the migrants from India to southeast Asia and eastern-Pacific Islands is a distinct possibility. Transplants could also been taken to the Americas. Sequences of more isolates from the path of spread of PRSV may provide clearer picture on PRSV evolution, and may explain the recombination between the Indian and American isolates. Recombination in PRSV is common. RDP (recombinantion detection programme) analysis of PRSV genome indicates that 5′ end of the genome is prone to recombination. Several sequences between 1–600 nt from the 5′ end of Indian PRSV seem to have recombined at 4 hot spots of isolates from Taiwan, 3–4 different hotspots of isolates from Thailand and China, 2 each from Hawaii, Mexico and Brazil. Interestingly the 5’ UTR seems to have moved around.14 Tospoviruses Tospoviruses belong to family Bunyaviridae, which has four other genera. Three of these genera, Orthobunyavirus, Nairovirus and Phlebovirus can replicate in vertebrates and vector insects. The fourth genus Hantavirus seems to have no vector. Tospoviruses, replicate both in vector thrips and host plants, and are emerging as the most destructive plant viruses in India and also other parts of the world. The tospoviruses occurring in Asia are most diverse.15 Generally, plant viruses do not kill their hosts, but the tospoviruses are the exception as they seem to be alien to plants. Tospoviruses have isometric particles of 80–120 nm containing tripartite genomic RNAs, designated as large, medium and small components. The genomic RNAs are tightly linked with ‘N’ protein, coded by the small RNA, forming ribonucleoproteins, which are encapsidated by a lipid membrane, consisting of two virus-coded glycoproteins and a membrane of host origin. Their structure suggests animal origin, finding a niche in plants. For a

Figure 9. Mung bean necrosis caused by GBNV

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Figure 10. Phylogeographic analysis of Tospoviruses based on nucleocapsid protein gene: Calla lily chlorotic spot virus (CCSV-Taiwan) AY867502; Capsicum chlorosis virus (CaCv-Thailand) NC008301; Gloxinia tospovirus (GTV-USA) AF059577; Groundnut bud necrosis virus (GBNV-India) AY871098; Impatiens necrotic spot virus (INSV-Japan) A109100; Iris yellow spot virus (IYSV-Netherland) AF001387; Melon severe mosaic tospovirus (MSMTV-Mexico) EU275149; Melon yellow spot virus (MYSV-Japan) NC008300; Peanut chlorotic fan spot virus (PCFSV-Taiwan) AF080526; Peanut yellow spot virus (PYSV-USA) AF013994; Physalis severe mottle virus (PhySMoV-Netherland) AF007151; Poligonum ring spot tospovirus (PoRSTV-Italy) EF445397; Tomato spotted wilt virus ( TSWVUSA) AY870391; Tomato yellow ring virus (TYRV-Iran) DQ810196; Tomato zonate spot virus (TZSV-China) NC010489; Watermelon bud necrosis virus ( WBNV-India) EU249351; Watermelon silver mottle virus (WsMoV-Japan) AB042650; Watermelon spotted wilt virus ( WBNVIndia) NC003843

long time tospoviruses were considered to be monotypic represented by Tomato spotted wilt virus (TSWV), distributed in the temperate and sub-tropical parts of the world, but now tospoviruses are represented by eight recognized and six tentative species, which are widely distributed and can infect about 1200 plant species; TSWV alone infects about 900 plant species. In India, occurrence of TSWV has not been detected so far, but two other tospoviruses - Groundnut bud necrosis virus (GBNV) and Watermelon bud necrosis virus (WBNV) - have emerged as the major pathogens of a wide range of crop plants, the natural host range of GBNV is wider, whereas WBNV seems to be restricted to cucurbits. In 2000, a severe epidemic GBNV occurred affecting groundnut in 0.25 million ha in Andhra Pradesh. This epidemic was caused by GBNV and an Ilarvirus (Tobacco

