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Mohenjo-daro_Priesterkönig At the Eurogenes blog there has been a lot of analysis of South Asian genetic history in light of ancient DNA recently. Part of this is probably due to the fact that “Euro” genes (that is, the genetic history of European peoples) are now understood to be inextricably tied to demographic pulses and shifts which are deeply rooted in Eur asian cultural revolutions over the past 4 to 10,000 years. Only a very small fraction of the ancestry of modern Europeans dates to the period before the Last Glacial Maximum ~20,000 years ago; at least according to ancient DNA. And most of the ancestry is conditional on events which occurred during the Holocene, the past 10,000 years.* To give a sense of how recent all this is, when the first cuneiform tablets were being written, the demographic-genetic revolution which was to begin the transformation of Northern Europeans into what we now know as Northern Europeans had not completed itself, and in many regions not even begun (e.g., the Swedish-Battle Axe culture begins in 2800 BCE, several hundred years after the earliest writing in Sumerian).

Screenshot 2016-05-28 16.24.36 They say you need two hands to clap. And India is the other hand that we have now when comes to understanding this process. There’s now a lot of circumstantial evidence to tie Indians to Europeans in moderately complex ways. To the left is a figure from the supplements of Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. You see that the phylogeny of R1a in South Asia really is a burst. There’s just not that much genetic difference between all of us South Asian R1a males, irrespective of region and caste. We’re pretty much all on a particular branch, Z93. Rare outside of South Asia today (it is found in the Altai and in Central Asia), it has been discovered in ancient males from the Srubna culture of eastern Ukraine ~4,000 years ago. In Europe R1a is found mostly in Northern Europe, and especially Eastern Europe. And yet if you look further up in the supplements you see that for haplogroup J2 most of the males are partitioned between South Asians and Southwest Europeans. Additionally, the two large branches of J2 have both South Asians and Southwest Europeans, suggesting that divergence in J2 predates the arrival of J2 bearing males to South Asia and Southwest Europe. Finally, unlike R1a you can see visually that the phylogeny of J2 is less explosive; there are more clean sequences of mutations to differentiate the various branches of this patrilineage. J2 is common, but it did not undergo nearly the same burst as R1a. It’s prevalence is due to more continuous and gradual demographic processes.

51IZQjMbVlL._SX346_BO1,204,203,200_ What does this mean? Various genome bloggers have been arguing since the late aughts that there seem to be two West Eurasian admixtures into South Asia, who are clearly a compound of West Eurasians and non-West Eurasians. This was supported to some extent by the 2013 publication of Genetic Evidence for Recent Population Mixture in India, which found evidence for more than one admixture event in a subset of populations. Then, ancient DNA from the Caucasus added more evidence, Upper Palaeolithic genomes reveal deep roots of modern Eurasians. If you dig deep into the paper you see that Indian populations which are likely to be due to one(ish) admixture event are best modeled as a synthesis between the Kotias Caucasus hunter-gatherer and a non-West Eurasian population (i.e., Ancient South Indians or ASI). But some groups, such as high caste North Indians, seem to be better modeled with ancient Eurasian steppe groups as the source population (these groups themselves have ancestry from a Kotias-related/descended group).

In 2016 the ultimate judge is going to be ancient DNA. In the next year or so I think it will tell the tale that we’ve been hearing in the winds of modern contemporary genetic variation. What I think is that it will confirm part of the narrative and model pushed forward in First Farmers, Peter Bellwood’s book from the middle aughts. The Dravidian languages were brought to India from West Asia in the early-to-middle Holocene by agriculturalists descended from or related to the hunter-gatherers of the Caucasus. They mixed with indigenous hunter-gatherer populations, and gave rise to the first people we would recognize as modern South Asians genetically. Eventually they built what we term the Indus Valley civilization. The relatively evenness of this mix between West Asian descended Ancestral North Indians (ANI) and ASI across South Asia is due to the fact that much of the subcontinent was sparsely populated, and the farmers demographically overwhelmed the indigenous groups. The fact the non-Brahmin upper and middle castes are genetically somewhat different from tribal populations and Dalits in South India is probably due to the fact that the indigenous populations were absorbed at the lower levels of the nascent civilization.

The arrival of Indo-Europeans may or may not have been an “invasion” in a classical sense, but it was highly disruptive. The phylogeny of R1a in South Asia is strongly indicative of an incredible reproductive advantage for males bearing this haplogroup. In fact, R1a is more expansive than Indo-Aryan languages, and is found across language and caste, including among tribal populations. Previously this was argued as a reason for why R1a in South Asia must be old and indigenous to South Asia. Next generation sequencing of the Y chromosome has looked closely, and that is unlikely. The expansion of R1a, and the South Asian branch, is very recent. It hints at cultural processes of male domination and elite diffusion of lineages which we do not have a good theoretical grasp of at this moment.

But this is not the end of the story. I have spoken only of West Eurasians. What of the other half of the ancestral glass, the ASI? I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. The closest modern population to the “pure” ASI ghost group are the Andaman Islanders, and they arrived where they are today not from the Indian subcontinent, but from Burma. There is now a modest amount of evidence through various angles that the ancestors of the Munda people of South Asia must have arrived as part of the Austro-Asiatic agricultural migrations from what is today interior South China. They are not primal. There is no reason to think that that this was the first eruption of humans from this region into South Asia. Those with more understanding of paleoclimatology need to weigh in, but it may be that in the drier conditions of the Pleistocene South Asia had a naturally smaller population than Southeast Asia, so that the latter was always going to be a source and the former a sink, in terms of demographics.

