October 9, 2015

First African ancient nuclear DNA

Major update (Feb 12 2016): the authors have publicly corrected their conclusions: the alleged Eurasian admixture in Yoruba and Mbuti does not exist. See HERE for further details.


Mota cave
Whatever we may think of the conclusions (see below), this study is a most important breakthrough because it shows that ancient DNA can be obtained from remains preserved in hostile (hot) conditions, removing the technical barriers for research in these areas, which make up most of the inhabited world. The method, which relies in the vault-like conditions of the inner petrous earbone, was demonstrated earlier this year by Pinhasi et al. (open access) and is in itself a technical revolution in ancient DNA research.

M. Gallego Llorente, E.R. Jones et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 2015. Pay per viewLINK [doi:10.1126/science.aad2879]

Supplementary materials are free (as usual) and most information seems to be there anyhow.

Abstract

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.


Massive and late European Neolithic-like migration into Africa, even into the Bushmen, Pygmy and Hadza hunter-gatherers?! Well, that's the thesis and the authors seem to have some reasons to believe it. However I am a bit skeptic to say the least. 

The logic behind Llorente & Jones' conclusions is that, when replacing the "non-admixed African" baseline from the usual reference populations such as the Yoruba (a major SW Nigerian population) and Mbuti (Eastern Pygmies from the Ituri jungle of NE Congo) to this newly sequenced paleo-Ethiopian genome from Mota cave, all Africans appear more similar to West Eurasians, particularly to the reference ancient farmer "Stuttgart" (LBK) or his closest modern relatives: Sardinians. 

However this is untrue for some of the populations from the same region as Mota: most Ethiopian populations actually show a slight but significant decrease in their putative Eurasian ancestry (table S5). This is very intriguing, as is the main thesis of the study, and I have the impression that at least part of that appearance of European-like admixture may be explained by ancient internal African structure rather than true immigration. This possibility is not addressed in the study, so we will have to wait for counter-studies, be them professional or amateur. It would not be the first case where a pioneer study "finds" things that become less clear as new research is done, I am thinking of course on stuff like the problematic "ANE" component of Lazaridis 2014 or the extreme "Indoeuropean admixture" conclusions of Haak & Lazaridis 2015, which are much milder and clinal in other comparable studies.

So let's keep calm and wait for more data or improved analyses.

Fig. S6. The proportion of West Eurasian ancestry in modern eastern African populations. λYoruba,Druze (using Yoruba as the non-admixed reference and Druze as the source), estimated for individuals belonging to a number of Ethiopian populations.



Affinities

Mota seems to be most akin to modern Ari people of SW Ethiopia, who speak an Omotic language. He is also rather similar to the Sandawe of Southern Tanzania, who speak a distinct click language. These similitudes underline the importance that "tribal" nations have, among other reasons, for deciphering the ancient African demographic landscape.  

Fig. S5. PCA showing the relationship between Mota and contemporary Ethiopian populations. Components were loaded on contemporary Ethiopian populations using ~480k SNPs, with Mota projected on these dimensions.


His mtDNA haplogroup is L3x2a (table S3), described by Behar 2008 in Ethiopia and the Arabian peninsula (but most likely original from The Horn) and his Y-DNA one is E1b1 (table S4), a major African haplogroup, most likely original from the same Upper Nile region, with some offshoots in West Eurasia.

He did not carry any known allele for lactase persistance (table S13) but he was homozygous for three alleles that seem to confer altitude adaptation (resistance to hypoxia, table S14). 

He had brown eyes and dark or black hair, skin color determination was inconclusive (the matter is still ill-understood) but he did not carry any European alleles associated with lighter pigmentation, so most likely he was black (or, with more chromatic descriptive precision, brown).


Neanderthal admixture testing

This seems to be the detail that most strongly supports the thesis of the study: Mota is even less akin to Neanderthals than modern Africans. From article S11:
The two African genomes, Yoruba and Mbuti, also have slightly positive D values, indicating that they are slightly more similar to Neanderthal than Mota is. This result is likely driven by the West Eurasian component found in modern Africans.

However when we look at the raw data (table S9), we can see that, while the Yoruba Neanderthal admixture estimate is slightly larger than the error margin, the Mbuti one is markedly smaller, so we can still consider the latter to be effectively zero or at the very least negligible. 

