rolloff analysis of South Indian Brahmins

Populations with 5+ individuals and which belonged no more than 5% in African or East Eurasian components at K=7 were retained. South Indian Brahmins were combined from the Iyer_D and Iyengar_D datasets of the Dodecad Project. Other populations were from the current version of the Old World dataset used for the K7b/K12b calculators.

The lowest f3 statistics were the following:

English_D North_Kannadi South_Indian_Brahmin -0.006119 0.000339 -18.06 236533
North_Kannadi Orkney_1KG South_Indian_Brahmin -0.005987 0.000311 -19.223 237162
Irish_D North_Kannadi South_Indian_Brahmin -0.005958 0.000317 -18.817 237023
British_Isles_D Chamar_M South_Indian_Brahmin -0.005931 0.000334 -17.757 237112
Dutch_D North_Kannadi South_Indian_Brahmin -0.005914 0.00034 -17.416 236008
British_Isles_D North_Kannadi South_Indian_Brahmin -0.005914 0.000342 -17.273 236064
North_Kannadi Baleares_1KG South_Indian_Brahmin -0.005878 0.000367 -16.012 235743
German_D North_Kannadi South_Indian_Brahmin -0.005838 0.000306 -19.048 237156
Georgian_D North_Kannadi South_Indian_Brahmin -0.005827 0.000366 -15.924 235091
CEU30 North_Kannadi South_Indian_Brahmin -0.005818 0.000315 -18.461 237266
Greek_D North_Kannadi South_Indian_Brahmin -0.005812 0.000314 -18.527 237028
Orcadian North_Kannadi South_Indian_Brahmin -0.005807 0.000329 -17.649 236669
Austrian_D North_Kannadi South_Indian_Brahmin -0.005803 0.000371 -15.659 235187
North_Kannadi Pais_Vasco_1KG South_Indian_Brahmin -0.005796 0.000337 -17.193 235754
British_D North_Kannadi South_Indian_Brahmin -0.005794 0.000336 -17.243 236613
Mixed_Germanic_D North_Kannadi South_Indian_Brahmin -0.005778 0.000344 -16.794 236047
French North_Kannadi South_Indian_Brahmin -0.005773 0.000312 -18.493 237461
North_Kannadi Cornwall_1KG South_Indian_Brahmin -0.00577 0.000306 -18.846 237375
Armenians Chamar_M South_Indian_Brahmin -0.005759 0.000279 -20.674 238398
Orkney_1KG Chamar_M South_Indian_Brahmin -0.005757 0.000287 -20.042 238463
Hungarians North_Kannadi South_Indian_Brahmin -0.005756 0.000311 -18.482 237196
Serb_D North_Kannadi South_Indian_Brahmin -0.005751 0.000371 -15.499 235625
Iraq_Jews Chamar_M South_Indian_Brahmin -0.005742 0.000303 -18.968 237341
Greek_D Chamar_M South_Indian_Brahmin -0.005736 0.000293 -19.57 238374
North_Kannadi Aragon_1KG South_Indian_Brahmin -0.005733 0.000347 -16.526 235610
Armenians_15_Y Chamar_M South_Indian_Brahmin -0.005723 0.000293 -19.5 237884
German_D Chamar_M South_Indian_Brahmin -0.005719 0.000294 -19.483 238514
Orcadian Chamar_M South_Indian_Brahmin -0.005701 0.000305 -18.707 237880
French_Basque North_Kannadi South_Indian_Brahmin -0.005698 0.000333 -17.104 237119

Links between Western Europe and South Asia have turned up in many of the Project's analyses (e.g., the West European in Dodecad v3, or the Gedrosia component in K12b, or even earlier the "Dagestan" component in both West Europe and South Asia). 

Of course, we don't have to imagine a migration all the way from the the British Isles to South Asia, anymore than we may imagine a migration from South America to Europe to explain the strong negative f3(European; Karitiana, Sardinian) signals previously detected. I don't know what to make of this tendency to minimize f3 for the "longest possible clines". 

In any case, I carried out rolloff analysis using Orcadians and North_Kannadi. This is not the strongest signal, but it is very close to it, and also has the twin advantages of involving public data (so the analysis can be repeated) and a large number of SNPs, which were 466,644 in total. The fit can be seen below:

This appears to be excellent visually. The inferred date from the jackknife is 110.155 +/- 11.345 generations, or 3,190 +/- 330 years, assuming as always a generation length of 29 years.

The obvious candidate for this admixture signal is of course the arrival of the Indo-Aryans into South Asia. 

Can we retire the 60,000-year old coastal Out of Africa?

A widely popularized story has become part of the mainstream view of modern human origins. I have seen it repeated countless times in print, and it has been picked up and repeated in popular magazines and documentaries. One day, it may be worth for someone to chart how this idea came to prominence and wide acceptance, despite having very little in its favor. You can read the final death cries of its supporters in a recent Nature special issue.

The idea can be expressed as follows:

"A very small group of humans left Africa 60 thousand years ago; they were on the brink of extinction, but they managed to follow the coastline of Asia, eventually reaching Australia, and subsequently expanding to colonize the interior of the Eurasian landmass"

I have recently become aware of several new papers that directly challenge this view. Instead of writing a new post about each of them, I've decided to combine them all in one post.

The first one by Delagnes et al. in the Journal of Human Evolution describes Shi’bat Dihya 1 and 2, a couple of ~55,000-year old inland human settlements in the Wadi Surdud basin (Yemen). 


From the paper:

Our fieldwork at the Wadi Surdud in Yemen demonstrates that during the period of the supposed expansion of modern humans out of Africa ca. 60-50 ka, and their rapid dispersal toward southeastern Asia along the western and southern Arabian coastlines, the interior of this region was, in fact, occupied by well-adapted human groups who developed their own local technological tradition, deeply rooted in the Middle Paleolithic. Future research will likely reveal whether the archaeological assemblages recovered from the Wadi Surdud can be associated with the descendents of anatomically modern human groups who occupied the Arabian Peninsula during MIS 5 or the southernmost expansion of the Neanderthals.

There is a paucity of old human remains from Arabia due to local conditions, so we cannot know for sure what morphology was associated with these archaeological cultures. If we take the finds that we do have at face value, we would conclude that the Neandertal range did not reach much to the south of Israel, since (i) no Neandertal remains have been found there, while (ii) modern human remains have.

This is further reinforced by the discovery of the Nubian Complex in southern Arabia with its clear African links; it is extremely difficult to assign that to Neandertals, because that would strongly imply presence of Neandertals in Africa for which there is also no evidence.