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streak virus (TSV). In subsequent years also, infection by these two viruses were common. Groundnut bud necrosis disease (GBND) caused by GBNV is a serious constraint in the production of groundnut throughout India. Occurrence of GBNV in groundnut has been known for a long time, but during the last decade the virus has also spread to other crops, like mungbean (Fig. 9), tomato and potato. One could argue that the virus was not detected earlier as the diagnostic tools were not available, but the diseases caused by tospoviruses are so destructive that these would not have been missed. For example, the destructive stem necrosis disease of potato, characterized by extensive stem and petiole necrosis, leaf distortions and stunting of plants. The disease is caused by GBNV. It emerged in central India in the early eighties. Since then, it has spread to other potato growing regions of the country, due to the introduction of susceptible genotypes in the GBNV endemic areas. GBNV is also fast spreading in tomato, particularly in southern and western India, and could assume serious proportion in these areas. WBNV emerged in the nineties as a devastating problem in watermelon cultivation in Karnataka. It has also spread to a limited extent in watermelon and cucumber in northern India and ridge-gourd in southern India.16 Other cucurbits may also be affected. Recently two other tospoviruses – Iris yellow spot virus (IYSV) and Capsicum chlorosis virus (CaCV) – are also reported to occur in the country. IYSV is fast spreading in onion growing areas in western India,17 and CaCV is emerging as a serious problem in chili pepper cultivation.18 Various genes of GBNV and WBNV genome are highly conserved sharing >95% identity. Phylogenetically tospoviruses occurring in Asia and the Americas form two major clusters.15 Three of the four tospoviruses occurring in India, i.e. CaCV, GBNV and WBNV, represent one branch of the Asian cluster, whereas IYSV represents another distinct branch, indicating a distant relationship from the other tospoviruses spreading in India. GBNV and WBNV have been found to occur only in India, whereas CaCV also occurs in Thailand and IYSV has a worldwide distribution. CaCV, GBNV and WBNV mainly infect plants grown through true seeds and tospoviruses are not seed-borne, which explains their restricted geographical distribution. In contrast to this IYSV infects bulbs crops, which are propagated by true seeds as well as vegetative propagules, which can carry viral infections. International trade in bulbs must have resulted in the wide distribution of IYSV, which seems to have originated in Europe. CaCV might have originated in Australasia, and introduced in India through infected transplants. CaCV has been detected in India only recently, but it might have been introduced many years ago and remained unnoticed. The two tospoviruses, GBNV and WBNV, which are endemic in India could have originated from CaCV. This analysis indicates that the tospoviruses occurring in India have originated along with some other tospoviruses reported from other parts of Asia (Fig.10). Some of these viruses also share sequences with tospovirus infecting Gloxinia in USA, suggesting genomic recombination amongst the tospoviruses. The oldest known tospovirus – Tomato

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spotted wilt virus (TSWV) does not occur in India, although the symptoms produced by GBNV on tomato look similar to those induced by TSWV. Absence of TSWV, which forms a separate branch of tospoviruses, suggests independent origin of TSWV and the two tospoviruses occurring in India. Ilarviruses During the last decade, TSV, an Ilarvirus has emerged as a destructive virus in a variety of crops particularly in southern India. The most serious incidence of the virus has been on the newly introduced hybrids of sunflowers. It has also spread to other crops like cucurbits, groundnut, legumes, cotton and okra. Emergence of TSV in India has not been understood. Phylogenetically isolates sequenced from India are close to other isolates found in other geographical regions, but the destruction caused by TSV to crops in India is unique. Ilarviruses are also emerging as constraint in the production temperate fruit crops like apple in the country.