This is potentially contradictory with the alleged 6-7% West Eurasian admixture that the study claims for Mbuti (table S5), which would be almost the same as that of Yorubas (7-8%), so I think that there is something not properly pondered and that, while Yorubas may have some (very minor?) West Eurasian admixture, the case for the Mbuti is very much suspect of false positive caused by confounding factors, such as ill understood ancient African diversity. 

Most strange is the case of Khoisan populations. While two of them (Nama and Khomani) do seem to have clear Eurasian admixture, as they stick up well above the average, several others (Xun, Juhoansi or GuiGhanaKgal) are very low when using Yoruba as reference and the tiny bit can be attributed to the pull effect caused by the mere fact that Yoruba and Khoisan are very different populations, which diverged (at least in the essentials) even before the Out-of-Africa migration took place. I strongly suspect that this confounding factor is also at play when comparing with Mota and even more strongly so, because Mota quite obviously lacks the later intra-African partial homogenization tendency caused by migrations such as the Nilotic or Bantu ones. 

Fig. S7. Maps showing the proportion of West Eurasian ancestry in African populations. The proportion of West Eurasian ancestry calculated using either (A), Druze. λMota,Druze, or (B), LBK, λMota,LBK, as a source, and Mota as the non-admixed African reference in both cases.



Early European farmers or...?

Sure, among the tested populations, Sardinians are the best apparent matches for the source of the alleged Eurasian admixture in Africa (tables S6 and S7). But next in line are Belorussians and Lithuanians, what is a bit perplexing, because in the European analyses these are two completely opposite poles along the PC1. Basques and Russians however are surprisingly bad matches, with French, Italian, Spaniards, etc. being in between. 

Among ancient populations, Stuttgart (LBK) appears as a good match when using a Yoruba reference but not so good when using a Mbuti one. Inversely, Lochsbour (Epi-Magdalenian) looks a very bad match when using Yoruba but a bit better when using Mbuti. As Mbuti seem still to be a more clear outgroup than Yoruba, I think that table S7 holds preference over S6. 

Hence I'd rather discard that the source of the apparent Eurasian admixture is LBK-like. However Sardinians (or a similar ancient population) are a better candidate. But what about Belorussians and Lithuanians, whose scores are also very high? Perplexing.

So basically I have all kind of doubts and I look forward to further research that may clarify them.

55 comments:

  1. Great news that viable ancient DNA has been retrieved from such conditions. In terms of their conclusions: supplementary data from other papers has shown a migration edge from Dinka into Sardinians and Stuttgart and a migration edge from Hadza into Lithuania!

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    1. Hey, Chris. I just re-read your comment and noticed the las part (for some reason it did not call my attention earlier). I know that some studies show a migration edge Dinka → LBK and some other (but not all) EEF-like peoples. But Hadza → Lithuanians is unknown for me, can you give me a reference? Thanks in advance.

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    2. Is from Hellenthal et al, 2014. But is unfortunately a Science article so is only available to subscribers. However the data from that paper is summarised here: admixturemap.paintmychromosomes.com

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    3. Thank you, Chris. I find difficult to use the page (unfamiliar with the method) but I think I could see it. In any case it's good to know the reference.

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  2. Could these results be explained by archaic African gene-flow into the ancestors of Mota?

    The results are very strange IMHO. Not the fact that there is admixture necessarily, but the fact that it is pretty homogenous across the board (from 6% in the Mbuti to 9% among the Luhya) among groups (West Africans, Bantus, South Sudanese, Khoe-San) with disparate population histories. For example, the Xun (who again generally lack Bantu or Cushitic admixture) possess just as much purport Eurasian admixture (7.6%) as the Yoruba (7.0-7.4%) according to these stats. The odd effect it has on Horners is also kind of weird, their % of Eurasian admixture actually decreases with Mota/LBK.

    Honestly, these authors might have captured evidence of "Basal Eurasians" without realizing it. Treemix consistently captures an admixture edge close to the Dinka and Hadza (but not really) to the root of groups like LBK.