In any case, if the model fits, eventually a preprint you must submit. I think the age of speculations will give way to the age of understanding, though I have no inside information at this point….


* To unpack this, take a conventional idea of Europe today, bounded by Gibraltar on the southwest, the Bosporus on the southeast, and in the far east the Urals and far southeast the Caucasus. The majority of Southern European ancestry seems to derive from Early European Farmers (EEF), and these almost certainly are from Anatolia. In Northern Europe the ancestry is a compound of EEF, Indo-Europeans from the east, and probably residual hunter-gatherers (some researchers believe nearly all of the hunter-gatherer ancestry in Northern Europe is actually from the Indo-Europeans and EEF, with no true relic populations by 5,000 BC). Of the original Yamnaya Indo-European ancestry, the ~25% or so that is Ancestral North Eurasia (ANE) probably is extra-European in provenance. Specifically, a migration out of central Siberia or thereabouts. Nearly half of the remaining is similar to EEF, but we now know it is likely derived from a different Near Eastern farming populations which descend in part from hunter-gatherers from the Caucasus. The balance is from indigenous European hunter-gatherer ancestry which amalgamated with ANE. This last portion is indigenous to Europe broadly construed before the Holocene. I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene.
 
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  1. “I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. ”

    I do not know the need to be so circumspect, screw OIT.
    Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene? There is very limited evidence of human population in the subcontinent before 10,000 BC. All the crops, all the human features (Dravidans) indicate a long transition from out of africa to “Into India”, but no evidence before 10 K ybp. So, there is no need to be coy to argue for everyone being intrusive into India.

    Separately, a question. All of south India shows significant contributions by ashmound building herders, with crops from Africa. Can you conjecture at what point they entered India. I am guessing not more than a thousand years before the first arrival of R1A. Is there a possibility these were the first of multiple “ASI” in Deccan?

    • Replies: @Megalophias
    Do you know of any studies on the population size/density of South Asia in the Upper Paleolithic? I haven't been able to find anything on the subject.
    , @Steve Sailer
    "Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene?"

    Was there anything that made India relatively unattractive to pre-agriculture hunter-gatherers? We're used to thinking of India as supporting a large population with its ample rains.

    Or is it simply that hunter-gatherers who didn't invent agriculture tend to make up a small fraction of today's population's ancestors? Did people invent agriculture independently in India or did only come in from the outside?
  2. @Vijay
    "I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. "

    I do not know the need to be so circumspect, screw OIT.
    Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene? There is very limited evidence of human population in the subcontinent before 10,000 BC. All the crops, all the human features (Dravidans) indicate a long transition from out of africa to "Into India", but no evidence before 10 K ybp. So, there is no need to be coy to argue for everyone being intrusive into India.

    Separately, a question. All of south India shows significant contributions by ashmound building herders, with crops from Africa. Can you conjecture at what point they entered India. I am guessing not more than a thousand years before the first arrival of R1A. Is there a possibility these were the first of multiple "ASI" in Deccan?

    Do you know of any studies on the population size/density of South Asia in the Upper Paleolithic? I haven’t been able to find anything on the subject.

    • Replies: @Vijay
    This is a million dollar question that is subject to controversy and has no precise answer.

    1. Note the later period of start of each of the "lithic" periods in India.

    2. I assume that you are talking about the period between 77 KYA and 10Kya.

    3. Conflicting models by Petragila group and Mellars et al on the actual date of "modern" human entrance OOA into India.

    3. Based on the toolset and hominid population in Indian continent in this period, a proposal is made by Mishra: highly competitive archaic hominids continued to exist in India preventing human dispersal into India until 57 K (MIS 3) before present. They write

    "We suggest that the Indian Subcontinent during MIS 5 times was occupied by a population derived from Homo erectus adapted to the Indian environment from Lower Pleistocene times onwards. This population would be archaic, and the Narmada hominin would be ancestral or a representative of it. Competition between Indian archaics and modern humans would have been intense since they were adapted to similar environments. Failure of modern humans to disperse into the Indian Subcontinent during MIS 5 was probably due to their failure to successfully compete with the Indian archaics during a period when the climatic conditions were favourable to both. However during the MIS 4 times, when the desert zones of Africa and Arabia were abandoned and more favourable zones in the Middle East such the Levant and Iran were occupied by Neanderthals, modern humans had more success in entering India and a major change in the Indian Palaeolithic record then occurred. The expansion of modern humans into India therefore coincides with the expansion of Neanderthals into the Middle East at the expense of modern humans and into Central Asia possibly at the expense of Denisovans."

    Because of the large presence of technologically competent hominids in India, I conjecture that "the later day" modern human population was small, scattered until MIS 3 or MIS 2, and difficult to count. However this does not consider people settling in the periphery in Andamans, Himalayas, and the coast, and their population is unknown in the 57 KYA through 29 KYA period.
  3. The phylogeny of R1a in South Asia is strongly indicative of an incredible reproductive advantage for males bearing this haplogroup. In fact, R1a is more expansive than Indo-Aryan languages, and is found across language and caste, including among tribal populations. It hints at cultural processes of male domination and elite diffusion of lineages which we do not have a good theoretical grasp of at this moment.

    Kings or chiefs fearing for the security of their realm who see a neighboring power being conquered by effective invaders, and want to have some of the interlopers ‘ military or organisational might, would invite high born members of the new neighboring elite into the unconquered realm and offer marriages and landholding in return for military allegiance. The French speaking Norman Lords of Anglo/ Gaelic Scotland became the key to its survival against Norman England for example. I expect some of the spread of R1a across language/ national barriers was due to such a process.