Conclusions Phylogeographically economically important viruses occurring in the Indian Subcontinent fall in three broad groups. One group is represented by badnaviruses, which infect vegetatively propogated plants like banana and citrus and seem to have evolved slowly and form phylogenetic clusters according to their host species, rather than their geographical distribution. The second group is represented by begomoviruses, which mainly infect plants grown through true seeds, are more diverse and seem to have undergone rapid mutations and recombinations, resulting in the fast emergence of new viruses and strains. These viruses appear to have evolved within specific geographic regions and form phylogeographic clusters. The third group is represented by ilar-, poty- and tospoviruses, which also evolve geographically but unlike the second group these viruses, have evolved slowly as they are not prone to rapid mutations and recombinations, but some of them are wide spread due to the movement of infected planting material. The tospoviruses appear to be conserved with occurrence of limited variability; this could be due to the possible origin of these viruses in insects. Whether the limited variation occurred to them during their replication in insects or plants remains to be seen. Vector transmission and human interventions have played important roles in the evolution and spread of plant viruses. Further work and sequencing of full genomes of different groups of viruses are expected to throw more light in the understanding of evolution of viruses. This is important as viral disease problems are threatening food production particularly in the tropics and semi-tropics. Acknowledgments: The authors thank Ms. Priyanka Singh, Ms. Suneha Upadhyaya and Ms. T. Vinutha for their help in bioinformatics and Mr. Zile Singh for logistic support.

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References 1. 2. 3. 4. 5.

6.

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Harper G, Julian OO, Harrison JSH, Hull RG (1999) Integration of banana streak badnavirus into the Musa genome: molecular and cytogenetic evidence. Virology 255:207–213 Harper G, Hull R (1998) Cloning and sequence analysis of Banana streak virus DNA. Virus Genes 17:271–278 Muhammad Shah NR, Claude F (2009) Evolution of geminiviruses and their satellites. FEBS letters 583:1825–1832 Varma A, Malathi VG (2003) Emerging geminivirus problems: a serious threat to crop production. Ann Appl Biol 142:145–164 Malathi VG, Radhkrishnan G, Varma A (2003) Cotton. In: Virus and Virus-like Diseases of Major Crops in Developing Countries. Loeberstein G, Thattappilly G (Eds.), Kluwer Academic Publishers, London, UK Varma A, Dhar AK Mandal B (1992) MYMV transmission and control in India. In: Mungbean Yellow Mosaic Disease. Green Sk, Kim D (Eds.), Asian Vegetable Research and Development Centre, Taipei John P, Sivalingam PN, Haq QMI, Kumar N, Mishra A, Briddon RW, Malathi VG (2008) Cowpea golden mosaic disease in Gujarat is caused by a Mungbean yellow mosaic India virus isolate with a DNA B variant. Arch Virol 153:1359–1365 Rouhibakhsh A, Malathi VG (2005) Severe leaf crinkle disease of cowpea – a new disease of cowpea in northern India caused by Mungbean yellow mosaic India virus and satellite DNA-ß. Plant Pathol 54:259 Praveen S, Dasgupta A, Varma A (2004) Phylogenetic analysis and homologies of the replicase of tomato leaf curl geminiviruses: implications for obtaining pathogen derived resistance. Virus Genes 28:195–199

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Senanayake DMJB, Mandal B, Lodha S, Varma A (2006) First report of Chilli leaf curl virus affecting chilli in India. Plant Pathol 55:13 (http://www.bspp.org.uk/ndr/july2004/ 2004-25.asp)

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Jain RK, Sharma J, Sivakumar AS, Sharma PK, Byadgi AS, Verma AK, Varma A (2004) Variability in the coat protein gene of Papaya ringspot virus isolates from multiple locations in India. Arch Virol 149:2435–2442

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Mangrauthia SK, Parameswari B, Praveen S, Jain RK (2009) Comparative genomics of Papaya ringspot virus pathotypes P and W from India. Arch Virol 154:727–730

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Gibbs AJ, Mackenzie AM, Wei1 KJ, Gibbs MJ (2008) The potyviruses of Australia. Arch Virol 153:1411–1420

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Mangrauthia SK, Parameswari B, Jain RK, Praveen S (2008) Role of genetic recombination in the molecular architecture of Papaya ringspot virus. Biochemical Genetics 46(11):835–846

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Pappu HR, Jones, RAC, Jain RK (2009) Global status of tospovirus epidemics in diverse cropping systems: Successes achieved and challenges ahead. Virus Research (in press)

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Jain RK, Bag S, Umamaheshwaran K, Mandal B (2007) Natural infection by tospovirus of cucurbitaceous and fabaceous vegetable crops in India. J Phytopsthol 155:22–25

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Ravi KS, Kirkaru AS, Winter AS (2006) Iris yellow spot virus in onions: a new tospovirus record from India. Plant Pathol 55:288