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    1. I don't see any reason for archaic flow specifically in that area, probably the cradle of the "sapiens" humankind, and not elsewhere. If anything I'd expect archaic admixture in Western and Southern Africans (has been suggested by some study and in West Africans would fit with some rare way too old Y-DNA lineages to be properly considered "sapiens"). So to your initial question: IMO nope.

      I totally agree that the results are extremely strange and I appreciate in your comment additional valid reasons to the ones I mentioned. I must say that your final suggestion makes at least some sense: "these authors might have captured evidence of "Basal Eurasians" without realizing it". But why would be "Basal Eurasian" more relevant to Lithuanians than to Basques?

      It's very perplexing and intriguing and I think we will be discussing about this for a long time before a good explanation is produced. Probably we need more data, as always. My suspicion, as stated in the main entry is that it has to do with poor addressing of the very large African diversity (and our lack of direct evidence about its ancient structure, continent-wide) and therefore with West Eurasians in general exerting a "pull" over all other African populations.

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    2. Who knows? But in light of Homo Naledi, we shouldn't be surprised if we run across evidence of archaic African gene-flow into ancient or otherwise (that is modern) populations on the continent. Minor archaic African gene-flow into Mota would explain the uniform increase of purport Eurasian ancestry across the entire continent among groups with disparate population histories, including: West Africans and Bantus (whose migration from their core region occurred 3,000 years ago), eastern and western pygmies (who split from an ancestral population ~20,000 years ago), the South Sudanese, and the Khoe and San (who split from an ancestral population ~35,000 years ago). That's six ancestral populations with the exact same proportion of "Eurasian admixture," which they received all within the last ~4,500 years; and we have no archeological or unipaternal evidence to speak of on top of that. Don't you find it odd that Mota appears "proto-Eurasian" in the formal PCAs (he clusters in close proximity to the Ari, Sandawe, and Masai)? Horners are also the only group of Africans that don't experience a significant increase in Eurasian ancestry in the Mota/LBK run. IMHO very minor but non-negilgible archaic African gene-flow into a "proto-Eurasian-/Basal Eurasian"-like African population like Mota (and hence Horners?) would explain a number of things: 1) the uniform increase of Eurasianess across the entire continent among 6 distinct ancestral populations, 2) the absence of that increase among Horners, 3) if we assume that the archaic strain in Mota is older than the Neanderthal split, the apperence of a Neanderthal affinity in groups like the Mbuti and Dinka, 4) theories that revolve around "Basal Eurasian" would also remain feasible. There's clearly something going on with Mota. Side note, the Mbuti are so isolated that they barely have any Bantu or Nilotic ancestry, despite speaking a NS language and being surrounded by such groups, yet Neolithic farmers managed to leave a bigger impact?

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    3. I agree that the results seem fishy, but I don't think archaic gene flow into Mota would explain them.

      The Eurasian ancestry estimate was based on an f4 ratio test: f4(Han, Orcadian; X, Stuttgart) / f4(Han, Orcadian; Mota, Stuttgart). The closer the African population X is related to Stuttgart, the smaller the positive value of the numerator. If the denominator were more positive than expected, that would inflate the result. However, to make the denominator higher Mota would need to share ancestry with Han that he didn't share with Orcadian. So the archaic African ancestry would have to impact China as well as Ethiopia, but not Europe.

      Likewise the Neanderthal ancestry estimates used Denisovan as an outgroup, so the archaic African ancestry would have to be related to Denisovans but not Neanderthals. But a direct test found no evidence of Denisovan affinity in Mota either.

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    4. Thanks for the explanation Capra; I expect a follow up study in the near future, probably by another team, that will shed more light on these results. Do you have any alternate theories?

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    5. To be honest, I have no idea at all.

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    6. @Capra: African archaic humans do not need to be related with Denisova/Heidelbergensis or Neanderthal at: they probably are just early offshoots of the same wider population that eventually evolved into H. sapiens, Homo rhodesiensis in rough terms, and that never migrated out of Africa.

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  3. Belorussian and Lithuanians score high?! It's just a matter of time until someone proposes a Yamnaya migration into Africa :)

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    1. XD

      But they do score very high, right after Sardinians in the Mbuti-controlled table, roughly same result in the Yoruba-controlled one. It's just weird and the explanation will have to be better than that.