  4. Rick says:

    “I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene.”

    You don’t even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.

    Most of the possibly Pleistocene ancestry is probably there in some kind of roundabout way… they entered early into the EEF or Yamnaya-like groups at the edges of Europe, and then rode their way (back) into Central Europe on the coat tails.

    • Replies: @Sean
    Y chromosome haplogroups like R1a may be a little deceptive, because they would have been affected by hierarchy, patriarchy, especially in combination with primogeniture, which I believe the Indo Europeans set much store by. A major Highland clan founder had Y chromosome success, see Somerled. Another aspect is that younger sons sharing the Y, but lacking position, may have been driven to strike out on their own. I suppose some other markers could have been selected through similar cultural change.
    , @notanon

    Most of the possibly Pleistocene ancestry is probably there in some kind of roundabout way
     
    "Most" seems likely although it seems some of R.E Howard's "dark, savage Picts" might have slipped in along the Atlantic coast somewhere.

    Probably not relevant to anything important except maybe minor phenotype differences.
  5. @Megalophias
    Do you know of any studies on the population size/density of South Asia in the Upper Paleolithic? I haven't been able to find anything on the subject.

    This is a million dollar question that is subject to controversy and has no precise answer.

    1. Note the later period of start of each of the “lithic” periods in India.

    2. I assume that you are talking about the period between 77 KYA and 10Kya.

    3. Conflicting models by Petragila group and Mellars et al on the actual date of “modern” human entrance OOA into India.

    3. Based on the toolset and hominid population in Indian continent in this period, a proposal is made by Mishra: highly competitive archaic hominids continued to exist in India preventing human dispersal into India until 57 K (MIS 3) before present. They write

    “We suggest that the Indian Subcontinent during MIS 5 times was occupied by a population derived from Homo erectus adapted to the Indian environment from Lower Pleistocene times onwards. This population would be archaic, and the Narmada hominin would be ancestral or a representative of it. Competition between Indian archaics and modern humans would have been intense since they were adapted to similar environments. Failure of modern humans to disperse into the Indian Subcontinent during MIS 5 was probably due to their failure to successfully compete with the Indian archaics during a period when the climatic conditions were favourable to both. However during the MIS 4 times, when the desert zones of Africa and Arabia were abandoned and more favourable zones in the Middle East such the Levant and Iran were occupied by Neanderthals, modern humans had more success in entering India and a major change in the Indian Palaeolithic record then occurred. The expansion of modern humans into India therefore coincides with the expansion of Neanderthals into the Middle East at the expense of modern humans and into Central Asia possibly at the expense of Denisovans.”

    Because of the large presence of technologically competent hominids in India, I conjecture that “the later day” modern human population was small, scattered until MIS 3 or MIS 2, and difficult to count. However this does not consider people settling in the periphery in Andamans, Himalayas, and the coast, and their population is unknown in the 57 KYA through 29 KYA period.

    • Replies: @Megalophias
    Thanks!

    I was thinking of the time from the beginning of the Upper Palaeolithic - probably around 50 000 years ago - to the mid-Holocene, not so much the Middle Palaeolithic. AFAIK there were people using a microlithic technology in Peninsular India and Sri Lanka and others making a Hoabinhian-like macrolithic technology in the sub-Himalayan region and East/Northeast India down through the Mesolithic.

    But I can't find even a guess at how many they were. Most of the sub-continent and especially the Indo-Gangetic plain is so densely settled, patchily researched, and subject to erosion and sedimentation that it's really hard to even get an idea of how much we know we don't know. There are a whole ton of distinct Indian mtDNA lineages, which has generally been taken to signify long-term high population size.
  6. Razib: (some researchers believe nearly all of the hunter-gatherer ancestry in Northern Europe is actually from the Indo-Europeans and EEF, with no true relic populations by 5,000 BC)

    Probably nearly all, though I expect there should be *some* local continuity with HGs, as there’s a finding from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720318/ – “Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome” that Median haplotype donation is highest from Loschbour to Scotland, Welsh, Ireland, English, Norwegian, French in descending order (Table S14.2 – http://www.pnas.org/content/suppl/2015/12/23/1518445113.DCSupplemental/pnas.1518445113.sapp.pdf).

    This is kind of interesting because these aren’t the populations that share the most ancestry with Loschbour when considering on unlinked sites, like in Identity-By-State (where instead the highest sharers tend to be Baltics and Northeast Europe, who here have relatively lower haplotype donation from Loschbour compared to the Northwest Europeans, at around the same level as the Spanish and North Italians). Haplotype donation would be more of a direct link, where measures like the IBS would indicate more that some similar population with different haplotypes would be a donor.

    Actually the haplotype donation from Loschbour to modern populations is the highest to modern populations out of all the other ancient samples they checked (from Neolithic and Bronze Age Irish and Central European groups), including a sample that shows very strong links to Celtic Britain. However, this is usually the case when donation goes from a very small group with restricted population size to a much larger group, so does not indicate a large overall contribution.

    (I think Razib’s referred to this before on this blog in the past, so this is more in case anyone was interested).

