What DNA Says About Aryan Invasion Theory -2

[dhu]

Overall, R1b shows unidirectional expansion into Europe. With some of the latter day Empires, there is some variation, but these are trivial..



Given the noncontroversial R1b case, it will be hard to argue for concentric expansion out of the "above the black sea" region for R1a1. All their plausibility arguments are being shorn. Concentric expansion is shown for the theological prop that it is.



Pattern that seems to be emerging is Europe as a battlefield between Mideasterners and S Asians. Indians do not even need any interests in psyops, these scenarios just seem to be gifted to them as a matter of course <img src='http://www.india-forum.com/forums/public/style_emoticons/<#EMO_DIR#>/wink.gif' class='bbc_emoticon' alt='' />..



Empires within India are not associated with population movements, probably a result of heathen dynamics (the king simply assumed a token suzerainty); that is, they are not colonial Empires.

[ramana]

Dhu, As usual please explain all this in a clear way on the blog for all others. I really like your statement about the difference in empires of India and other normatized people.

[ramana]

Neither Neandthral nor Homo Sapiens

Neither Neanderthal nor sapiens: new human relative IDed

By John Timmer | Last updated about 2 hours ago

At a press conference yesterday, researchers announced the completely unexpected: a Siberian cave has yielded evidence of an entirely unknown human relative that appears to have shared Asia with both modern humans and Neanderthals less than 50,000 years ago. The find comes courtesy of a single bone from individual's hand. Lest you think that paleontologists are overinterpreting a tiny fragment, it wasn't the shape of the bone that indicates the presence of a new species—it was the DNA that it contained.



The paper that describes the finding comes courtesy of the Max Planck Institute's Svante Pääbo, who has been actively pursuing the sequencing of the Neanderthal genome. It seems likely that this particular bone fragment was targeted due to suspicions that it might also provide an additional Neanderthal sequence. The site, called Denisova, is in the Altai Mountains of southern Siberia, an area that has had hominins present as early as 125,000 years ago. The sample itself came from a layer of material that dates from between 30,000 and 50,000 years ago. Neanderthal DNA was found in a sample from the same time period less than 100km away, while artifacts indicate that modern humans were also present in the region by 40,000 years ago.



So, there was no apparent reason to suspect that the bone would yield anything more than a familiar sequence. And in fact, most of the first half of the paper simply describes the methods used to construct a complete sequence of the mitochondrial DNA, including over 150-fold coverage of the genome, and an alignment program designed to account for the errors typical of ancient DNA sequences. About the only surprise here is that Pääbo's group has switched from using 454 sequencing machines to those made by Illumina.



Various checks indicate that the sequence the authors obtained contains damage that's typical of ancient DNA, and that it all comes from a single individual. So far, quite typical.



Things got quite unusual when they attempted to align the sequence to the mitochondrial DNA from the hominin species that were likely to be present at that time and place: human and Neanderthal. Instead of clustering with one or the other, the Denisova mitochondrial genome was a clear outlier, having about 385 differences with the typical human mitochondrial genome. In contrast, Neanderthals only differ from modern humans by an average of 202. The obvious interpretation is that the Denisova lineage split off before modern humans and Neanderthals did. If we accept that Neanderthals are a distinct species of hominin (and we do), then this sample clearly represents yet another one.



Building a tree with the chimpanzee genomes and assuming a divergence time of 6 million years, the data indicates that the Denisova lineage diverged about a million years ago. At that point, Homo Erectus was already a global species, but our human ancestors were still in Africa. That suggests that the Denisova variant probably originated in, or at least near, Africa as well, although there's no way to tell whether it was a distinct species before it started migrating, or whether it became an isolated population because of a migration.



The paper is in the format of a Nature letter, which allows only a paragraph for discussion. The authors use that space primarily to note that, 40,000 years ago, southern Siberia was a very busy place as far as hominins are concerned, with at least three different species present within a very narrow time frame. If we accept that the Indonesian hobbits are yet another distinct species—and the relevant community seems to be leaning that way—then it appears that there were at least four distinct hominin species cohabiting the globe in the very recent past.