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    2. I already did :)

      Miners looking for the gold mines of West Africa via Egypt - Nubia - Sahel

      only 40% serious though

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    3. There's been other studies that show a minor contribution from Africa to the Baltic (Hazda to Lithuanian if I recall). I think it's likely a minor African input into WHG during the Upper Paleolithic. The signal is strongest around the Baltic due to the increased WHG ancestry there.

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    4. By the way, now Eurogenes' latest Treemix is showing a 24% migration edge from Mota (ancient Ethiopian hunter-gatherer) into 'CHG' (Caucasus Hunter-Gatherer).

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    5. That's interesting because in the paper they "find" that CHG are pure "Basal Eurasian" (unlike WHG) and also say something about not having East African admixture. That's very perplexing and something that must be looked upon in depth. Ancient African admixture or maybe a Red Sea/West Asian ancient population may be among the possible answers. But very murky anyhow.

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  4. Concerning Table_S6/S7:

    Is it really that surprising, that the source of West-Eurasian admixture in sub-Saharan pops. highlights Sardinians, the most dominant South_European (Mediterranean) and Lithuanians, the most dominant North_Europeans (Baltic); Simply showing that West-Eurasian admixture in sub-Saharan pops. is pan-European; That LBK plays a role (though less in the more isolated pygmies) does illustrate a Neolithic infusion as also Sikora et al 2014 illustrated by TreeMix analysis (Supp.Info. Figure_S6);

    This study: Supp.Info.p.15
    " LBK (an early Neolithic farmer) and Sardinians are the two most likely sources (showing the most negative admixture f3values) for the Eurasian admixture in the Ari. A number of other analyses have shown Sardinians to be the closest contemporary population to early Neolithic farmers that came into Europe from the Near East (9), as contemporary populations from that region have been affected by large-scale populations movements in the last few millennia (65). Thus, the West Eurasian backflow originated from the direct descendants of the same early farmers who brought agriculture into Europe. Given that we have a putative source for the West Eurasian component, we can re-estimate its extent by using LBK as its source in our estimation of the f4ratio, from which λMota,LBK can be derived without having to worry about West African ancestry in the source (as we had to for the Druze; Fig. S7). "

    However, if i understood this study correctly than 'Mota' himself had NO west-Eurasian ancestry where as the Ari (his closest modern remnants) do; Either he was isolated or the infusion simply occurred later; Something also his appearance reveals, he was most def. dark; heterozygous at rs6119471 and homozygous ancestral at rs1426654 and rs16891982, in that regard dark as the European Hunter-Gatherers; He did not posses these derived mutations that are found in Neolithic farmers of Europe (Otzi/Gokham/Stuttgart);

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    1. "if i understood this study correctly than 'Mota' himself had NO west-Eurasian ancestry where as the Ari (his closest modern remnants) do"

      Yes. But not just the Ari: every single modern African population, even the most isolate hunter-gatherers... And that's the hard to accept part, more so as the frequencies look way too similar to established farmers', so it rather appears as a missing baseline and that Mota's distinctiveness is the one that needs explanation.

      "in that regard dark as the European Hunter-Gatherers"...

      Rather as modern Africans. In any case it's a default assumption, because we can't tell skin color from our present genetic knowledge. Half of the genetic factors are not understood and there's also a 20% of non-genetic factors involved. We can be safer re. eye and hair color, or at least the authors are.

      "He did not posses these derived mutations that are found in Neolithic farmers of Europe (Otzi/Gokham/Stuttgart)"...

      He did not possess the blue eyes of European HGs either. I'm not sure why are you comparing with Europeans anyhow.

      "Simply showing that West-Eurasian admixture in sub-Saharan pops. is pan-European"...

      Or whatever else. I still think it is an artifact caused by ill-understanding ancient African diversity. I just don't make sense of a hyper-soluble drop of European blood reaching equally the Yoruba farmers and the Xun hunter-gatherers. It's nonsense and time will provide a better explanation, I'm sure.

      Remember also that statistical analysis (what is always applied to autosomal genetics, necessarily) is not rocket science: it's statistics after all. Take a deep breath and wait a few months, years maybe, for improved understanding.