But, I think we can infer at least three things:

• People thrived inland during the supposed Out of Africa; if there were any Out-of-Africans around this time did not have to "follow the coast".
• It is becoming increasingly difficult to discount the pre-100ka Mt. Carmel (Qafzeh/Skhul) modern humans as the Out-of-Africa that failed: together with Jebel Faya, and the Nubian Complex we are now getting a picture of thriving populations in the Near East and Arabia prior to 60ka. There is every reason to believe that pre-100ka modern humans in the Levant and probably elsewhere did not disappear to make way for the hypothesized second 60ka Out-of-Africa wave.
• If people without a modern technological package were living in the Wadi Surdud, the idea that they are descended from recent Out-of-Africans with all the technological bells and whistles of modernity disappears: these are people rooted in the local traditions, without any signs of recent African descent.

The second article is a review of the prehistory of the Arabian peninsula by Groucutt and Petraglia in Evolutionary Anthropology. One of the points made by the author, quite often forgotten in recent attempts to discover patterns of human dispersals from modern populations, is that populations don't stay put for tens of thousands of years:

As genetic studies of Arabian populations have increased in scale, they reveal a complex pattern.22–25 Such studies show that modern Arabian populations are mostly derived from Western Asia, reflecting dispersals since the Last Glacial Maximum (LGM). In some areas, however, there are relatively high levels of ‘‘African’’ lineages, which have generally been attributed to historical processes such as slavery.26,27 Genetic evidence, then, is poorly placed to elucidate the position of Arabia in the dispersal of hominin populations. Likewise, the extinction of regional populations means they will not be represented in contemporary genetic structure. In this situation, archeology, in the context of paleoenvironmental fluctuation, offers a key way to elucidate the dispersal of hominin populations into Arabia and their subsequent evolutionary and cultural trajectories.

In Europe where we have the best ancient DNA record, there is substantial evidence for major genetic change over the span of a few thousand years. We have evidence of substantial gene flow into East Africa over the last few thousand years. And, of course, in Africa itself we have substantial evidence for gene flow whether it is related to Bantu farmers or Nilo-Saharan pastoralists.

The authors' overall conclusion:

In general, indications of possible population connections to surrounding regions remain rather speculative, and this is compounded by the absence of fossil evidence. We suggest, however, that the emerging picture suggests a general lack of connections between Africa and Arabia after MIS 5, the last interglacial. Instead, there are perhaps indications that Arabia sometimes saw connections to the Levant.

The third paper is a book chapter by Petraglia, Groucutt, and Blinkhorn. There is plenty of interest here, but what caught my attention is this map of paleorivers in the Arabian and Thar deserts. We so often think of deserts as eternal entitities, and looking at the present-day landscape one would of course conclude that migrating humans would be stark mad to venture far from the coast.

An interesting bit from the paper:

Upper Palaeolithic stone tool industries (typified by the production of long,thin ‘blades’ as well as, often, evidence of ‘art’ and symbolism), appear in the Levant at about 47–45 ka but seem to be rare to absent in Arabia. Maher (2009) comprehensively discusses potentially later Pleistocene sites in Arabia, most of which she identifies as being located in the north-west and south-west of the peninsula. The Qaryat al-Faw site is a possible Late Pleistocene locality, containing laminar technology reminiscent of Levantine Upper and Epi-Palaeolithic assemblages (Edens 2001). The overall lack of Upper Palaeolithic technologies either suggests that human populations were not presentin MIS 3, or that Middle Palaeolithic technologies were used until more sophisticatedtechnologies were developed in the Holocene (Crassardet al.2006, Crassard 2007). Ineither case, the nature of environmental conditions is a critical factor in determining the character of human occupations and material culture. 

and:

Upper Palaeolithic industries are present in the Thar but the ages of many of these sites remain unknown. An assemblage dated to ca. 26 ka has been identified as UpperPalaeolithic at 16R Dune, although the sample size is too low for easy technological comparisons to be made (Achyuthanet al.2007). It can be reasonably hypothesised thatmany Upper Palaeolithic assemblages, containing blade and microblade technologies,date to ca. 35 ka and after (Petraglia et al.2009). Microblade innovations have beentied to more efficient hunting strategies in the face of environmental deterioration andpopulation increase at ca. 35 ka (Petraglia et al.2009). 

There is a widespread belief in the simultaneous spread of Upper Paleolithic technology and modern human populations in Eurasia. But, this is not what the actual evidence shows us. However, the evidence for an earlier appearance of UP industries in the Levant than either Arabia or India makes this hypothesis problematic. It renders the coastal migration hypothesis doubly so, because if modern humans with new technology followed the coast all the way to Australia then it is troublesome that the MP stone tools persist in the regions most adjacent to this migration route. A better explanation may be that the UP revolution should be decoupled from the migration paths of modern humans, and that it was a cultural phenomenon which originated probably in the Levant, rather than being part and parcel of the early migrating humans wherever they were found.

The final article by Dennell and Petraglia argues that the modern humans appear in South Asia long before the conventional 60-40ky time frame. A quote from the paper is useful to remember, and echoes the above discussion:

In the Levant, both Neanderthals and H.sapiens used Mousterian stone-tool assemblages, and in East and North Africa, early H. sapiens used the same lithic tool-kits as their predecessors. This indicates that stone tools are a poor indicator of the species of the hominin that made them: changes in hominin type did not necessarily result in changes in lithic technology. Conversely, unchanging lithic traditions need not imply that the type of hom-inin that used them remained the same. As example, in mainland and island Southeast Asia, there is no equivalent of the Upper Palaeolithic, and“Mode 1”, technologically-simpleflake and core assemblages persist into the late Pleistocene and even inplaces the Holocene, even though the species of hominin that made them changed from H. erectus to H. sapiens. This is in sharp contrast to a region such as western Europe, where the shift from the Middle to Upper Palaeolithic was associated with the replacement of Neanderthals by H. sapiens, leaving aside a much-contested debate over the status of so-called “transitional industries” that could have been made by either. Changes in lithic technology in southern Asia are likely to have been more subtle, and discernible only through more rigorous quantitative analysis than merely noting the size andfrequency of a few common elements

I would say that "Mode 4-5 => Modern human" is quite probably true, but "Mode 1-3 => Not modern human" is not. In a sense, this is a little sad, because the more advanced modes appear much later than the hypothesized appearance of modern humans in most places of the world, so they are not of actually much use in determining when they arrived. The paleoanthropological record is a better guide, but, it is also quite sparse or hotly contested in many areas of Eurasia.

To conclude a long post: the evidence for 60,000 year old Out-of-Africa is weak:

• No specific ties with Africa at this or later times
• Clearest evidence of ties between Arabia and Africa during MIS5
• Evidence for strong populations in Asia at this time, inconsistent with the failure of the modern humans sampled at Mt. Carmel in the Levant prior to 100,000 years
• Presence of primitive stone tools does not necessarily indicate absence of modern humans
• Genetic studies of modern populations should not be used as if these populations are direct descendants of first modern humans in same locales

All in all, I'd say that my "two deserts" theory whereby a Green Sahara pumped early modern humans to Asia prior to 100,000 years ago and then a deteriorating Arabian desert pumped them out post-70,000 years ago is not obviously wrong. Perhaps the pre-100ky wave went much further to the east, to India and Southeast Asia.