As surprising as that is, it's only a small fraction of the implications of this work. For starters, there's the whole idea that we can identify a new species without having any idea what it actually looked like—in fact, without having any idea of whether it would be physically distinct enough from any of the other hominin species around that we'd even have known it were a separate species based on the bones.



The authors also briefly touched on a separate issue: this ability will be unevenly distributed in space and time. DNA simply lasts longer in cool climates, as evidenced by the recent announcement that DNA had been obtained from a polar bear sample that was over 100,000 years old. So, any species that was stuck near the equator—like the hobbits—are unlikely to be in on the DNA revolution. This is especially unfortunate given the fact that, as noted above, a lot of the most interesting action in hominin origins seem to have been taking place in Africa.



Then there's the whole question of what else we might be missing. Avoiding contamination issues with modern DNA is easiest if the entire excavation is designed around a sterile technique from the start, meaning bones that have been previously excavated aren't ideal. At the moment, at least, sequencing from a single sample is also pretty labor intensive (this paper had seven authors), meaning we aren't likely to be able to just start sequencing any bone fragments we stumble across. Figuring out how to prioritize what might be informative will be a real challenge.



If that seems like a lot of questions for a short and fairly technical paper (and it is), it's a product of the fact that this paper seems truly exceptional. Because of the rich history of most fields of science, there aren't a whole lot of truly unexpected results, since you typically know that there are people working in a given area. But this finding is truly a stunning one, and really seems to be a complete surprise.



Nature, 2010. DOI: 10.1038/nature08976 (About DOIs).

One of these days they will find the "vanara' gene and then the story of mythology collpases into reality.

[acharya]

Pre-history rewritten as new human discovered

ABC Online - David Mark - ‎24 minutes ago‎

Scientists in Germany have discovered a new human species that lived in Siberia around 30000 to 50000 years ago. The evidence changes the ...

Fingerbone points to a new type of human who fell off the family tree 30000 ...



Times Online - Mark Henderson - ‎41 minutes ago‎

A new species of ancient human that lived side by side with Homo sapiens and Neanderthals as recently as 30000 years ago has been discovered, rewriting the ...



http://news.google.com/news/more?pz=1&cf...VPdr8_FIgM

[dhu]

[url="http://news.bbc.co.uk/2/hi/uk_news/8602358.stm"] Non-native animals cause rural problems, charity warns[/url]



It appears the Chinese Muntjac is causing a major ruckus in massa junior. However, it must be remembered that the muntjac is native to India as well.

[dhu]

Read Sahoo: 2005, Sharma: 2009 and Underhill: 2009. Every genetic marker once used as “proof” of a foreign incursion is in fact native to India.

[acharya]

Signs of Neanderthals Mating With Humans

http://www.nytimes.com/2010/05/07/scienc...rthal.html



Johannes Krause MPI-EVA

The Vindija cave in Croatia where three small Neanderthal bones were found.

By NICHOLAS WADE

Published: May 6, 2010

Neanderthals mated with some modern humans after all and left their imprint in the human genome, a team of biologists has reported in the first detailed analysis of the Neanderthal genetic sequence.

Max-Planck-Institute EVA

The Neanderthal DNA that Svante Pääbo analyzed came from these three bones.

The biologists, led by Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have been slowly reconstructing the genome of Neanderthals, the stocky hunters that dominated Europe until 30,000 years ago, by extracting the fragments of DNA that still exist in their fossil bones. Just last year, when the biologists first announced that they had decoded the Neanderthal genome, they reported no significant evidence of interbreeding.



Scientists say they have recovered 60 percent of the genome so far and hope to complete it. By comparing that genome with those of various present day humans, the team concluded that about 1 percent to 4 percent of the genome of non-Africans today is derived from Neanderthals. But the Neanderthal DNA does not seem to have played a great role in human evolution, they said.