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    2. " Yes. But not just the Ari: every single modern African population, even the most isolate hunter-gatherers... And that's the hard to accept part, more so as the frequencies look way too similar to established farmers', so it rather appears as a missing baseline and that Mota's distinctiveness is the one that needs explanation. "

      Exactly, west-Eurasian exists in all sub-Saharan pops. - Figure S7 illustrares that just fine. However the fact that Mota himself had none is interesting given that Mota is only 4500BP;

      "In any case it's a default assumption, because we can't tell skin color from our present genetic knowledge."

      The Genes and Markers for skin-pigmentation and eye-pigmentation and their mutational effects are well known. 8plex has a tested (2013) accuracy rate (skin/eye) of >90%; What can not be accuratly determined is the exect hair-color, while the basic hair shading (light/dark) on the other hand can be accuratly determined.

      I was just comparing an ancient African with ancient Europeans, may they be of the Hunter-Gatherer pop. or the Farmers pop. The appearance is another interesting insight of this study (i think);

      "Or whatever else. I still think it is an artifact caused by ill-understanding ancient African diversity. I just don't make sense of a hyper-soluble drop of European blood reaching equally the Yoruba farmers and the Xun hunter-gatherers. It's nonsense and time will provide a better explanation, I'm sure."

      Firslty it has to be asserted that such a west-Eurasian infusion must have occurred after Mota; And even if it was an entire millenium after Mota (~1500BC) - now, do you have any substantial clue about inner-African migrations within these 3000 years (til 1500AD) ? or even in the following 500 years from sporadic to extensive European colonisation? You dont and i dont;

      It is known that the Farmers of south-Europe and the Farmers of north-Europe were of the same stock (i.e. a physical migration across Europe), based on this fact it is almost certain to assume that thus the Farmers of Anatolia were also of that very same stock; But what is known about the Hunter-Gatherers of Anatolia and how (if at all) different they were to the European counterpart; The Hunter-Gatherers of Anatolia are the key to this, for if Neolithic Anatolia had an identical population as Europe (certain on the Farmers part), a migration from there during the Chalcolithic/early Bronze-age into East Africa (Figure S7) is the most likliest, and than inner-African; My two sesterces.

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    3. PS: The skin-pigmentation in is given as inconclusive (Table S11) because its i based on 8plex; and 8plex (concerning skin-pigmentation) "utilizes only homozygous genotypes" {Hunt et al 2013); And as noted in my first post, Mota is heterozygous at rs6119471;

      The 8plex test is only conclusive with homozygous genotypes and as such extremely reliable with an error-rate of 0-1%; And the majority of the samples had homozygous genotypes (75% n=803 / 62% n=212); And most (if not all?) ancient Europeans tested displayed homozygous genotypes;

      What one can however still conclude based on the results (even based on 8plex criteria) is that Mota did not have Light or Light-Medium skin-pigmentation;

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    4. "such a west-Eurasian infusion must have occurred after Mota"

      Not necessarily if:
      a) Mota had archaic African (Homo rhodesiensis) admixture, as has been suggested by some commenter above, or if...
      b) The admixture is real but much older and Mota was shielded of it thanks to isolation

      Finally it can be a mere artifact, which will be highlighted if independent research on the same issue fails to produce the same results.

      Re. skin pigmentation issues, see: http://forwhattheywereweare.blogspot.com/2013/04/eye-and-skin-pigmentation-genetics-cape.html - More than half of the genetics involved are still undetermined.

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    5. "based on this fact it is almost certain to assume that thus the Farmers of Anatolia were also of that very same stock"...

      Not necessarily. Mainline European Neolithic originates in Greece and not directly nor too obviously in Anatolia. There is probably some connection but I don't expect it to be a mere replica of EEF data but something a bit more complex. Why? Because West Anatolian Neolithic (and not all Anatolian Neolithic cultures, as there are several, with important differences), while interconnected by trans-Aegean relations to Greek Neolithic and maybe partly sharing the same origin further East (not necessarily in South Anatolia, it could be Cyprus or even the Levant, at least in part), they also show neat differences, particularly at the Turkish Thracia's cultural divide: with Balcanic ("Bulgarian") early Neolithic and Marmara Sea coastal (NW Anatolian) one being clearly distinct in culture and not getting mixed at all.