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Krishnareddy M, Usha Rani R, Kumar A, Madhavi Reddy K, Pappu HR (2008) Capsicum chlorosis virus (Genus Tospovirus) infecting Chili pepper (Capsicum annuum) in India. Plant Dis 92:1469

7 Evolution of HIV-1 in India Pradeep Seth Seth Research Foundation, Gurgaon, Haryana, India [email protected]

Abstracts: Nearly 25 years after the discovery of the human immunodeficiency virus type 1 (HIV-1) effective control of the AIDS pandemic remains elusive. At the root of this challenge is the evolution of this virus to elude immune control. Error-prone nature of replication and retro-transcription is the hallmark of this virus. This fidelity of replication in HIV-1is due to the absence of proof-reading/repair and post-replicative error correction mechanisms that normally operate during replication of DNA Viruses. Advances in sequencing technology and expanded disease surveillance have allowed researchers to characterize the variation in HIV-1 around the world and within individual patient overtime. Although HIV-1 has been classified into distinct subtypes, the classification does not reflect dynamic genetic evolution of HIV-1 through which new strains are constantly emerging. The resultant viral diversity has implications for differential rates of disease progression in different geographical areas, differential responses to antiretroviral therapy (including the development of resistance), and vaccine development. In this review evolution of HIV-1 in India is discussed. Keywords: HIV, Evolution, Phylogenetic analysis, HIV-1 subtypes, HIV-1 diversity “Everything changes and moves and that movement is God.” —Leo Tolstoy in War and Peace- Book-14 Chapter XV

Introduction Since the unfolding of the AIDS epidemic in the early 1980s, there has been an increasing interest in the emergence and evolution of infectious diseases. It has become extremely important to investigate the factors that allowed new infections like HIV to appear, or older ones to reappear and then to track their spread through populations. These tracks form part of science of molecular epidemiology. Traditionally serology has been used to trace the spread of infectious diseases. These days comparative analysis of gene sequence data is being undertaken to V. P. Sharma (ed.), Nature at Work: Ongoing Saga of Evolution © The National Academy of Sciences, India 2010

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study spread of infectious diseases. Meaning thereby, phylogenetic-trees have become an important analytical tool to track the spread of infections through populations. Since DNA sequences provide the most detailed information possible for any organism in evolutionary studies, this information is recognized as an invaluable document of history of life on earth. There are two types of HIV: a highly virulent global type (HIV-1) and a somewhat less virulent strain HIV-2 found mostly in West Africa. Many African monkeys are commonly infected at high frequencies with HIV like viruses known as simian immunodeficiency viruses (SIV). Therefore, African monkeys are almost certainly the animal reservoir that ultimately gave us the HIV. HIV-1 and HIV-2 are most closely related to different primate species: HIV-1 to the viruses found in chimpanzees (SIV-CPZ) and HIV-2 to those found in sooty mangabey monkeys (SIV-SM). Sootey mangabey monkeys are likely direct source of HIV-2 since these are West African monkeys and HIV-2 also is found predominantly in West Africa. On the other hand, since chimpanzees are rarely infected with SIV-CPZ in the wild they are less likely to be the direct source of HIV-1. However, it is possible that an unknown SIV from other monkey species may be the ancestor of both HIV-1 and SIV-CPZ. Nonetheless, separation of HIV-1 and HIV-2 on phylogenetic tree suggests that they must have entered human populations on different occasions. HIV-1 genetic diversity over time is driven by two factors namely the high error rate of the viral reverse transcriptase and the rapid turn over of HIV-1 in infected individuals. Recombination events, pressures generated by the host immune responses, and antiviral drugs further contribute to differential viral genetic evolution. Globally circulating strains exhibit an extraordinary degree of genetic diversity, which may influence several aspects of their biology such as infectivity, transmissibility and immunogenicity. Molecular analyses of various HIV isolates reveal sequence variations over many parts of the viral genome. Sequences derived from these HIV-1 strains have historically been classified on the basis of their Phylogenetic relationship. The groups were originally named M (major), O (outlier), and N (non-M, non-O).1 The last two groups (N and O) remain essentially restricted to West Africa, whereas the M group comprises a number of viruses that dominate the global AIDS epidemic. Since HIV-1 M group began its expansion in humans roughly 70 years ago, it has diversified rapidly, now comprising a number of different subtypes and circulating recombinant forms. Based on the sequence of the envelope glycoproteins, genetic subtypes including CRFs (circulating recombinant forms) have been identified in group M, whereas subtypes within group O remain unidentified. Subtypes are genetically defined lineages that can be resolved through phylogenetic analysis of the HIV-1 M group viruses as well-defined clades or branches in a tree. CRF describes a recombinant