Experts believe that the Neanderthal genome sequence will be of extraordinary importance in understanding human evolutionary history since the two species split some 600,000 years ago.



So far, the team has identified only about 100 genes — surprisingly few — that have contributed to the evolution of modern humans since the split. The nature of the genes in humans that differ from those of Neanderthals is of particular interest because they bear on what it means to be human, or at least not Neanderthal. Some of the genes seem to be involved in cognitive function and others in bone structure.



“Seven years ago, I really thought that it would remain impossible in my lifetime to sequence the whole Neanderthal genome,” Dr. Paabo said at a news conference. But the Leipzig team’s second conclusion, that there was probably interbreeding between Neanderthals and modern humans before Europeans and Asians split, is being met with reserve by some archaeologists.



A degree of interbreeding between modern humans and Neanderthals in Europe would not be greatly surprising given that the species overlapped there from 44,000 years ago when modern humans first entered Europe to 30,000 years ago when the last Neanderthals fell extinct. Archaeologists have been debating for years whether the fossil record shows evidence of individuals with mixed features.



But the new analysis, which is based solely on genetics and statistical calculations, is more difficult to match with the archaeological record. The Leipzig scientists assert that the interbreeding did not occur in Europe but in the Middle East and at a much earlier period, some 100,000 to 60,000 years ago, before the modern human populations of Europe and East Asia split. There is much less archaeological evidence for an overlap between modern humans and Neanderthals at this time and place.



Dr. Paabo has pioneered the extraction and analysis of ancient DNA from fossil bones, overcoming daunting obstacles over the last 13 years in his pursuit of the Neanderthal genome. Perhaps the most serious is that most Neanderthal bones are extensively contaminated with modern human DNA, which is highly similar to Neanderthal DNA. The DNA he has analyzed comes from three small bones from the Vindija cave in Croatia.



“This is a fabulous achievement,” said Ian Tattersall, a paleontologist at the American Museum of Natural History in New York, referring to the draft Neanderthal genome that Dr. Paabo’s team describes in Thursday’s issue of Science.



But he and other archaeologists questioned some of the interpretations put forward by Dr. Paabo and his chief colleagues, Richard E. Green of the Leipzig institute, and David Reich of Harvard Medical School. Geneticists have been making increasingly valuable contributions to human prehistory, but their work depends heavily on complex mathematical statistics that make their arguments hard to follow. And the statistical insights, however informative, do not have the solidity of an archaeological fact.



“This is probably not the authors’ last word, and they are obviously groping to explain what they have found,” Dr. Tattersall said.



Richard Klein, a paleontologist at Stanford, said the authors’ theory of an early interbreeding episode did not seem to have taken full account of the archaeological background. “They are basically saying, ‘Here are our data, you have to accept it.’ But the little part I can judge seems to me to be problematic, so I have to worry about the rest,” he said.



In an earlier report on the Neanderthal genome, the reported DNA sequences were found by other geneticists to be extensively contaminated with human DNA. Dr. Paabo’s group has taken extra precautions but it remains to be seen how successful they have been, Dr. Klein said, especially as another group at the Leipzig institute, presumably using the same methods, has obtained results that Dr. Paabo said he could not confirm.



Dr. Paabo said that episode of human-Neanderthal breeding implied by Dr. Reich’s statistics most plausibly occurred “in the Middle East where the first modern humans appear before 100,000 years ago and there were Neanderthals until 60,000 years ago.” According to Dr. Klein, people in Africa expanded their range and reached just Israel during a warm period some 120,000 years ago. They retreated during a cold period some 80,000 years ago and were replaced by Neanderthals. It is not clear whether or not they overlapped with Neanderthals, he said.



These humans, in any case, were not fully modern and they did not expand from Africa, an episode that occurred some 30,000 years later. If there was any interbreeding, the flow of genes should have been both ways, Dr. Klein said, but Dr. Paabo’s group sees evidence for gene flow only from Neanderthals to modern humans.