      Re. Europe the process is fairly clear:

      1. First Neolithic in Greece (notably Thessaly but a distinct one also in Crete) with founders partly arriving from West Asia, probably via coastal migration but also mixing with local "UHG" natives, maybe at 25% levels.

      2a. Painted Pottery Neolithic in the Balcans, excepted the Adriatic area.
      2b. Impressed Pottery Neolithic in Epirus and the Adriatic coasts, quickly crossing to South Italy.

      3a. Linear Pottery (LBK, "Danubian") Neolithic in Central Europe (not "Northern Europe"!)
      3b. Cardium Pottery Neolithic in the Western Mediterranean

      Then it gets a bit more complicated:
      → Parts of the Balcans (Thessaly, Macedonia, Serbia) seem invaded by peoples related to Halafian culture, initiating the Dimini-Vinca complex, c. 5000 BCE.
      → Soon after, Danubian-derived branches (Cucuteni, Boian) take over the Eastern Balcans and West Ukraine in complex fusion with previous layers.
      → In SW Europe there is a complex "Epi-Cardial" phase, which may have implied greater admixture with WHGs, as suggested by La Mina and Atapuerca data.
      → In Atlantic Europe there is a complex array of unique cultures that may well be related to even greater WHG admixture: Portuguese Megalithism (1000 years older than any other, epi-Cardial?), Roucadour (epi-Cardial?), La Hoguette in the Rhine-Seine area (epi-Cardial?), Limburg Pottery culture in Belgium and nearby areas (aborigine?), etc.
      → Based on some of these, there is a Megalithic boom since c. 4000 BCE, which is directly related to the first Neolithic in Britain, Ireland, Denmark and South Sweden, and probably other Atlantic areas (Galicia, Low Germany and Netherlands).

      It's off topic but really there's nothing as simple about European Neolithic as you seem to believe, with most (~80%) of the modern West Eurasian variation (~PC1) spread along the axis between EEFs (Stuttgart, Ötzi, etc., modern Sardinians too) and "MN" (or Chalcolithic) Atlantic populations (to which Basques would be closest, although a bit more extreme maybe in their WHG admixture). This axis is also the one that differentiates Europeans from West Asians.

      West Asian Neolithic was probably even more complex and at least two distinct ancient populations can be inferred from modern data: (a) an "Arab-like" one, which would be related to EEFs and (b) a "Caucasian-like" one, which would have left their external legacy mostly in South and Central Asia but also in Eastern Europe (Kurgan peoples). It's parsimonious to infer that the former were centered in the Levant and maybe somewhat homogenized with PPNB, while the latter would rather be centered in the Zagros originally. Less clear is what South Anatolian Neolithic groups (Çatal Höyuk and such) would be like.

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    6. Well now, seems i was correct:
      http://www.biorxiv.org/content/early/2015/10/10/016477.abstract?%3Fcollection=

      " The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers "

      This was clear to me simply based on Archaeology and the most recent genetic results (Haak et al 2015 and all before him >>> Keller et al 2011) and i am certain the Neolithic Levantine Farmers werent that different as well; In Haak et al 2015 [(K=16) Figure 2b)] the Neolithic Farmers were of one common ancestry (admixture) that differed from the pre-existing Hunter-Gatherers and the only diffs. between the Farmers pops. was the extent of inter-mixture with these pre-existing Hunter-Gatherers i.e. the gradient of HG-admixture; And Spain_MN does not differ in that manner from any other Neolithic-Farmer group i.e. other than having more HG-admixture than their predecessors Spain_EN (Cardial), yet almost identical to the contemporary MN Baalberge and Esperstedt farmers;

      Also in that manner, the Sardinians are not of any special Farmers-group, they are simply the population with the highest inheritance of the Neolithic Farmers and it is quite high: "Sardinians are the population that is closest to early European farmers with an estimated ~90% descent from them" {Haak et al supp. p.120}; One can consider the Sardinians as the last remnants of Neolithic-Europeans; Figure2a also illustrates what countless studies before illustrated, isolated Sardinians with Neolithic-Farmers clustering close and with (incl. Spain_MN);

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    7. What it seems is that NW Anatolian early farmers from near the Marmara Sea were similar to mainline European early farmers (from probably Thessaly). The latter still have some extra Paleoeuropean admixture.