    • Replies: @Shaikorth
    Short IBD segments and Chromopainter chunks aren't quite the same thing, but this IBD map (by Srkz, you've probably seen these before) shows the peak of Loschbour and Bichon IBD in Northeast Europe, a pattern similar to that with unlinked loci. Is the difference using Chromopainter due to the method or the samples/SNP dataset?

    http://oi68.tinypic.com/mhav7r.jpg
  7. @Matt_
    Razib: (some researchers believe nearly all of the hunter-gatherer ancestry in Northern Europe is actually from the Indo-Europeans and EEF, with no true relic populations by 5,000 BC)

    Probably nearly all, though I expect there should be *some* local continuity with HGs, as there's a finding from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720318/ - "Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome" that Median haplotype donation is highest from Loschbour to Scotland, Welsh, Ireland, English, Norwegian, French in descending order (Table S14.2 - http://www.pnas.org/content/suppl/2015/12/23/1518445113.DCSupplemental/pnas.1518445113.sapp.pdf).

    This is kind of interesting because these aren't the populations that share the most ancestry with Loschbour when considering on unlinked sites, like in Identity-By-State (where instead the highest sharers tend to be Baltics and Northeast Europe, who here have relatively lower haplotype donation from Loschbour compared to the Northwest Europeans, at around the same level as the Spanish and North Italians). Haplotype donation would be more of a direct link, where measures like the IBS would indicate more that some similar population with different haplotypes would be a donor.

    Actually the haplotype donation from Loschbour to modern populations is the highest to modern populations out of all the other ancient samples they checked (from Neolithic and Bronze Age Irish and Central European groups), including a sample that shows very strong links to Celtic Britain. However, this is usually the case when donation goes from a very small group with restricted population size to a much larger group, so does not indicate a large overall contribution.

    (I think Razib's referred to this before on this blog in the past, so this is more in case anyone was interested).

    Short IBD segments and Chromopainter chunks aren’t quite the same thing, but this IBD map (by Srkz, you’ve probably seen these before) shows the peak of Loschbour and Bichon IBD in Northeast Europe, a pattern similar to that with unlinked loci. Is the difference using Chromopainter due to the method or the samples/SNP dataset?

  8. Another reference to Rakhigarhi ancient DNA studies in the news –
    http://www.tribuneindia.com/news/haryana/democracy-has-roots-in-harappa/233774.html

    ‘“We are close to a breakthrough to reconstruct the lives of people of the Harappan civilisation. The excavation has failed to answer several questions related to these people. DNA samples are being analysed by South Korea’s Seoul National University College of Medicine, and Centre for Cellular and Molecular Biology, Hyderabad. The similar investigation will be carried out at Howard University, Cambridge University andthe Copenhagen University in Denmark,” Shinde said, adding the results would be published in ‘Nature’ or ‘Science’ magazine.’

  9. , possibly due to Cassidy et all using a full coverage loschbour genome and comparing to higher coverage samples used for hellenthal et al 2014? The more full the coverage the more power to detect it is actually IBD? Idk what skrz is using. Posting from my phone so can’t check, but that’s what I’d look to as an explanation. Other possibility is the shorter the class of IBD segment gets the more it should converge with results for unlinked loci.

  10. The chromopainter analysis used higher coverage ancients merged with genotype data from Illumina 660W array of Hellenthal 2014, so no high coverage sequences for moderns.

    Srkz uses a merger of the usual datasets like Human Origins, 1000genomes, EBC data AFAIK.

    • Replies: @Matt_
    Might be worth running those differences against Srkz himself and see what his take on it is? If you're in a forum where you chat with him. I'd be interested to hear what you find if you get a chance to run it past him.
  11. Has there been any genetic research on the negroid-like peoples of Southern Asia, eg the Andamanese? This posits extensive connections between Africa and Southern India/Oceana http://www.raceandhistory.com/historicalviews/Sudroid.htm

  12. @Shaikorth
    The chromopainter analysis used higher coverage ancients merged with genotype data from Illumina 660W array of Hellenthal 2014, so no high coverage sequences for moderns.

    Srkz uses a merger of the usual datasets like Human Origins, 1000genomes, EBC data AFAIK.

    Might be worth running those differences against Srkz himself and see what his take on it is? If you’re in a forum where you chat with him. I’d be interested to hear what you find if you get a chance to run it past him.

  13. Sean says:
    @Rick
    "I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene."

    You don't even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.

    Most of the possibly Pleistocene ancestry is probably there in some kind of roundabout way... they entered early into the EEF or Yamnaya-like groups at the edges of Europe, and then rode their way (back) into Central Europe on the coat tails.

    Y chromosome haplogroups like R1a may be a little deceptive, because they would have been affected by hierarchy, patriarchy, especially in combination with primogeniture, which I believe the Indo Europeans set much store by. A major Highland clan founder had Y chromosome success, see Somerled. Another aspect is that younger sons sharing the Y, but lacking position, may have been driven to strike out on their own. I suppose some other markers could have been selected through similar cultural change.

    • Replies: @Rick
    Thanks for the info Sean, I totally agree. I have no idea how that relates to my own statement, but it sounds like we are all good on R1a possibilities.
  14. @Sean
    Y chromosome haplogroups like R1a may be a little deceptive, because they would have been affected by hierarchy, patriarchy, especially in combination with primogeniture, which I believe the Indo Europeans set much store by. A major Highland clan founder had Y chromosome success, see Somerled. Another aspect is that younger sons sharing the Y, but lacking position, may have been driven to strike out on their own. I suppose some other markers could have been selected through similar cultural change.

    Thanks for the info Sean, I totally agree. I have no idea how that relates to my own statement, but it sounds like we are all good on R1a possibilities.

    • Replies: @Sean

    You don't even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.
     