The Leipzig group’s interbreeding theory would undercut the present belief that all human populations today draw from the same gene pool that existed a mere 50,000 years ago. “What we falsify here is the strong out-of-Africa hypothesis that everyone comes from the same population,” Dr. Paabo said.



In his and Dr. Reich’s view, Neanderthals interbred only with non-Africans, the people who left Africa, which would mean that non-Africans drew from a second gene pool not available to Africans.

[ramana]

SOURCE

June 13, 2010





Home > 2010 Issues > June 13, 2010





Special Report



Mystery of our origins

India has one of the largest human biodiversity pools

By Dr Lalji Singh



India represents one of the largest human biodiversity pool in the world. There are 532 tribes, 72 primitive tribes and 36 hunters and gatherers. Although the genome sequences of any two unrelated people differ by just 0.1 per cent, that tiny slice of genetic material is a rich source of information. It provides clues that can help reconstruct the historical origins of modern populations.



The kings of South India, like the Chola and the Pandya dynasties, relate their lineages back to Manu. The Matsya Purana moreover makes Manu, the progenitor of all the Aryans, originally a south Indian king, Satyavrata. Hence these are not only traditions that make the Dravidian descendants of Vedic rishis and kings, but those that make the Aryans of North India descendants of Dravidian kings.



Dr Lalji Singh, former Director of Centre for Cellular and Molecular Biology (CCMB), Hyderabad, delivered the seventeenth Bhaorao Deoras Memorial Lecture in Lucknow on May 12. This article is based on that lecture.



SINCE the dawn of civilisation, man has been asking questions such as ‘who are we?’ and ‘where have we come from?’ Until 1858 it was universal belief that man is special creation of God. In 1858, based on phenotypic transition of various organisms including plant and animal species, Charles Darwin proposed the theory of evolution and wrote a book The Origin of Species. Eight years later in 1871, he wrote a book The Descent of Man. Based on the anatomical similarities, he declared that the chimpanzee and the gorilla are our closest living relatives and predicted that the earliest ancestors of humans would turn up in Africa, where our ape kins live today. Now it is widely accepted view that modern human diverged from a common ancestor of chimpanzee and human nearly 6-7 million years ago. Based on fossil records found in Africa, it is now believed that modern human originated from a single mother about 160,000 years ago in East Africa. East-African mega-droughts between 135 and 75 thousand years ago, when the water volume of the lake Malawi was reduced by at least 95 per cent, could have caused their migration out of Africa. The obvious question to ask is which route did they take? Our study of the tribes of Andaman and Nicobar Islands using complete mitochondrial DNA sequences, and its comparison with the mitochondrial DNA sequences of the world populations available in the database, led to the theory of southern coastal route of migration through India, against the prevailing view of northern route of migration via Middle East, Europe, south-east Asia, Australia and then to India. Our earlier study revealed that Negrito tribes of Andaman and Nicobar Islands, such as Onge, Jarawa, Great Andamanese and Sentinelese, are probably the descendants of the first man who moved out of Africa.



This raised many questions such as: (i) what is the origin of mainland tribal and caste populations?; (ii) are there any population(s) in mainland India, which are close to Andamanese?; (iii) how much affinities the Indian populations have with Andamanese?; (iv) did the Indians contribute to the early human spread?



In order to answer these questions and to explore the ancient history of India we have harnessed genomic technology.



Ancient roots for India’s rich diversity

India represents one of the largest human biodiversity pool in the world. There are 532 tribes, 72 primitive tribes and 36 hunters and gatherers. Although the genome sequences of any two unrelated people differ by just 0.1 per cent, that tiny slice of genetic material is a rich source of information. It provides clues that can help reconstruct the historical origins of modern populations. It also points to genetic variations that heighten the risk of certain diseases. In recent years, maps of human genetic variation have opened a window onto the diversity of populations across the world, yet India has been largely unrepresented until now.