But, early modern humans may not have been as dominant as we often think, irrespective of when they dispersed: evidence of archaic humans persists in parts of the world down to the Holocene, and so do the simple stone tools of the Middle Paleolithic. Plus the fact that 2/2 of archaic hominins sampled so far show differential relationships to modern human groups, some of them quite unexpected (Denisova with Melanesians) ought to clue us in to the very real possibility that our distant past was quite more complex than we could ever imagine.

Journal of Human Evolution http://dx.doi.org/10.1016/j.jhevol.2012.03.008

Inland human settlement in southern Arabia 55,000 years ago. New evidence from the Wadi Surdud Middle Paleolithic site complex, western Yemen

Anne Delagnes et al.

The recovery at Shi’bat Dihya 1 (SD1) of a dense Middle Paleolithic human occupation dated to 55 ka BP sheds new light on the role of the Arabian Peninsula at the time of the alleged expansion of modern humans out of Africa. SD1 is part of a complex of Middle Paleolithic sites cut by the Wadi Surdud and interstratified within an alluvial sedimentary basin in the foothills that connect the Yemeni highlands with the Tihama coastal plain. A number of environmental proxies indicate arid conditions throughout a sequence that extends between 63 and 42 ka BP. The lithic industry is geared toward the production of a variety of end products: blades, pointed blades, pointed flakes and Levallois-like flakes with long unmodified cutting edges, made from locally available rhyolite. The occasional exploitation of other local raw materials, that fulfill distinct complementary needs, highlights the multi-functional nature of the occupation. The slightly younger Shi’bat Dihya 2 (SD2) site is characterized by a less elaborate production of flakes, together with some elements (blades and pointed flakes) similar to those found at SD1, and may indicate a cultural continuity between the two sites. The technological behaviors of the SD1 toolmakers present similarities with those documented from a number of nearly contemporaneous assemblages from southern Arabia, the Levant, the Horn of Africa and North Africa. However, they do not directly conform to any of the techno-complexes typical of the late Middle Paleolithic or late Middle Stone Age from these regions. This period would have witnessed the development of local Middle Paleolithic traditions in the Arabian Peninsula, which suggests more complex settlement dynamics and possible population interactions than commonly inferred by the current models of modern human expansion out of Africa.

Link

Evolutionary Anthropology DOI: 10.1002/evan.21308

The prehistory of the Arabian peninsula: Deserts, dispersals, and demography

Huw S. Groucutt, Michael D. Petraglia

As a geographic connection between Africa and the rest of Eurasia, the Arabian Peninsula occupies a central position in elucidating hominin evolution and dispersals. Arabia has been characterized by extreme environmental fluctuation in the Quaternary, with profound evolutionary and demographic consequences. Despite the importance of the region, Arabia remains understudied. Recent years, however, have seen major developments in environmental studies and archeology, revealing that the region contains important records that should play a significant role in future paleoanthropological narratives.1–3 The emerging picture of Arabia suggests that numerous dispersals of hominin populations into the region occurred. Populations subsequently followed autochthonous trajectories, creating a distinctive regional archeological record. Debates continue on the respective roles of regional hominin extinctions and population continuity, with the latter suggesting adaptation to arid conditions.

Link

HOMININ EVOLUTIONARY HISTORY IN THE ARABIAN DESERT AND THE THAR DESERT

Michael D. Petraglia, Huw Groucutt and James Blinkhorn

Link

Quaternary Science Reviews Volume 47, 30 July 2012, Pages 15–22

The dispersal of Homo sapiens across southern Asia: how early, how often, how complex?

Robin Dennell, Michael D. Petraglia


The timing and the paths of colonization of southern Asia by Homo sapiens are poorly known, though many population geneticists, paleoanthropologists, and archaeologists have contended that this process began with dispersal from East Africa, and occurred between 60,000 and 40,000 years ago. However, the evidence for this scenario is very weak, particularly the lack of human skeletal evidence between the Levant and Borneo before 40 ka, and other explanations are possible. Here we argue that environmental and archaeological information is increasingly indicating the likelihood that H. sapiens exited Africa much earlier than commonly thought, and may have colonized much of southern Asia well before 60,000 years ago. Additionally, we cannot exclude the possibility that several dispersal events occurred, from both North and East Africa, nor the likelihood that early populations of H. sapiens in southern Asia interbred with indigenous populations of Neanderthals, Denisovans and Homoerectus. The population history of southern Asia during the Upper Pleistocene is likely far more complex than currently envisaged.


Link

SMBE 2012 abstracts (Part II)

Some more abstracts from SMBE 2012.

The Neolithic trace in mitochondrial haplogroup U8 

Joana Barbosa Pereira 1,2 , Marta Daniela Costa 1,2 , Pedro Soares 2 , Luísa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,  3 Faculdade de Medicina da  Universidade do Porto, Porto, Portugal,  4 School of Applied Sciences, University of Huddersfield, Huddersfield, UK  

The mitochondrial DNA (mtDNA) still remains an important marker in the study of human history, especially if  considering the increasing amount of data available. Among the several questions regarding human history that are  under debate, the model of expansion of agriculture into Europe from its source in the Near East is still unclear. Recent  studies have indicated that clusters belonging to haplogroup K, a major clade from U8, might be related with the  Neolithic expansions. Therefore, it is crucial to identify the founder lineages of the Neolithic in Europe so that we may  understand the real genetic input of the first Near Eastern farmers in the current European population and comprehend  how agriculture spread so quickly throughout all Europe.  In order to achieve this goal, a total of 55 U8 samples from the Near East, Europe and North Africa were selected for  complete characterisation of mtDNA. A maximum-parsimonious phylogenetic tree was constructed using all published  sequences available so far. Coalescence ages of specific clades were estimated using ρ statistic, maximum likelihood  and Bayesian methods considering a mutation rate for the complete molecule corrected for purifying selection.   Our results show that U8 dates to ~37-54 thousand years ago (ka) suggesting that this haplogroup might have been  carried by the first modern humans to arrive in Europe, ~50 ka. Haplogroup K most likely originated in the Near East  ~23-32 ka where it might have remained during the Last Glacial Maximum, between 26-19 years ago. The majority of K  subclades date to the Late Glacial and are related with the repopulation of Europe from the southern refugia areas. Only  a few lineages appear to reflect post glacial, Neolithic or post-Neolithic expansions, mostly occurring within Europe. The  major part of the lineages dating to the Neolithic period seems to have an European origin with exception of haplogroup  K1a4 and K1a3. Clade K1a4 appears to be originated from the Near East where it also reaches its highest peak of  diversity. Despite the main clades of K1a4 arose in the Near East during the Late Glacial, its subclade K1a4a1 dates to  ~9-11 ka and is most likely related with the Neolithic dispersal to Europe. Similarly, K1a3 probably originated in the Near  East during the Late Glacial and its subclade K1a1a dispersed into Europe ~11-13 ka alongside with the expansion of  agriculture. 