    Sounded think Euro hunter gatherers are comparable to the Neanderthals in their lack of influence on modern European DNA. That maybe was true of men, but females?

    [are you purpose writing like a neanderthal? ;-) ]

  15. Sean says:
    @Rick
    Thanks for the info Sean, I totally agree. I have no idea how that relates to my own statement, but it sounds like we are all good on R1a possibilities.

    You don’t even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.

    Sounded think Euro hunter gatherers are comparable to the Neanderthals in their lack of influence on modern European DNA. That maybe was true of men, but females?

    [are you purpose writing like a neanderthal? 😉 ]

    • Replies: @Shaikorth
    Unlike Neanderthals, all but the very earliest AMH hunter-gatherers in Europe were still closer to modern Europeans than any other present population so even if moderns do not have direct ancestry from them they have ancestry from similar groups elsewhere.

    IBS (genomewide similarity) heatmaps show that they just became more distinctly modern European-like as time went on.

    GoyetQ116, Aurignacian: http://oi66.tinypic.com/2d6uth.jpg

    Vestonice16, Gravettian: http://oi64.tinypic.com/2hwp9y1.jpg
  16. Apropos of nothing at all but…I am continually amazed at how few people know the linguistic connection between the West and the Asian sub-continent.

  17. @Sean

    You don't even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.
     
    Sounded think Euro hunter gatherers are comparable to the Neanderthals in their lack of influence on modern European DNA. That maybe was true of men, but females?

    [are you purpose writing like a neanderthal? ;-) ]

    Unlike Neanderthals, all but the very earliest AMH hunter-gatherers in Europe were still closer to modern Europeans than any other present population so even if moderns do not have direct ancestry from them they have ancestry from similar groups elsewhere.

    IBS (genomewide similarity) heatmaps show that they just became more distinctly modern European-like as time went on.

    GoyetQ116, Aurignacian:

    Vestonice16, Gravettian:

    • Replies: @Sean

    Sailboats with masts needing stability achieve this with rigid spreaders of the guy wires or rigging. Vasily Alexeyev achieved the spreading of the muscles to enhance stability with girth. In contrast to the manoeuver of abdominal hollowing (not recommended), try performing the abdominal brace
     
    Neanderthals' physique, especially their flaring lower ribcage, seem to be made primarily for core stability to aid in using a stabbing spear. No one looks like that now.

    so even if moderns do not have direct ancestry from them
     
    That there is no direct ancestry would require Euro HG ancestry becoming extinct in its original territory and some aspects of it flourishing prodigiously millennia later in the Yamnaya but, ONLY AFTER THEY GOT to Europe
  18. @Vijay
    "I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. "

    I do not know the need to be so circumspect, screw OIT.
    Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene? There is very limited evidence of human population in the subcontinent before 10,000 BC. All the crops, all the human features (Dravidans) indicate a long transition from out of africa to "Into India", but no evidence before 10 K ybp. So, there is no need to be coy to argue for everyone being intrusive into India.

    Separately, a question. All of south India shows significant contributions by ashmound building herders, with crops from Africa. Can you conjecture at what point they entered India. I am guessing not more than a thousand years before the first arrival of R1A. Is there a possibility these were the first of multiple "ASI" in Deccan?

    “Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene?”

    Was there anything that made India relatively unattractive to pre-agriculture hunter-gatherers? We’re used to thinking of India as supporting a large population with its ample rains.

    Or is it simply that hunter-gatherers who didn’t invent agriculture tend to make up a small fraction of today’s population’s ancestors? Did people invent agriculture independently in India or did only come in from the outside?

    • Replies: @Davidski

    Did people invent agriculture independently in India or did only come in from the outside?
     
    Both, but mainly from the outside, including from West and East Asia. Here's the latest on the topic. Open access...

    Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age

    http://hol.sagepub.com/content/early/2016/06/01/0959683616650268.abstract
    , @Wizard of Oz
    A related question prompted by the possibility that the Indian population was small before the Holocene is why those who became Australian Aborigines kept on moving - and what routes they took. For much of the time between the arrival of the first humans in Australia some 50 to 60,ooo years ago and the Holocene there would have been much more land extending from the coasts of what is now south and south east Asia. That, on the face of it, doesn't seem to require the future Aborignes to move on and finally cross 90 km or so of sea between East Timor and NW Australia. But perhaps life was so easy (as it is today for Sri Lankans living as fishermen and eating lots of fruit) that populations grew and moving on along the coast just seemed easy and natural. The interior of south India may have suffered too much from dangerous jungles and their wild animals and snakes, disease, and occasional devastating droughts as well as typhoons and thus inhibited population growth until the farmers started cutting down lots of trees. But my speculations don't give me much explanation for the different patterns of settlement and migration of the short curly crinkly haired Andaman Islanders and other pygmy like people, some of whom reached Australia and were photographed looking just like the pygmies they were in NE Australia in the 1940s.
  19. @Steve Sailer
    "Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene?"

    Was there anything that made India relatively unattractive to pre-agriculture hunter-gatherers? We're used to thinking of India as supporting a large population with its ample rains.

    Or is it simply that hunter-gatherers who didn't invent agriculture tend to make up a small fraction of today's population's ancestors? Did people invent agriculture independently in India or did only come in from the outside?

    Did people invent agriculture independently in India or did only come in from the outside?