To shed light on the genetic variability across the Indian subcontinent, we analysed 132 Indian samples from 25 groups on an Affymetrix 6.0 array, yielding data for 587,753 SNPs after restricting to markers with good completeness. To span the widest range of ancestry in India, we sampled tribal groups from 13 states and 6 language families (Indo-European, Dravidian, Austro-Asiatic, Tibeto-Burman, Great Andamanese and Jarawa-Onge). We also sampled caste groups mostly from Uttar Pradesh and Andhra Pradesh to permit comparison of traditionally "upper" and "lower" caste groups after controlling for geography. With tens of thousands of independent loci, we could estimate Fst (F-statistics) - accurately with just 2-9 samples per groups (with average standard error of + 0.0011). We also merged our data with 155 European (CEU), Chinese (CHB), and West African (YRI) samples from HapMap, and 938 samples from the Human Genome Diversity Panel (HGDP).



We analysed these data to address five questions about Indian genetics and history. Does the Indian subcontinent harbour more structure than Europe? Has strong endogamy been a long-standing feature of Indian groups? Do nearly all Indians descend from a mixture of populations, one of which was related to Central Asians, Middle Easterners and Europeans and probably lived in north India? Are tribal groups systematically different from castes, and do some tribal groups provide a good approximation for the ancestral populations of India? What is the origin of the indigenous Andaman Islanders?



All mainland Indian groups have inherited a mixture of ancestries

We provide strong evidence for two ancient and genetically divergent populations that are ancestral to most Indian groups today. One, the "Ancestral North Indians" (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, while the other, the "Ancestral South Indians" (ASI), is not close to any group outside the subcontinent. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39-71 per cent, and is higher in traditionally upper caste groups and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India.



The finding that nearly all Indian groups descend from mixtures of two ancestral populations applies to traditional "tribes" as well as "castes". It is impossible to distinguish castes from tribes using the data. The genetics prove that they are not systematically different. This supports the view that castes grew directly out of tribal-like organisations during the formation of Indian society. The one exception to the finding, that all Indian groups are mixed, is the indigenous people of the Andaman Islands, an archipelago in the Indian Ocean with a census of only a few hundred today. The Andamanese appear to be related exclusively to the Ancestral South Indian lineage and therefore lack Ancestral North Indian ancestry. In this sense, they are unique. Understanding their origins provides a window to look into the history of the Ancestral South Indians, and the period of tens of thousands years ago when they diverged from other Eurasians. Our project to sample the disappearing tribes of the Andaman Islands has been more successful than we hoped, as the Andamanese are the only surviving remnant of the ancient colonisers of South Asia.



Medical Implications

Our findings revealed that many groups in modern India descend from a small number of founding individuals, and have since been genetically isolated from other groups. In scientific parlance, this is called a "founder event". It has medical implications for Indian populations. Recessive hereditary diseases - single gene disorders that occur only when an individual carries two malfunctioning copies of the relevant gene - are likely to be common in populations descended from so few ‘founder’ individuals. Mapping the causal genes will help to address this problem. The widespread history of founder events in Indian populations helps to explain why the incidence of genetic diseases among Indians is different from the rest of the world. For example, an ancient deletion of 25 bp in the cardiac myosin-binding proteins-C gene (MYBPC3) is associated with heritable cardiomyopathies as well as with an increased risk of heart failure. Its prevalence is high (~4 per cent) in the general populations from the Indian subcontinent. However, this mutation is completely absent among the people from the rest of the world.



The finding that a large proportion of modern Indians descended from founder events means that India is genetically not a single large population; instead it is best described as many smaller isolated populations. Founder events in other groups, such as Finns and Ashkenazi Jews, are well-known to increase the incidence of recessive genetic diseases; and our study predicts that the same will be true for many groups in India. It is important to carry out a systematic survey of Indian groups to identify which ones descend from the strongest founder events. Further studies of these groups should lead to the rapid discovery of genes that cause devastating diseases, and thus will help in the clinical care of individuals and their families who are at risk.