Late Glacial Expansions in Europe revealed through the fine-resolution characterisation of mtDNA haplogroup  U8 

Marta Daniela Costa 1,2 , Joana Barbosa Pereira 1,2 , Pedro Soares 2 , Luisa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal,  3 Faculdade de  Medicina, Universidade do Porto, Porto, Portugal,  4 School of Applied Sciences, University of Huddersfield, Huddersfield,  UK  

The maternally inherited and fast evolving mitochondrial DNA (mtDNA) molecule is a highly informative tool with which  to reconstruct human prehistory. This has become even more true in recent years, as mtDNA based studies are  becoming more robust and powerful due to the availability of complete mtDNA genomes. These allow better mutation  rate estimates and fine-resolution characterisation of the phylogeography of mtDNA haplogroups, or named  clades.  MtDNA haplogroup K, the major subclade of U8, occurs at low frequencies through West Eurasian populations,  and is much more common in Ashkenazi Jews. However, the lack of variation on the first hypervariable segment (HVSI) has precluded any meaningful phylogeographic analysis to date. We therefore completely sequenced 50 haplogroup  K and 5 non-K U8 mtDNA samples from across Europe and the Near East, and combined them with 343 genomes  previously deposited in GenBank, in order to reconstruct a detailed phylogenetic tree. By combining several inference  methods, including maximum parsimony, maximum likelihood and Bayesian inference it was possible to trace the  timescale and geography of the main expansions and dispersals associated with this lineage. We confirmed that  haplogroup K, dating to ~32 thousand years (ka) ago, descended from the U8 clade, which coalesces ~48 ka ago. The  latter is close to the timing of the first arrival of modern humans in Europe and U8 could be one of the few surviving  mtDNA lineages brought by the first settlers from the Near East. U8 split into the widespread U8b, at ~43 ka, and U8a,  which seems to have expanded only in Europe ~24 ka ago. Considering the pattern of diversity and the geographic  distribution, haplogroup K is most likely to have arisen in the Near East, ~32 ka ago. However, some subclades were  evidently carried to Europe during the Last Glacial Maximum (LGM). We observed significant expansions of haplogroup  K lineages in the Late Glacial period (14-19 ka), reflecting expansions out of refuge areas in southwest and possibly  also southeast Europe. 

Reticulated origin of domesticated tetraploid wheat 

Peter Civan Centro de Ciencias do Mar, Universidade do Algarve, Faro, Portugal  

The past 15 years have witnessed a notable scientific interest in the topic of crop domestication and the emergence of  agriculture in the Near East. Multi-disciplinary approaches brought a significant amount of new data and a multitude of  hypotheses and interpretations. However, some seemingly conflicting evidence, especially in the case of emmer wheat,  caused certain controversy and a broad scientific consensus on the circumstances of the wheat domestication has not  been reached, yet.  The past phylogenetic research has translated the issue of wheat domestication into somewhat simplistic mono- /polyphyletic dilemma, where the monophyletic origin of a crop signalizes rapid and geographically localized  domestication, while the polyphyletic evidence suggests independent, geographically separated domestication events.  Interestingly, the genome-wide and haplotypic data analyzed in several studies did not yield consistent results and the  proposed scenarios are usually in conflict with the archaeological evidence of lengthy domestication.  Here I suggest that the main cause of the above mentioned inconsistencies might lie in the inadequacy of the divergent,  tree-like evolutional model. The inconsistent phylogenetic results and implicit archaeological evidence indicate a  reticulate (rather than divergent) origin of domesticated emmer. Reticulated genealogy cannot be properly represented  on a phylogenetic tree; hence different sets of samples and genetic loci are prone to conclude different domestication  scenarios. On a genome-wide super-tree, the conflicting phylogenetic signals are suppressed and the origin of  domesticated crop may appear monophyletic, leading to misinterpretations of the circumstances of the Neolithic  transition.  The network analysis of multi-locus sequence data available for tetraploid wheat clearly supports the reticulated origin of  domesticated emmer and durum wheat. The concept of reticulated genealogy of domesticated wheat sheds new light  onto the emergence of Near-Eastern agriculture and is in agreement with current archaeological evidence of protracted  and dispersed emmer domestication.

High-coverage population genomics of diverse African hunter-gatherers 

Joseph Lachance 1 , Benjamin Vernot 2 , Clara Elbers 1 , Bart Ferwerda 1 , Alain Froment 3 , Jean-Marie Bodo 4 , Godfrey  Lema 5 , Thomas Nyambo 5 , Timothy Rebbeck 1 , Kun Zhang 6 , Joshua Akey 2 , Sarah Tishkoff 1 1 University of Pennsylvania, Philadelphia, PA, USA,  2 University of Washington, Seattle, WA, USA,  3 IRD-MNHN, Musee  de l'Homme, Paris, France,  4 Ministere de la Recherche Scientifique et de l’Innovation, Yaounde, Cameroon,  5 Muhimbili  University College of Health Sciences, Dar es Salaam, Tanzania,  6 University of California at San Diego, San Diego, CA,  USA     

In addition to their distinctive subsistence patterns, African hunter-gatherers belong to some of the most genetically  diverse populations on Earth.  To infer demographic history and detect signatures of natural selection, we sequenced  the whole genomes of five individuals in each of three geographically and linguistically diverse African hunter-gatherer  populations at >60x coverage.  In these 15 genomes we identify 13.4 million variants, many of which are novel,  substantially increasing the set of known human variation.  These variants result in allele frequency distributions that are  free of SNP ascertainment bias.  This genetic data is used to infer population divergence times and demographic history  (including population bottlenecks and inbreeding).  We find that natural selection continues to shape the genomes of  hunter-gatherers, and that deleterious genetic variation is found at similar levels for hunter-gatherers and African  populations with agricultural or pastoral subsistence patterns.  In addition, the genomes of each hunter-gatherer  population contain unique signatures of local adaptation.  These highly-divergent genomic regions include genes  involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.