    Both, but mainly from the outside, including from West and East Asia. Here’s the latest on the topic. Open access…

    Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age

    http://hol.sagepub.com/content/early/2016/06/01/0959683616650268.abstract

  20. I saw this paper earlier this week. To me the most fascinating portion was the conclusion that African Americans with higher levels of white admixture preferentially migrated to the north. There are obviously a few possible explanations for this. The paper prefers the explanation that lighter-skinned blacks had higher economic standing in the South, and were thus more capable of affording the move. I’m sure others would prefer the HBD explanation. But it makes me wonder how other voluntary migrations resulted in distribution of ancestry (or even traits) which were not identical to their originating area.

    • Replies: @Karl Zimmerman
    Ahh shit. I meant to put this in the open thread. Feel free to delete.
  21. @Vijay
    This is a million dollar question that is subject to controversy and has no precise answer.

    1. Note the later period of start of each of the "lithic" periods in India.

    2. I assume that you are talking about the period between 77 KYA and 10Kya.

    3. Conflicting models by Petragila group and Mellars et al on the actual date of "modern" human entrance OOA into India.

    3. Based on the toolset and hominid population in Indian continent in this period, a proposal is made by Mishra: highly competitive archaic hominids continued to exist in India preventing human dispersal into India until 57 K (MIS 3) before present. They write

    "We suggest that the Indian Subcontinent during MIS 5 times was occupied by a population derived from Homo erectus adapted to the Indian environment from Lower Pleistocene times onwards. This population would be archaic, and the Narmada hominin would be ancestral or a representative of it. Competition between Indian archaics and modern humans would have been intense since they were adapted to similar environments. Failure of modern humans to disperse into the Indian Subcontinent during MIS 5 was probably due to their failure to successfully compete with the Indian archaics during a period when the climatic conditions were favourable to both. However during the MIS 4 times, when the desert zones of Africa and Arabia were abandoned and more favourable zones in the Middle East such the Levant and Iran were occupied by Neanderthals, modern humans had more success in entering India and a major change in the Indian Palaeolithic record then occurred. The expansion of modern humans into India therefore coincides with the expansion of Neanderthals into the Middle East at the expense of modern humans and into Central Asia possibly at the expense of Denisovans."

    Because of the large presence of technologically competent hominids in India, I conjecture that "the later day" modern human population was small, scattered until MIS 3 or MIS 2, and difficult to count. However this does not consider people settling in the periphery in Andamans, Himalayas, and the coast, and their population is unknown in the 57 KYA through 29 KYA period.

    Thanks!

    I was thinking of the time from the beginning of the Upper Palaeolithic – probably around 50 000 years ago – to the mid-Holocene, not so much the Middle Palaeolithic. AFAIK there were people using a microlithic technology in Peninsular India and Sri Lanka and others making a Hoabinhian-like macrolithic technology in the sub-Himalayan region and East/Northeast India down through the Mesolithic.

    But I can’t find even a guess at how many they were. Most of the sub-continent and especially the Indo-Gangetic plain is so densely settled, patchily researched, and subject to erosion and sedimentation that it’s really hard to even get an idea of how much we know we don’t know. There are a whole ton of distinct Indian mtDNA lineages, which has generally been taken to signify long-term high population size.

  22. @Karl Zimmerman
    I saw this paper earlier this week. To me the most fascinating portion was the conclusion that African Americans with higher levels of white admixture preferentially migrated to the north. There are obviously a few possible explanations for this. The paper prefers the explanation that lighter-skinned blacks had higher economic standing in the South, and were thus more capable of affording the move. I'm sure others would prefer the HBD explanation. But it makes me wonder how other voluntary migrations resulted in distribution of ancestry (or even traits) which were not identical to their originating area.

    Ahh shit. I meant to put this in the open thread. Feel free to delete.

  23. @Rick
    "I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene."

    You don't even have to do detailed math on this one. All of the genetic markers (SNPs and haplogroups) show that much much more than a simple majority of modern European ancestry is intrusive since the Pleistocene.

    Most of the possibly Pleistocene ancestry is probably there in some kind of roundabout way... they entered early into the EEF or Yamnaya-like groups at the edges of Europe, and then rode their way (back) into Central Europe on the coat tails.

    Most of the possibly Pleistocene ancestry is probably there in some kind of roundabout way

    “Most” seems likely although it seems some of R.E Howard’s “dark, savage Picts” might have slipped in along the Atlantic coast somewhere.

    Probably not relevant to anything important except maybe minor phenotype differences.

  24. Maybe I missed some big new developments here? Last I heard modern Europeans were supposed to be descended mainly from a mix of Middle Neolithic farmers and East European pastoralists, and Eastern Europe is still Europe.

    The Middle Neolithic guys were supposed to have picked up a good deal of additional western hunter-gatherer ancestry over what their predecessors had, which would then make a modest but significant contribution to modern (West and Central) Europeans. This would make sense in the framework of static and moving frontiers – once the initial surge of colonization had taken up the suitable farmland, there would be mixture with the remaining foragers across ecological boundaries, with new mixed populations taking part in later expansions. A likely candidate for north-central Europe would be the sedentary foragers of the rich South Baltic coast (Ertebølle etc) mixing with Early Neolithic people to form the Funnelbeaker culture.

    The Eastern European side is supposed to be about half eastern hunter-gatherer, which probably has some contribution from Central Asia/Siberia, but I know of no compelling reason to suppose they aren’t mainly native to the region. So that is a large chunk of European ancestry again, even if from a different part of Europe.

    As for Y chromosomes, the major R1a and R1b lineages could perfectly well have been in Eastern Europe since the Pleistocene, and I don’t see why most of the surviving I lineages shouldn’t ultimately derive from native foragers as well.