Indo-European family of language and the concept of Aryan and Dravidian

The story of Indo-European family of languages was proposed by Sir William Jones before the Asiatic Society at Calcutta in 1786 (Jones, 1786). The Indo-European concept was a real breakthrough of scientific linguistics, linking languages widely separated in space, forming two blocks - an eastern one of Persian and Indic languages and a western European block, separated from one another by Semitic and Turkic languages. The Indo-European concept was anything but obvious - the idea, that is, that the two blocks of languages, so distant from one another, are nevertheless related to one another. Its discovery by Jones and others not only created a new science of language but it radically recorded existing ideas about the relations among different natives or races of people. Jones (1746-1794) was an employee of the East India Company who developed the Indo-European concept. He also made important identifications of words in the Romanic or Gypsy languages with Sanskrit (Jones, 1786). Marsdens’ (William Marsdens 1754-1836) early paper, comparing the Gypsy language with Hindustani, makes him one of the co-discoverers of its Indian origins.



Max Muller, who was one of the first to apply the Aryan name to the Indo-European concept identified the racial-linguistic entity as racially white and was instrumental in the formation of the racial theory of Indian civilisation.



The kings of South India, like the Chola and the Pandya dynasties, relate their lineages back to Manu. The Matsya Purana moreover makes Manu, the progenitor of all the Aryans, originally a south Indian king, Satyavrata. Hence these are not only traditions that make the Dravidian descendants of Vedic rishis and kings, but those that make the Aryans of North India descendants of Dravidian kings. The two cultures are so intimately related that it is difficult to say which came first.



The present research findings are consistent with the view of one school of thoughts that the Aryans and Dravidians are part of the same culture and we need not speak of them as separate. However, it contradicts the second school of historians such as Max Muller who for the first time applied the Aryan name to the Indo-European concept. It strongly suggests that dividing them and placing them at odds with each other serves the interest of neither but only serves to damage their common culture.



Our study is important in highlighting important questions still open for future research. One priority is to estimate a date for the ANI-ASI mixture; this may be possible by studying the length of stretches of ANI ancestry in modern Indian samples. Inferring a date is important, as we expect that it would shed light on the historical process leading to the present day structure of Indian groups. A second priority would be to follow up on the observation that many Indian descended from a small number of founders. The groups with the strongest founder effects can then be analysed to identify genetic variants that we predict will account for substantial rates of recessive disease in these groups. Have Eurasians descended from the Ancestral North Indians? This is the question we would like to address in our future research activities.



Suggested reading

Dandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS et al. (2009) A common Cardiac Myosin Binding Protein C variant associated with cardiomyopathies in South Asia. Nature Genetics 41, 187-191.



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



Scholz CA, Johnson TC, Cohen AS, King JW et al. (2007) East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins. Proc. Natl. Acad. Sci. (USA) 104, 16416-16421.



Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC et al. (2003) Genetic affinities of the Andaman Islanders, a vanishing human population. Curr Biol. 21, 86-93.



Thangaraj K, Chaubey G, Kivisile T, Reddy AG, Singh V, Rasalkar A, Singh L (2005) Reconstructing the origin of Andaman Islanders. Science 308, 996.



Thangaraj K, Chaubey G, Kivisile T, Reddy AG, Singh V, Rasalkar A, Singh L (2006) Response to comment on "Reconstructing the origin of Andaman Islanders". Science 311, 470b.



Trautmann TR (2004) Discovering Aryan and Dravidian in British India. Historiographia Linguistica. XXXI : 1, 33-58.



The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861.



(The witer is Bhatnagar Fellow (CSIR) and former Director of Centre for Cellular and Molecular Biology, Hyderabad)

[dhu]

Some DNA forum deleted its content on R. Also when doing basic search for R1a1, the only results are about the Indian origin including David Faux's statement. Gura is in major tailspin dive.