Reconstructing past Native American genetic diversity in Puerto Rico from contemporary populations Marina Muzzio 1,2 , Fouad Zakharia 1 , Karla Sandoval 1 , Jake K. Byrnes 3 , Andres Moreno-Estrada 1 , Simon Gravel 1 , Eimear  Kenny 1 , Juan L. Rodriguez-Flores 5 , Chris R. Gignoux 6 , Wilfried Guiblet 4 , Julie Dutil 7 , The 1000 Genomes Consortium 0 ,  Andres Ruiz-Linares 8 , David Reich 9,10 , Taras K. Oleksyk 4 , Juan Carlos Martinez-Cruzado 4 , Esteban Gonzalez  Burchard 6 , Carlos D. Bustamante 1 1 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA,  2 Facultad de Ciencias  Naturales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina,  3 Ancestry. com®, San Francisco,  California, USA,  4 Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico,  5 Department  of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA,  6 Institute for Human Genetics,  University of California San Francisco, San Francisco, California, USA,  7 Ponce School of Medicine, Ponce, Puerto Rico, 8 Department of Genetics, Evolution and Environment. University College London, London, UK,  9 Department of  Genetics, Harvard Medical School, Boston, Massachusetts, USA,  10 Broad Institute of MIT and Harvard, Cambridge,  Massachusetts, USA  

The Caribbean region has a rich cultural and biological diversity, including several countries with different languages,  and important historical events like the arrival of the Europeans in the late fifteenth century affected it deeply. Although it  has been said that two main Native American groups peopled the Caribbean at the time of Columbus’s voyages—the  Arawakan-speaking Tainos and the Caribs—this model has been questioned because it comes from the descriptions  written by the conquerors. The archaeological record shows a richer picture of trade among the islands, cultural change  and diversity than what colonial documents depict, from the early settlements around 8000 B.P. to the chiefdoms and  towns at the time of contact. How this area was peopled and how its inhabitants interacted with the surrounding  continent are questions that remain to be answered due to the fragmentary nature of the historical and archaeological  records.   
We aim to reconstruct the Native American genetic diversity from the time of the Spanish arrival at the island of Puerto  Rico from its contemporary population. We seek to find out how the original peopling of Puerto Rico occurred, along  with which contemporary Native American populations are the most closely related to the Native tracks found. We used  PCAdmix to trace Native American segments in admixed individuals, thus enabling us to reconstruct the original native  lineages previous to the European and African contact.   

Specifically, we generated local ancestry calls for the 70 parents of the 35 complete Puerto Rican trios from the wholegenome and Illumina Omni 2.5M chip Genotype data of the 1000 Genomes Project, both to examine genome-wide  admixture patterns and to infer demographic historical events from ancestry tract length distributions and an ancestryspecific PCA approach, adding 55 Native American groups as potential source populations (N=475 genotyped through  Illumina’s 650K array) and 15 selected Mexican trios (genotyped on Affymetrix’s 6.0 array, including about 906,000  SNPs) to provide population context. ADMIXTURE analysis has shown that in Puerto Rico there is no single source of  contribution for the Native component. Rather, this component seems to include a mixture of major Mexican and  Andean components with little contributions from the Amazonian isolates. On the other hand, the ancestry-specific PCA  plotted the Puerto Rican Native segments tightly clustered with the Native segments of groups from the same language  family as the Tainos (Equatorial-Tucanoan), showing a clear association between linguistics and genetics instead of a  geographical one.

 Inference of demographic history and natural selection in African Pygmy populations from whole-genome  sequencing data

 Martin Sikora 1 , Etienne Patin 2 , Helio Costa 1 , Katherine Siddle 2 , Brenna M Henn 1 , Jeffrey M Kidd 1,3 , Ryosuke Kita 1 ,  Carlos D Bustamante 1 , Lluis Quintana-Murci 2 1 Department of Genetics, School of Medicine, Stanford Uni, Stanford, CA, USA,  2 Unit of Human Evolutionary Genetics,  Institut Pasteur, CNRS URA3012, Paris, France,  3 Departments of Human Genetics and Computational Medicine and  Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA     

The Pygmy populations of Central Africa are some of the last remaining hunter-gatherers among present-day human  populations, and can be broadly classified into two geographically separated groups, the Western and Eastern Pygmies.  Compared to their neighboring populations of predominantly Bantu origin, Pygmy populations show distinct cultural and  physical characteristics, most notably short stature, often referred to as the “Pygmy phenotype”. Given their distinct  physical characteristics, the questions of the demographic history and origin of the Pygmy phenotype have attracted  much attention. Previous studies have shown an ancient divergence (~60,000 years ago) of the ancestors of modernday Pygmies from non-Pygmies, and a more recent split of the Eastern and Western Pygmy groups. However, these  studies were generally based on a relatively small set of markers, precluding accurate estimations of demographic  parameters. Furthermore, despite the considerable interest, to date there is still little known about the genetic basis of  the small stature phenotype of Pygmy populations.   

In order to address these questions, we sequenced the genomes of 47 individuals from three populations: 20 Baka, a  Pygmy hunter-gatherer population from the Western subgroup of the African Pygmies; 20 Nzebi, a neighboring nonPygmy agriculturist population from the Bantu ethnolinguistic group; as well as 7 Mbuti, Eastern Pygmy population, from  the Human Genome Diversity Project (HGDP). We performed whole-genome sequencing using Illumina Hi-Seq 2000 to  a median sequencing depth of 5.5x per individual. After stringent quality control filters, we call over 17 Million SNPs  across the three populations, 32% of them novel (relative to dbSNP 132). Genotype accuracy after imputation was  assessed using genotype data from the Illumina OMNI1 SNP array, and error rates were found to be comparable to  other low-coverage studies (< 3% for most individuals). Preliminary results show relatively low genetic differentiation  between the Baka and the Nzebi (mean FST = 0.026), whereas the Mbuti show higher differentiation to both Baka and  Nzebi (mean FST = 0.060 and 0.070, respectively). Furthermore, we find that alleles previously found to be associated with height in other populations are not enriched for the “small” alleles in the Pygmy populations. We find a number of  highly differentiated genomic regions as candidate loci for height differentiation, which will be verified using simulations  under the best-fit demographic model, inferred from multi-dimensional allele frequency spectra using DaDi. Our dataset  will allow a detailed investigation of the demographic history and the genomics of adaptation in these populations.

Genetic structure in North African human populations and the gene flow to Southern Europe

Laura R Botigué 1 , Brenna M Henn 2 , Simon Gravel 2 , Jaume Bertranpetit 1 , Carlos D Bustamante 2 , David Comas 1 1 Institut de Biologia Evolutiva (IBE, CSIC-UPF), Barcelona, Spain,  2 Stanford University, Stanford CA, USA Despite being in the African continent and at the shores of the Mediterranean, North African populations might have  experienced a different population history compared to their neighbours. However, the extent of their genetic divergence  and gene flow from neighbouring populations is poorly understood. In order to establish the genetic structure of North  Africans and the gene flow with the Near East, Europe and sub-Saharan Africa, a genomewide SNP genotyping array  data (730,000 sites) from several North African and Spanish populations were analysed and compared to a set of  African, European and Middle Eastern samples. We identify a complex pattern of autochthonous, European, Near  Eastern, and sub-Saharan components in extant North African populations; where the autochthonous component  diverged from the European and Near Eastern component more than 12,000 years ago, pointing to a pre-Neolithic  ‘‘back-to-Africa’’ gene flow. To estimate the time of migration from sub-Saharan populations into North Africa, we  implement a maximum likelihood dating method based on the frequency and length distribution of migrant tracts, which  has suggested a migration of western African origin into Morocco ~1,200 years ago and a migration of individuals with  Nilotic ancestry into Egypt ~ 750 years ago.  We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African  ancestry that is highest in southwestern Europe and decreases in northern latitudes. The elevated shared African  ancestry in SW Europe (up to 20% of the individuals’ genomes) can be traced to populations in the North African  Maghreb. Our results, based on both allele-frequencies and shared haplotypes, demonstrate that recent migrations from  North Africa substantially contribute to the higher genetic diversity in southwestern Europe