    • Replies: @Razib Khan
    The Middle Neolithic guys were supposed to have picked up a good deal of additional western hunter-gatherer ancestry over what their predecessors had, which would then make a modest but significant contribution to modern (West and Central) Europeans.

    what % are u estimating. if you're going to dispute, actually state the numbers. (i know it's complicated because EEF might be part WHG, but admixturegraph estimates partition that out)

    The Eastern European side is supposed to be about half eastern hunter-gatherer, which probably has some contribution from Central Asia/Siberia, but I know of no compelling reason to suppose they aren’t mainly native to the region. So that is a large chunk of European ancestry again, even if from a different part of Europe.

    it's not some. EHG is 50% ANE. the consensus seems to be that ANE is east of the urals, as the pleistocene samples which are ~100% ANE are from that region.

    i put this in the note, but you just ignored it:

    yamnaya = 50% CHGish/(25% ANE 25% WHG)

    so mostly non-european. northern euroopeans are steppe + minority EEF + some WHG. that is pretty clearly mostly non-european (steppe is mostly non-european, EEF is mostly non-european*. southern europeans are mostly EEF.

    the key is how much of the "WHG bounce back" is from reservoir populations. that is the wild card.

    * EEF is assumed to be admixed btwn basal eurasian and WHG. but the latest work strongly implies that basal eurasian was intrusive to a WHG-like population in west asia. so the admixture probably predated in southern europe in large part.

  25. @Megalophias
    Maybe I missed some big new developments here? Last I heard modern Europeans were supposed to be descended mainly from a mix of Middle Neolithic farmers and East European pastoralists, and Eastern Europe is still Europe.

    The Middle Neolithic guys were supposed to have picked up a good deal of additional western hunter-gatherer ancestry over what their predecessors had, which would then make a modest but significant contribution to modern (West and Central) Europeans. This would make sense in the framework of static and moving frontiers - once the initial surge of colonization had taken up the suitable farmland, there would be mixture with the remaining foragers across ecological boundaries, with new mixed populations taking part in later expansions. A likely candidate for north-central Europe would be the sedentary foragers of the rich South Baltic coast (Ertebølle etc) mixing with Early Neolithic people to form the Funnelbeaker culture.

    The Eastern European side is supposed to be about half eastern hunter-gatherer, which probably has some contribution from Central Asia/Siberia, but I know of no compelling reason to suppose they aren't mainly native to the region. So that is a large chunk of European ancestry again, even if from a different part of Europe.

    As for Y chromosomes, the major R1a and R1b lineages could perfectly well have been in Eastern Europe since the Pleistocene, and I don't see why most of the surviving I lineages shouldn't ultimately derive from native foragers as well.

    The Middle Neolithic guys were supposed to have picked up a good deal of additional western hunter-gatherer ancestry over what their predecessors had, which would then make a modest but significant contribution to modern (West and Central) Europeans.

    what % are u estimating. if you’re going to dispute, actually state the numbers. (i know it’s complicated because EEF might be part WHG, but admixturegraph estimates partition that out)

    The Eastern European side is supposed to be about half eastern hunter-gatherer, which probably has some contribution from Central Asia/Siberia, but I know of no compelling reason to suppose they aren’t mainly native to the region. So that is a large chunk of European ancestry again, even if from a different part of Europe.

    it’s not some. EHG is 50% ANE. the consensus seems to be that ANE is east of the urals, as the pleistocene samples which are ~100% ANE are from that region.

    i put this in the note, but you just ignored it:

    yamnaya = 50% CHGish/(25% ANE 25% WHG)

    so mostly non-european. northern euroopeans are steppe + minority EEF + some WHG. that is pretty clearly mostly non-european (steppe is mostly non-european, EEF is mostly non-european*. southern europeans are mostly EEF.

    the key is how much of the “WHG bounce back” is from reservoir populations. that is the wild card.

    * EEF is assumed to be admixed btwn basal eurasian and WHG. but the latest work strongly implies that basal eurasian was intrusive to a WHG-like population in west asia. so the admixture probably predated in southern europe in large part.

    • Replies: @Megalophias
    I guess it wasn't clear, I was responding to the "comparable to Neanderthals" and "all in a roundabout way" comments, not to your estimate that most modern European ancestry came into Europe during the Holocene. That I expect is true.

    Haak et al estimated 38-40% ANE to 60-62% WHG for EHG, and couldn't distinguish whether it was EHG, ANE, or WHG which was admixed, if not something more complicated. If someone has resolved the question, I haven't heard. We don't yet have East European samples after Kostenki14 and before the Mesolithic which would tell us how far west ANE was before the end of the Pleistocene, and what exactly its relationship is to EHG.

    The best fitting admixture proportions for three Middle Neolithic populations were 82.5%, 78.8%, or 66.2% Early Neolithic to 17.5%, 21.2%, or 33.8% Loschbour. Mathieson et al modelled Chalcolithic Iberians as 77% Anatolia Neolithic and 23% WHG, which did not differ significantly from Middle Neolithic Iberians but was more than Early Neolithic. Ballynahatty was calculated at 42±2% WHG. Assuming Yamna is 50% EHG then it would be 30% WHG. Any mix of Yamna and Middle Neolithic will be on the order of 20-30% WHG using these estimates. The Irish Bronze Age people who succeeded Ballynahatty were estimated to have 67-86% Middle Neolithic ancestry giving 26±12% WHG exclusive of the Yamnaya component.