[dhu]

Latest Autosomal study (which supersedes the jokers' favorite) confirms the well-known conclusions from uniparental lineages, that India is the source population for an earlier eastern lineage at 90K and a later western one at 45K (with another later trajectory of Indian r1a1 into the west in the holocene). It is now impossible for these jokers to use homogeneity of the western lines as a support for autogenesis, since the same type of homogeneity is seen in native American lines but with a clear progenitor in interior asia. It's over for gora and his slaves.

[HareKrishna]

[quote name='dhu' date='03 August 2010 - 07:27 AM' timestamp='1280800195' post='107732']

Latest Autosomal study (which supersedes the jokers' favorite) confirms the well-known conclusions from uniparental lineages, that India is the source population for an earlier eastern lineage at 90K and a later western one at 45K (with another later trajectory of Indian r1a1 into the west in the holocene). It is now impossible for these jokers to use homogeneity of the western lines as a support for autogenesis, since the same type of homogeneity is seen in native American lines but with a clear progenitor in interior asia. It's over for gora and his slaves.

[/quote]

any new study beside underhill one?

[dhu]

search "New paper on human autosomal phylogenetics" this is tamacha to all remaining jokers posing hope in autosomals. Autosomals are only good for degree of inbreeding and do not indicate descent.

[acharya]

http://leherensuge.blogspot.com/2010/07/...somal.html

THURSDAY, JULY 22, 2010

New paper on human autosomal phylogenetics



A reader points me to a new quite interesting paper on human phylogeny from the viewpoint of autosomal DNA mainly.



Jinchuang Xing et al. Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics 2010. Pay per view.



A copy can be found at ZohoViewer and the supplementary material is also freely available.



Abstract



High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

manju said...

Most importantly a clearly distinct South Asian component (purple) has been detected and is strong enough to make up 50% of the Pakistani gene pool and almost the totality of some South Indian populations



Very revealing. Isn't it? Matches with so-called South Asia specific mtDNA in that region. Autosomal analysis is not really helpful. It's a red-herring. We should concentrate on uniparental lineages only to understand linguistic distribution. As I have argued the local matrilineages establish themselves in overall genome over time even when patrilineages keep chaging.



I suppose Newar has only ~25% East Asian patrilineages(compared ~70% South Asian patrilineages). But their matrilineages are predominantly East Asia thus overall they are closer to East Asian.

[HareKrishna]

Himalaya is the first COLD region touched by humans.

Very probably the birth place of the mongoloid yellow race.

Mystery solved...maybe.

[ramana]

News Report in Pioneer...

FLASH | Tuesday, August 24, 2010 | Email | Print | | Back





Hitler possibly had Jewish, African roots



IANS | London



Nazi leader Adolf Hitler possibly had Jewish as well as African ancestors - communities whom he had pledged to exterminate, new DNA tests have revealed.



Daily Express Tuesday reported that samples taken from Hitler's relatives link him to both the Jewish community and people from North Africa.



Jean-Paul Mulders, a journalist, was able to investigate Hitler’s DNA after he managed to lay his hands on a serviette dropped by the dictator’s great-nephew Alexander Stuart-Houston who lives in New York. A serviette is a small square of cloth or paper used while eating to protect the clothes, wipe the mouth and hand.



He got a second sample from an Austrian cousin of Hitler, a farmer known as Norbert H, the media report said.



The DNA tests threw up a startling result.



It revealed a form of the Y-chromosome that is rare in Germany and the rest of Western Europe, but common among Jewish and North African groups.



Experts now think that Hitler had migrant relatives who settled in his homeland.



Mulders said both the test samples had a form of genetic material known as Haplopgroup E1b1b, proving an "irrefutable link" to the Nazi leader.



"It is most commonly found in the Berbers of Morocco, in Algeria, Libya and Tunisia, as well as among Ashkenazi and Sephardic Jews. One can from this postulate that Hitler was related to people whom he despised," the Belgian journalist was quoted as saying.