Estimating a date of mixture of ancestral South Asian populations

Priya Moorjani 1,2 , Nick Patterson 2 , Periasamy Govindaraj 3 , Danish Saleheen 4 , John Danesh 4 , Lalji Singh* 3,5 ,  Kumarasamy Thangaraj* 3 , David Reich* 1,2 1 Harvard University, Boston, Massachusetts, USA,  2 Broad Institute, Cambridge, Massachusetts, USA,  3 Centre for  Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India,  4 Dept of Public Health and Care, University of  Cambridge, Cambridge, UK,  5 Genome Foundation, Hyderabad, Andhra Pradesh, India Linguistic and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of  two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and  Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and  ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the  ANI-ASI mixture is unknown. Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI  mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using  admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking  Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that  occurred within the last four thousand years, a cultural shift led to widespread endogamy, decreasing the rate of  additional mixture.   

Long IBD in Europeans and recent population history 

Peter Ralph, Graham Coop  UC Davis, Davis, CA, USA  

Numbers of common ancestors shared at various points in time across populations  can tell us about recent demography, migration, and population movements.  These rates of shared ancestry over tens of generations can be inferred from  genomic data, thereby dramatically increasing our ability to infer population  history much more recent than was previously possible with population genetic  techniques.  We have analyzed patterns of IBD in a dataset of thousands of  Europeans from across the continent, which provide a window into recent  European geographic structure and migration.   

Gene flow between human populations during the exodus from Africa, and the timeline of recent human  evolution  

Aylwyn Scally, Richard Durbin  Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK 

We present a novel test for historical gene flow between populations using unphased genotypes in present-day  individuals, based on the sharing of derived alleles and making a minimal set of assumptions about their demographic  history. We apply this test to data for three human individuals of African, European and Asian ancestry. We find that the  joint distribution of European and Asian genotypes is compatible with these populations having separated cleanly at  some time in the past without subsequent genetic exchange. However the same is not true of the European-African and  Asian-African distributions, which instead suggest an extended period of continued exchange between African and nonAfrican populations after their initial separation. 

We discuss this in comparison with recent models and estimates of separation time between these populations. We  also consider the impact of recent direct experimental studies of the human mutation rate, which suggest rates of  around 0.5 × 10 -9  bp -1  y -1 , substantially lower than prior estimates of 1 × 10 -9  bp -1  y -1  obtained from calibration against  the primate fossil record. We show that in several places the lower rate, implying older dates, yields better agreement  between genetic and non-genetic (paleoanthropological and archaeological) evidence for events surrounding the  exodus of modern humans from Africa and their dispersion worldwide.

Long-term presence versus recent admixture: Bayesian and approximate-Bayesian analyses of genetic  diversity of human populations in Central Asia 

Friso Palstra, Evelyne Heyer, Frederic Austerlitz  Eco-anthropologie et Ethnobiologie UMR 7206 CNRS, Equipe Genetique des Populations Humaines, Museum National  d'Histoire Naturelle, Paris, France 

A long-standing goal in population genetics is to unravel the relative importance of evolutionary forces that shape  genetic diversity. Here we focus on human populations in Central Asia, a region that has long been known to contain  the highest genetic diversity on the Eurasian continent. However, whether this variation principally reflects long-term  presence, or rather the result of admixture associated with repeated migrations into this region in more recent historical  times, remains unclear. Here we investigate the underlying demographic history of Central Asian populations in explicit  relation to Western Europe, Eastern Asia and the Middle East. For this purpose we employ both full Bayesian and  approximate-Bayesian analyses of nuclear genetic diversity in 20 unlinked non-coding resequenced DNA regions,  known to be at least 200 kb apart from any known gene, mRNA or spliced EST (total length of 24 kb), and 22 unlinked  microsatellite loci.   

Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be  best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians)  with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications  that this region might have genetically influenced Western European populations, rather than vice versa. A further  evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of  establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the  approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate  the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both  long-term presence and admixture in more recent historical times. 

Population structure and evidence of selection in the Khoe-San and Coloured populations from southern Africa 

Carina Schlebusch 1 , Pontus Skoglund 1 , Per Sjödin 1 , Lucie Gattepaille 1 , Sen Li 1 , Flora Jay 2 , Dena Hernandez 3 , Andrew  Singleton 3 , Michael Blum 2 , Himla Soodyall 4,5 , Mattias Jakobsson 1 1 Uppsala University, Uppsala, Sweden,  2 Université Joseph Fourier, Grenoble, France,  3 National Institute on Aging (NIH),  Bethesda, USA,  4 University of the Witwatersrand, Johannesburg, South Africa,  5 National Health Laboratory Service,  Johannesburg, South Africa  

The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of  hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking  groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Mitochondrial DNA, Y-chromosome  and autosomal studies conducted on a few San groups revealed that they harbour some of the most divergent lineages  found in living peoples throughout the world.   

We used autosomal data to characterize patterns of genetic variation among southern African individuals in order to  understand human evolutionary history, in particular the demographic history of Africa. To this end, we successfully  genotyped ~ 2.3 million genome wide SNP markers in 220 individuals, comprising seven Khoe-San, two Coloured and  two Bantu-speaking groups from southern Africa. After quality filtering, the data were combined with publicly available  SNP data from other African populations to investigate stratification and demography of African populations.  

We also  applied a newly developed method of estimating population topology and divergence times. Genotypes and inferred  haplotypes were used to assess genetic diversity, patterns of haplotype variation and linkage disequilibrium in different  populations.  We found that six of the seven Khoe-San populations form a common population lineage basal to all other modern  human populations. The studied Khoe-San populations are genetically distinct, with diverse histories of gene flow with  surrounding populations. A clear geographic structuring among Khoe-San groups was observed, the northern and  southern Khoe-San groups were most distinct from each other with the central Khoe-San group being intermediate. The  Khwe group contained variation that distinguished it from other Khoe-San groups. Population divergence within the  Khoe-San group is approximately 1/3 as ancient as the divergence of the Khoe-San as a whole to other human  populations (on the same order as the time of divergence between West Africans and Eurasians). Genetic diversity in  some, but not all, Khoe-San populations is among the highest worldwide, but it is influenced by recent admixture. We  furthermore find evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups, possibly related to the  introduction of pastoralism to southern Africa.   