    Where else would the WHG resurgence come from?
  26. @Razib Khan
    The Middle Neolithic guys were supposed to have picked up a good deal of additional western hunter-gatherer ancestry over what their predecessors had, which would then make a modest but significant contribution to modern (West and Central) Europeans.

    what % are u estimating. if you're going to dispute, actually state the numbers. (i know it's complicated because EEF might be part WHG, but admixturegraph estimates partition that out)

    The Eastern European side is supposed to be about half eastern hunter-gatherer, which probably has some contribution from Central Asia/Siberia, but I know of no compelling reason to suppose they aren’t mainly native to the region. So that is a large chunk of European ancestry again, even if from a different part of Europe.

    it's not some. EHG is 50% ANE. the consensus seems to be that ANE is east of the urals, as the pleistocene samples which are ~100% ANE are from that region.

    i put this in the note, but you just ignored it:

    yamnaya = 50% CHGish/(25% ANE 25% WHG)

    so mostly non-european. northern euroopeans are steppe + minority EEF + some WHG. that is pretty clearly mostly non-european (steppe is mostly non-european, EEF is mostly non-european*. southern europeans are mostly EEF.

    the key is how much of the "WHG bounce back" is from reservoir populations. that is the wild card.

    * EEF is assumed to be admixed btwn basal eurasian and WHG. but the latest work strongly implies that basal eurasian was intrusive to a WHG-like population in west asia. so the admixture probably predated in southern europe in large part.

    I guess it wasn’t clear, I was responding to the “comparable to Neanderthals” and “all in a roundabout way” comments, not to your estimate that most modern European ancestry came into Europe during the Holocene. That I expect is true.

    Haak et al estimated 38-40% ANE to 60-62% WHG for EHG, and couldn’t distinguish whether it was EHG, ANE, or WHG which was admixed, if not something more complicated. If someone has resolved the question, I haven’t heard. We don’t yet have East European samples after Kostenki14 and before the Mesolithic which would tell us how far west ANE was before the end of the Pleistocene, and what exactly its relationship is to EHG.

    The best fitting admixture proportions for three Middle Neolithic populations were 82.5%, 78.8%, or 66.2% Early Neolithic to 17.5%, 21.2%, or 33.8% Loschbour. Mathieson et al modelled Chalcolithic Iberians as 77% Anatolia Neolithic and 23% WHG, which did not differ significantly from Middle Neolithic Iberians but was more than Early Neolithic. Ballynahatty was calculated at 42±2% WHG. Assuming Yamna is 50% EHG then it would be 30% WHG. Any mix of Yamna and Middle Neolithic will be on the order of 20-30% WHG using these estimates. The Irish Bronze Age people who succeeded Ballynahatty were estimated to have 67-86% Middle Neolithic ancestry giving 26±12% WHG exclusive of the Yamnaya component.

    Where else would the WHG resurgence come from?

  27. @Shaikorth
    Unlike Neanderthals, all but the very earliest AMH hunter-gatherers in Europe were still closer to modern Europeans than any other present population so even if moderns do not have direct ancestry from them they have ancestry from similar groups elsewhere.

    IBS (genomewide similarity) heatmaps show that they just became more distinctly modern European-like as time went on.

    GoyetQ116, Aurignacian: http://oi66.tinypic.com/2d6uth.jpg

    Vestonice16, Gravettian: http://oi64.tinypic.com/2hwp9y1.jpg

    Sailboats with masts needing stability achieve this with rigid spreaders of the guy wires or rigging. Vasily Alexeyev achieved the spreading of the muscles to enhance stability with girth. In contrast to the manoeuver of abdominal hollowing (not recommended), try performing the abdominal brace

    Neanderthals’ physique, especially their flaring lower ribcage, seem to be made primarily for core stability to aid in using a stabbing spear. No one looks like that now.

    so even if moderns do not have direct ancestry from them

    That there is no direct ancestry would require Euro HG ancestry becoming extinct in its original territory and some aspects of it flourishing prodigiously millennia later in the Yamnaya but, ONLY AFTER THEY GOT to Europe

  28. @Steve Sailer
    "Was there ever a large human population in Indian subcontinent after the Toba catstrope and before the holocene?"

    Was there anything that made India relatively unattractive to pre-agriculture hunter-gatherers? We're used to thinking of India as supporting a large population with its ample rains.

    Or is it simply that hunter-gatherers who didn't invent agriculture tend to make up a small fraction of today's population's ancestors? Did people invent agriculture independently in India or did only come in from the outside?

    A related question prompted by the possibility that the Indian population was small before the Holocene is why those who became Australian Aborigines kept on moving – and what routes they took. For much of the time between the arrival of the first humans in Australia some 50 to 60,ooo years ago and the Holocene there would have been much more land extending from the coasts of what is now south and south east Asia. That, on the face of it, doesn’t seem to require the future Aborignes to move on and finally cross 90 km or so of sea between East Timor and NW Australia. But perhaps life was so easy (as it is today for Sri Lankans living as fishermen and eating lots of fruit) that populations grew and moving on along the coast just seemed easy and natural. The interior of south India may have suffered too much from dangerous jungles and their wild animals and snakes, disease, and occasional devastating droughts as well as typhoons and thus inhibited population growth until the farmers started cutting down lots of trees. But my speculations don’t give me much explanation for the different patterns of settlement and migration of the short curly crinkly haired Andaman Islanders and other pygmy like people, some of whom reached Australia and were photographed looking just like the pygmies they were in NE Australia in the 1940s.

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