Ronny Decorte, a genetic specialist in Belgium, said: "Hitler would not have been pleased about this.



"Race and blood was central in the world of the Nazis. Hitler’s concern over his descent was not unjustified. He was apparently not ‘pure’ or ‘Aryan’."

[dhu]

More on the neanderthal-human interface limiting migration into eurostan



[url="http://www.msnbc.msn.com/id/40605372/ns/technology_and_science-science/"]Lost civilization may have been beneath Persian Gulf[/url]

Veiled beneath the Persian Gulf, a once-fertile landmass may have supported some of the earliest humans outside Africa some 75,000 to 100,000 years ago, a new review of research suggests.

..

"Given the presence of Neanderthal communities in the upper reaches of the Tigris and Euphrates River, as well as in the eastern Mediterranean region, this may very well have been the contact zone between moderns and Neanderthals," Rose told LiveScience.

..

[dhu]

minor blizzard hits london:

London's Heathrow Airport now filled to overflowing with stranded passengers. Broken glass, vomit, urine & feces on floors. Photos banned.

Now imagine ice age..

[HareKrishna]

[quote name='dhu' date='22 December 2010 - 05:07 AM' timestamp='1292974179' post='109957']

minor blizzard hits london:







Now imagine ice age..

[/quote]

no global warming?

[dhu]

Passengers at Moscow's Sheremetyevo Airport have been stranded for days thanks to an ice storm. So they did what any reasonable person trapped in an airport for days would do: They "attacked several employees." [RIA Novosti]

More ice age antics

[dhu]

Posting in full. With this discovery, it is the end of the 30K timeline for R in CAsia. R1a1 is indeed the postglacial signature of the gypsy horde. The prior trailblazing input into Europe was IJ.



[url="http://www.economist.com/node/17797276"]The old man of the mountain returns[/url]

More evidence for a previously unknown species of human

SVANTE PAABO, the DNA palaeontologist whose work provided the inspiration for “Jurassic Park”, has produced a nice Christmas present for students of human evolution. He and his colleagues have confirmed, using the creature’s whole genome, that a fossil finger bone which is at least 30,000 years old, and which was found in a cave in the Altai mountains of Siberia, comes from a previously unknown human species. That was all but certain from their previous study of the creature’s mitochondrial DNA (an abundant form of the molecule found in cells’ powerpacks), released in March. The latest analysis, published in Nature on December 23rd, removes any doubt—and adds a tooth to the meagre stock of evidence from the new species that modern science is able to examine.



This discovery is extraordinary on many levels. Perhaps the most important is that one small group of modern humans who live far away from Siberia—the Melanesian islanders of the Pacific Ocean—have picked up a block of genes from the newly discovered species on their (or, rather, their ancestors’) travels. Genetic evidence of the Melanesians’ journey from the African cradle of Homo sapiens, which started (like that of all non-African people) about 60,000 years ago when a band of adventurers crossed the straits of Bab el Mandeb, from modern Djibouti to modern Yemen, suggests they then continued along the south coast of Asia, never going far inland. For the necessary interbreeding to have happened, Dr Paabo’s new species would thus have to have been spread over a vast area of Asia. Yet it has left no previously identified traces.



To be fair, Asia has not, so far, been a rich source of human fossils—unlike Africa, where many sites in the east and the south have yielded ancestral humans, and Europe, where Neanderthals have been found by the hundred. Good Asian fossils come only from China (Peking Man, a type of Homo erectus) and Indonesia (Java Man, another erectus, and Homo floresiensis, the much-maligned “hobbit” of the island of Flores). Stone tools abound, but human bones from other Asian sites are almost as rare as hens’ teeth. The few that do exist are now, of course, the subject of intense scrutiny and much debate about whether they, too, belong to the new species.



What this discovery ought to provide, then, is the impetus to start looking much harder for human fossils in Asia. The new species, which has yet to be named, clearly lived all over the place. If, despite that, it remained hidden until now, who knows what other species of human might also be out there?