We searched for signatures of selection in the different population groups by scanning for differentiated genome-regions  between populations and scanning for extended runs of haplotype homozygosity within populations. By means of the  selection scans, we found evidence for diverse adaptations in groups with different demographic histories and modes of  subsistence. 

Impacts of life-style on human evolutionary history: A genome-wide comparison of herder and farmer  populations in Central Asia 

Michael C. Fontaine 1,2 , Laure Segurel 2,3 , Christine Lonjou 4 , Tatiana Hegay 5 , Almaz Aldashev 6 , Evelyne Heyer 2 , Frederic  Austerlitz 1,2 1 Ecology, Systematics & Evolution. UMR8079 Univ. Paris Sud - CNRS - AgroParisTech, Orsay, France,  2 EcoAnthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cite, Paris, France, 3 Department of Human Genetics, University of Chicago, Chicago, USA,  4 C2BiG (Centre de  Bioinformatique/Biostatistique Genomique d’Ile de France), Plateforme Post-genomique P3S, Hopital Pitie Salpetriere,  Paris, France,  5 Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan,  6 Institute of Molecular  Biology and Medicine, National Center of Cardiology and Internal Medicine, Bishkek,  

Kyrgyzstan Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of habitats and  dietary components. These aspects of human environments have changed dramatically during human evolution, giving  rise to new selective pressures. Here we focused on two populations in Central Asia with long-term contrasted lifestyles:  Kyrgyz’s that are traditionally nomadic herders, with a traditional diet based on meat and milk products, and Tajiks that  are traditionally agriculturalists, with a traditional diet based mostly on cereals. We genotyped 93 individuals for more  than 600,000 SNP markers (Human-660W-Quad-V1.0 from Illumina) spread across the genome. We first analysed the  population structure of these two populations in the world-wide context by combining our results with other available  genome-wide data. Principal component and Bayesian clustering analyses revealed that Tajiks and Kirgiz’s are both  admixed populations which differed however from each other with respect to their ancestry proportions: Tajiks display a  much larger proportion of common ancestry with European populations while Kirgiz’s share a larger common ancestry  with Asiatic populations. We then examined the region of the genome displaying unusual population differentiation  between these two populations to detect natural selection and checked whether they were specific to Central Asia or  not. We complemented these analyses with haplotype-based analyses of selection. 

Bayesian inference of the demographic history of Niger-Congo speaking populations 

Isabel Alves 1,2 , Lounès Chikhi 2,3 , Laurent Excoffier 1,4 1 CMPG, Institute of Ecology and Evolution, Berne, Switzerland,  2 Population and Conservation Genetics Group, Instituto  Gulbenkian de Ciência, Oeiras, Portugal,  3 CNRS, Université Paul Sabatier, ENFA, Toulouse, France,  4 Swiss Institute of  Bioinformatics, Lausanne, Switzerland  

The Niger-Congo phylum encompasses more than 1500 languages spread over sub-Saharan Africa. This current wide  range is mostly due to the spread of Bantu-speaking people across sub-equatorial regions in the last 4000-5000 years.  Although several genetic studies have focused on the evolutionary history of Bantu-speaking groups, much less effort  has been put into the relationship between Bantu and non-Bantu Niger-Congo groups. Additionally, archaeological and  linguistic evidence suggest that the spread of these populations occurred in distinct directions from the core region  located in what is now the border between Nigeria and Cameroon towards West and South Africa, respectively. We  have performed coalescent simulations within an approximate Bayesian computation (ABC) framework in order to  statistically evaluate the relative probability of alternative models of the spread of Niger-Congo speakers and to infer  demographic parameters underlying these important migration events. We have analysed 61 high-quality microsatellite  markers, genotyped in 130 individuals from three Bantu and three non Bantu-speaking populations, representing a  "Southern wave" or the Bantu expansion, and a "Western wave", respectively. Preliminary results suggest that models  inspired by a spatial spread of the populations are better supported than classical isolation with migration (IM) models.  We also find that Niger-Congo populations currently maintain high levels of gene flow with their neighbours, and that  they expanded from a single source between 200 and 600 generations, even though available genetic data do not  provide enough information to accurately infer these demographic parameters.

A genetic study of skin pigmentation variation in India  

Mircea Iliescu1 , Chandana Basu Mallick 2,3 , Niraj Rai 4 , Anshuman Mishra 4 , Gyaneshwer Chaubey 2 , Rakesh Tamang 4 ,  Märt Möls 3 , Rie Goto 1 , Georgi Hudjashov 2,3 , Srilakshmi Raj 1 , Ramasamy Pitchappan 5 , CG Nicholas Mascie-Taylor 1 , Lalji  Singh 4,6 , Marta Mirazon-Lahr 7 , Mait Metspalu 2,3 , Kumarasamy Thangaraj 4 , Toomas Kivisild 1,3 1 Division of Biological Anthropology, University of Cambridge, Cambridge, UK,  2 Evolutionary Biology Group, Estonian  Biocentre, Tartu, Estonia,  3 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia,  4 Centre for Cellular  and Molecular Biology, Hyderabad, India,  5 Chettinad Academy of Research and Education, Chettinad Health City,  Chennai, India,  6 Banaras Hindu University, Varanasi, India,  7 Leverhulme Centre for Human Evolutionary Studies,  Division of Biological Anthropology, University of Cambridge, Cambridge, UK  

Human skin colour is a polygenic trait that is primarily determined by the amount and type of melanin produced in the  skin. The pigmentation variation between human populations across the world is highly correlated with geographic  latitude and the amount of UV radiation. Association studies together with research involving different model organisms  and coat colour variation have largely contributed to the identification of more than 378 pigmentation candidate genes.  These include TYR OCA2, that are known to cause albinism, MC1R responsible for the red hair phenotype, and genes  such as MATP, SLC24A5 and ASIP that are involved in normal pigmentation variation. In particular, SLC24A5 has been  shown to explain one third of the pigmentation difference between Europeans and Africans. However, the same gene  cannot explain the lighter East Asian phenotype; therefore, light pigmentation could be the result of convergent  evolution. A study on UK residents of Pakistani, Indian and Bangladeshi descent found significant association of  SLC24A5, SLC45A2 and TYR genes with skin colour. While these genes may explain a significant proportion of  interethnic differences in skin colour, it is not clear how much variation such genes explain within Indian populations  who are known for their high level of diversity of pigmentation. We have tested 15 candidate SNPs for association with  melanin index in a large sample of 1300 individuals, from three related castes native to South India. Using logistic  regression model we found that SLC24A5 functional SNP, rs1426654, is strongly associated with pigmentation in our  sample and explains alone more than half of the skin colour difference between the light and the dark group of  individuals. Conversely, the other tested SNPs fail to show any significance; this strongly argues in favour of one gene  having a major effect on skin pigmentation within ethnic groups of South India, with other genes having small additional  effects on this trait. We genotyped the SLC24A5 variant in over 40 populations across India and found that latitudinal  differences alone cannot explain its frequency patterns in the subcontinent. Key questions arising from this research are  when and where did the light skin variant enter South Asia and the manner and reason for it spreading across the Indian  sub-continent. Hence, a comprehensive view of skin colour evolution requires that in depth sequence information be  corroborated with population (genetic) history and with ancient DNA data of past populations of Eurasia. 