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lineage that plays an important role in the HIV-1 epidemic. The CRF members must share an identical mosaic structure, that is, they have descended from the same recombination event(s).

HIV-1 Genetic subtypes On the basis of their Phylogenetic relationships, group M viruses have been classified into nine subtypes or clades (A to K; except E and I). Virus strains representing the genetic subtypes E and I have not yet been found. The viruses originally identified as subtype E (the predominant group of viruses involved in heterosexual transmission in Thailand) and I (a small group of viruses from Mediterranean region) are now considered inter-subtype recombinants and have been termed CRF01_AE and CRF04_cpx, respectively. Disproportionate spread of different lineages of group M viruses has been taken to indicate that specific biological differences may exist among various subtypes. Therefore, the phylogenetic analysis of subtype sequences remains an important molecular epidemiological tool with which to track the course of group M pandemic. Existence of viral subtypes or clades may be the result of a ‘founder effect’ in which certain variants of the virus become founders of a subepidemic because they happen to be involved in an extensive transmission chain. In this scenario, the subtypes may be similar biologically even though they are genetically very different. Alternatively, it is likely that certain characteristics of subtypes allowed them to out-compete less-fit viral variants. Despite the lack of clear correlations subtypes and overt biological characteristics, other more subtle phenotypic distinctions have been reported such as the pattern of co-receptors usage. There is growing evidence that the subtype C has a preponderance of ‘non-syncytia inducing’ viruses which bind to CCR5 receptors in addition to CD4 receptors present on the target cells and lack ‘syncytia inducing’ viruses that use CXC4 and CD4 receptors to infect the target cells. Distinctive RNA secondary structure in the important regulatory domain, TAR is a property associated uniquely with subtype A and viruses having AE mosaic. Thirdly different subtypes differ in susceptibilities to antiretroviral drugs. In addition, difference between subtypes is reflected in subtype specific pattern of genetic variation. There is an elevated rate of non-synonymous substitution in the third variable loop of subtype D viruses, compared with other subtypes.2 Most interesting feature of these subtypes is geographic predilection of their distribution worldwide. It is possible that these subtypes may have spread through different populations at different times and by different routes. For example, subtype A is composed of two sub-subtypes (A1 and A2), both of which appear to have a widespread geographic distribution3 and is commonly found in sub-Saharan Africa and Russia where it is predominantly transmitted through heterosexual

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intercourse.4 It may be one of the oldest of all subtypes. In contrast, subtype B is associated with the HIV epidemic among homosexual men and injecting drug users in North and South Americas, Europe, Japan and Australia. The most prevalent HIV-1 subtype in the global epidemic is subtype C which is dominant in India, Ethiopia, South Africa, Zimbabwe, Botswana and China and is transmitted through heterosexual intercourse. Interestingly HIV-1 viral lineages of O and N are mainly confined to West Africa and phylogenetically these are separated from the other HIV-1 sequences suggesting multiple entry of the viruses into humans.