Y-STR haplotype shared between Roma and South Indians

Gene. 2012 May 17. [Epub ahead of print]

Ancestral modal Y-STR haplotype shared among Romani and South Indian populations.

Regueiro M, Rivera L, Chennakrishnaiah S, Popovic B, Andjus S, Milasin J, Herrera RJ.

Abstract

One of the primary unanswered questions regarding the dispersal of Romani populations concerns the geographical region and/or the Indian caste/tribe that gave rise to the proto-Romani group. To shed light on this matter, 161 Y-chromosomes from Roma, residing in two different provinces of Serbian, were analyzed. Our results indicate that the paternal gene pool of both groups is shaped by several strata, the most prominent of which, H1-M52, comprises almost half of each collection's patrilineages. The high frequency of M52 chromosomes in the two Roma populations examined may suggest that they descend from a single founder that has its origins in the Indian subcontinent. Moreover, when the Y-STR profiles of haplogroup H derived individuals in our Roma populations were compared to those typed in the South Indian emigrants from Malaysia and groups from Madras, Karnataka (Lingayat and Vokkaliga castes) and tribal Soligas, sharing of the two most common haplotypes was observed. These similarities suggest that South India may have been one of the contributors to the proto-Romanis. European genetic signatures (i.e., haplogroups E1b1b1a1b -V13, G2a-P15, I-M258, J2-M172 and R1-M173), on the other hand, were also detected in both groups, but at varying frequencies. The divergent European genetic signals in each collection are likely the result of differential gene flow and/or admixture with the European host populations but may also be attributed to dissimilar endogamous practices following the initial founder effect. Our data also supports the notion that a number of haplogroups including G2a-P15, J2a3b-M67(xM92), I-M258 and E1b1b1-M35 were incorporated into the proto-Romani paternal lineages as migrants moved from northern India through Southwestern Asia, the Middle East and/or Anatolia into the Balkans.

Link

Y chromosomes in Haiti and Jamaica (Simms et al. 2012)

The paper investigates the different signals of patrilineal ancestry in two Caribbean islands, finding the expect signals of European and African ancestry, as well as minor other signals from the New World, East Asia, and even South Asia.

I will just point out the presence of a DE* chromosome in Jamaica. Such chromosomes have occasionally turned up in both Asia and Africa, and they ought to be an object of further study, preferrably with full Y-chromosome sequencing technology, since a better resolution of the DE-YAP haplogroup's structure will go a long way towards solving many puzzles about prehistory.

Am J Phys Anthropol. 2012 May 11. doi: 10.1002/ajpa.22090.

Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow.

Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ.

Abstract

Although previous studies have characterized the genetic structure of populations from Haiti and Jamaica using classical and autosomal STR polymorphisms, the patrilineal influences that are present in these countries have yet to be explored. To address this lacuna, the current study aims to investigate, for the first time, the potential impact of different ancestral sources, unique colonial histories, and distinct family structures on the paternal profile of both groups. According to previous reports examining populations from the Americas, island-specific demographic histories can greatly impact population structure, including various patterns of sex-biased gene flow. Also, given the contrasting autosomal profiles provided in our earlier study (Simms et al.: Am J Phys Anthropol 142 (2010) 49-66), we hypothesize that the degree and directionality of gene flow from Europeans, Africans, Amerindians, and East Asians are dissimilar in the two countries. To test this premise, 177 high-resolution Y-chromosome binary markers and 17 Y-STR loci were typed in Haiti (n = 123) and Jamaica (n = 159) and subsequently utilized for phylogenetic comparisons to available reference collections encompassing Africa, Europe, Asia (East and South), and the New World. Our results reveal that both studied populations exhibit a predominantly South-Saharan paternal component, with haplogroups A1b-V152, A3-M32, B2-M182, E1a-M33, E1b1a-M2, E2b-M98, and R1b2-V88 comprising 77.2% and 66.7% of the Haitian and Jamaican paternal gene pools, respectively. Yet, European derived chromosomes (i.e., haplogroups G2a*-P15, I-M258, R1b1b-M269, and T-M184) were detected at commensurate levels in Haiti (20.3%) and Jamaica (18.9%), whereas Y-haplogroups indicative of Chinese [O-M175 (3.8%)] and Indian [H-M69 (0.6%) and L-M20 (0.6%)] ancestry were restricted to Jamaica.

Link

Genetic affinities of Central Indian tribals

PLoS ONE 7(2): e32546. doi:10.1371/journal.pone.0032546

Genetic Affinities of the Central Indian Tribal Populations

Gunjan Sharma et al.

Abstract
Background

The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers.

Methodology/Principal Findings

Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results.

Conclusions/Significance

Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.

Link

Population structure in South Asia (Metspalu et al. 2011)

I haven't read the paper fully yet (it's open access), but the abstract seems to agree with what I've written both here and over at the Dodecad blog, about South Asians being primarily a West Asian/South Asian variable mix. I will try to get and analyze the new data from the paper; it is strange that every time I am just about ready to release the new version of Dodecad v4, I discover a source of new data!

The American Journal of Human Genetics, Volume 89, Issue 6, 731-744, 9 December 2011

Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

Mait Metspalu et al.


South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.

Link

Terai and Duars Y-chromosomes

I had not even heard of these populations until today; hopefully South Asian experts elsewhere in the blogosphere will chime in.

J Hum Genet. 2011 Sep 8. doi: 10.1038/jhg.2011.98. [Epub ahead of print]

Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India.

Debnath M, Palanichamy MG, Mitra B, Jin JQ, Chaudhuri TK, Zhang YP.

Abstract
The sub-Himalayan Terai and Duars, the important outermost zones comprising the plains of East India, are known as the reservoirs of ethnic diversity. Analysis of the paternal genetic diversity of the populations inhabiting these regions and their genetic relationships with adjacent Himalayan and other Asian populations has not been addressed empirically. In the present investigation, we undertook a Y-chromosome phylogeographic study on 10 populations (n=375) representing four different linguistic groups from the sub-Himalayan Terai and Duars regions of East India. The high-resolution analysis of Y-chromosome haplogroup variations based on 76 binary markers revealed that the sub-Himalayan paternal gene pool is extremely heterogeneous. Three major haplogroups, namely H, O and R, are shared across the four linguistic groups. The Indo-European-speaking castes exhibit more haplogroup diversity than the tribal groups. The findings of the present investigation suggest that the sub-Himalayan gene pools have received predominant Southeast Asian contribution. In addition, the presence of Northeast and South Asian signatures illustrate multiple events of population migrations as well as extensive genetic admixture amongst the linguistic groups.

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