Subtype C: The expanding pandemic One of the most dramatic changes in the HIV/AIDS has been the rapid emergence and devastating spread of subtype C viruses. HIV-1 C accounts for 56% of all circulating viruses and is the most commonly transmitted subtype worldwide. The subtype C epidemic has now become the most predominant subtype in Southern African countries and Indian subcontinent where HIV prevalence is the highest in the world. The proportionate increase in C viruses relative to other HIV strains suggest that subtype C may be more easily transmitted or that it has a higher level of “fitness” at the population level. One possible explanation is that founder effects relating to the ongoing introduction of subtype C into new population groups with different host factors, or different social and sexual practices, may be responsible for the rapid spread. However, founder and host effects cannot account for the fact that C viruses are overtaking preexisting virus subtypes in several different geographical regions. It is increasing evident that additional (non-host) viral factors are also contributing to the rapid spread of HIV-1 C. Viral studies indicate that subtype C has distinct genetic and phenotypic properties that differentiate it from other HIV-1 subtypes. Subtype C viruses have an extra NF-κB binding site in the long terminal repeat,5 a prematurely truncated Rev protein or a 5-amino-acid insertion in Vpu6 may influence viral gene expression, altering transmissibility and pathogenesis of C viruses. Factors related to C viral entry and pathogenesis such as CCR5 and non-syncytium-inducing properties of C isolates, may also contribute to the increased spread of C viruses. Interestingly, though both subtype B and C are spreading exponentially in Brazil, the subtype C growth rate is about twice that of subtype B there; thus providing evidence of a different epidemic potential between two HIV-1 subtypes7.

Geographical distribution of HIV-1 subtypes Epidemiological and Phylogenetic studies have also shown that HIV-1 clades are unequally spread out throughout the world.8 The HIV epidemic in Africa began in the late 1970s and, during the late 1980s, gradually spread to the South of the continent. Though Africa is considered home of all HIV-1 subtypes, their

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spread to other continents is attributed to some groups of individuals, particularly travelers, who contribute to the initiation of local epidemics worldwide. These groups include, in particular, immigrants, IV drug users, tourists, truck drivers, military troops and seamen. The global view on the contribution of travel to HIV-1 spread usually derives from the prevalence of non-B subtypes in various countries.9 The prevalence of non-B infections has indeed markedly increased in recent years in several European countries.9,10 Recent immigrants from areas of high HIV-1 endemicity and European travelers have been shown to contribute in large part to the increase in the prevalence of non-B infections in western and northern Europe. There is no doubt that it is high risk human behavior and not occupation that determines HIV-1 infection risk. Predominance of subtype B in the western countries including Japan and Australia is attributed to transmission among homosexual men and is generally thought to be spreading separately from that among IV drug users and heterosexual individuals. However, in India subtype C predominance even among homosexual men and IV drug users suggests interplay of host genetic factors and the virus in determining geographical distribution of HIV-1 subtypes. Among the HIV-1 group M viruses, HIV-1 subtype C is by far the most prevalent HIV in the world and is linked to heterosexual transmission. It was first discovered in North-east Africa in the early 1980s11,12 and has since moved to the southern parts of Africa. In addition, the subtype C epidemic has spread to East and Central Africa where it is becoming predominant subtype.13,14 From Africa, it has spread to India, Brazil and South and Central China where is appears to have been introduced from India.15 In England and Wales, preponderance of subtype C infections has been observed among HIV-infected heterosexual STI clinic attendees, particularly in younger age groups, suggesting recent acquisition of this viral strain.16

The Indian scenario In India HIV infection was first reported in 1986 in six commercial sex workers in the State of Tamil Nadu and since then it has been reported from all the States and Union Territories. India now holds dubious distinction of accounting second largest number of HIV infections in the world following South Africa. With an estimated 2.5 million people living with HIV infection in adult population (15–49 years) by 2008, India accounts for 13% of global HIV prevalence.17 Tracking the epidemic and implementing effective programmes is made difficult by the fact that there is no one epidemic in India. Rather, there are several localized sub-epidemics reflecting the diversity in social-cultural patterns and multiple vulnerabilities present in the country. Though the overall national prevalence is low, six states have reached high prevalence (>1%): Manipur,

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Nagaland, Andhra Pradesh, Tamil Nadu, Karnataka and Maharashtra. Certain districts in Goa and Gujarat have also reported high prevalence. Sexual transmission is driving the AIDS epidemic in India. This route accounts for about 86% of HIV infections in the country. Remaining 14% are accounted for by other routes namely blood transfusion, mother-child transmission and IV drug use, particularly in North-east India. Over one-third of all HIV infections occur in young people in the age group 15–24 years. Early studies have indicated the presence of both HIV-1 and HIV-2 in India.18,19 Subsequent studies further emphasized a predominance of subtype C strains in India, which were found to cluster with South African isolates.20,21 Other HIV-1 subtypes, A and B, have been reported in India between 1980s and early 1990s among the recipients of blood and blood products and IV drug users, respectively, suggesting multiple introductions of HIV-1 in this country. Subtype A strains were found to be related to Central and East African subtype and subtype B strains obtained from Manipur were related to subtype B sequences circulating in Thailand.21 However, recent studies have clearly shown that subtype C strains have displaced subtype B in the IV drug users in that part of India.22,23 The trends across the country show that there is no explosive HIV epidemic in India as a whole. However, there are serious sub-national epidemics in various parts of the country with rapid spread and evidence of high prevalence of HIV among both sexual transmitted infections (STI) and antenatal clinic attendees in different sites located in States of Andhra Pradesh, Maharashtra, Tamil Nadu, Gujarat, Pondicherry, Assam, Bihar, Chhatisgarh, Delhi, Haryana, Himachal Pradesh, Kerala, Orissa, Goa and Manipur. In high prevalence states the epidemic appears to be spreading gradually from urban to rural areas and from high-risk behavior groups to the general population. The epidemic continues to shift towards women with an estimated 39% of the infected being women17. An explosive epidemic driven by intravenous drug use has unfolded in the state of Manipur (North-east India) bordering Myanmar and is close to the Golden Triangle composed of Thailand, East Myanmar and West Laos and is the hub of international drug trafficking. A recent study documents that two-thirds HIV infections in this region of India are caused by subtype C and subtype B (Thai B) accounts for 20% of infections.22 The presence of multiple subtypes circulating in Manipur suggests the likelihood of recombinant viruses evolving in this region. Indeed, this has been corroborated by a recent study which reported presence of B/C recombinants from this region.24 Apart from north-eastern states there are also sporadic reports of the presence of A/C and B/C recombinants from West and South India.25,26 The occurrence of HIV-1 recombination in nature is borne out by the identification of genomes that are recombinants between different HIV-1 subtypes.27 Some of these recombinant viruses have become fixed in the human

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population and are referred to as circulating recombinant forms (CRFs), and in at least a few cases CRFs have become the predominant strain in specific geographic areas of infection such as A/E recombinants in Thailand and B/C recombinants in parts of Southeast Asia and China. HIV-1 recombinants are estimated to contribute to 10–40% and 10–30% of the infections in Africa and Asia, respectively. The identification of subtypes and CRFs provides a means of tracking dissemination of the pandemic worldwide. To delineate the molecular features of HIV-1 strains circulating in India, Phylogenetic analyses of sequences of Indian subtype C isolates along with a small number of subtype sequences from other countries revealed that almost all sequences from India form a distinct lineage within subtype C (CIN). Overall CIN lineage sequences were more closely related to each other (level of diversity, 10.2%) than to subtype C sequences from Botswana, Burundi, South Africa, Tanzania and Zimbabwe (range 15.3 to 20.7%). Suggesting thereby, much of the current Indian epidemic is descended from a single introduction into the country.28 In an assessment of the Phylogenetic relationships among subtype C sequences from eleven different countries including India, an overall star-like phylogeny was observed.29 Unlike sequences from South Africa and Botswana, which are scattered in numerous lineages, almost all sequences from India formed a monophyletic lineage, which is lying close to the sequences. Sequences from India generally clustered together more than sequences from other countries. Genetic characterization of the virus during the early seroconversion stage is crucial as the virus isolated is closely related to the transmitted strain and hence immunologically naïve. Phylogenetic analyses of Indian subtype C envelope sequences obtained from early seroconverts indicated that the Indian sequences not only clustered within the C clade but also clustered away from the African subtype C sequences.30 Moreover, a recent study demonstrating lower diversity within immunodominant epitopes and a tight clustering of Indian isolates29 suggested that production of a vaccine particularly against Indian subtype C may not be an unattainable and daunting task.

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