      It's plausible that the Paleoeuropean in these West Anatolian farmers came from Thessaly anyhow, as the evidence for Epipaleolithic in all West Anatolia is missing in the archaeological record. Another possiblity is of course that the Epipaleolithic populations in Western Anatolia and the Southern Balcans were roughly the same, implying pre-Neolithic navigation and major exchange but this is undocumented archaeologically, so more likely is that Greek and West Anatolian early farmers had a similar founder population and then exchanged a lot across the Aegean.

      We cannot extrapolate Western Anatolian farmers to other parts of Anatolia, notably the much older Neolithic of Southern Anatolia (Çatal Höyuk, etc.) As of now, it's at least as likely that the early Aegean farmers came from the Levant (via Cyprus), skipping or barely touching South Anatolia. A key hotspot seems to be in the so-called "Lakes Region" of south-central Anatolia, first West of the classical South Anatolian farmer area, where coastal sites are older, supporting the coastal migration hypothesis.

      I would not talk of "Neolithic Farmers" as a single simple population anyhow, not in West Asia for sure and not in Europe either. Even mainline Neolithic peoples of Thessalian roots are much more clinally different than you suggest (notice that PC1, horizontal, is massively compressed, while PC2 is much expanded - else it'd be almost a line and we could not appreciate the Eastern European admixture): the main gradient (by far) of European variability in the West Eurasian plot is the one between Anatolian early farmers and WHGs via Chalcolithic Iberians and Basques. So ancient farmers were very diverse and this diversity is caused primarily by greater or lesser WHG admixture.

      "the Sardinians are not of any special Farmers-group"

      Not sure where I said that (did I?) but anyhow, they are clearly representing best low-to-middle WHG admixture populations, while Basques probably represent best high WHG admixture populations of the Atlantic Neolithic, so far lacking ancient samples (except Gökhem) but almost necessarily real.

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    9. I have yet to see data that suggests an "Atlantic-farmer" type in contrast to any other farmer type; And Gökhem doesnt suggest that either, on the contrary; All that has been published so far suggests a uniform EN Farmer group that with gradual time and geograhic progression intermixed with the pre-esxisting WHGs; MN Farmers differ from EN Farmers in only that regard (gradient of WHD admix.), and it is not very substantial; Yet, whether contemporay farmer groups amongst themselves or in comparison with ancestral farmer groups - every admixture-analyses showed them to share an overwhelming common ancestry; Also illustarted on p.41 of the supp.;

      PS; Not sure if you are referring to the PCA plot (p.10) but the Chalcolithic_Iberians cluster closer to the modern Sardinians (highest EEF) than to modern Basques;

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    10. On the contrary, what I see is that Basque and Burgundian ancient mtDNA samples reinforce the idea of a group of populations in the Atlantic Basin that is more modern-like than known "MN/Chalcolithic" populations (in both mtDNA pool and LCT) and also has more HG admixture than them. Gökhem are related no doubt but they seem a bit less modern and less HG than expected, although their position depends on the analysis and let's not forget there are four samples, not just one.

      References you should read and consider:

      1. Gurgy ("modern" mtDNA pool before its time, just like some ancient Basques, see fig. 4 particularly)
      → http://forwhattheywereweare.blogspot.com/2015/05/neolithic-mtdna-from-seine-basin.html

      2. LCT allele was fixated first in a Basque Chalcolithic subpopulation (AFAWK), notice that Gökhem is also high in this allele, and nobody else was in those dates: → http://forwhattheywereweare.blogspot.com/2012/01/caught-in-act-lactose-intolerant-and.html

      3. Ancient Basque (and others') mtDNA history, notably Paternabidea shows early modernity and the cline between the Ebro and the coast in the early Neolithic shows a diversity that is like ATP vs WHG (in just 100 Km!):
      → http://forwhattheywereweare.blogspot.com/2013/09/basque-and-other-european-origins.html

      4. Alentoft's ADMIXTURE analysis, like many of Davidiski's ones, as well as others, show no signature of steppe admixture in Basques and produces a much more clinal (and logical) such effect: http://forwhattheywereweare.blogspot.com/2015/06/alentoft-2015-more-ancient-dna-from.html

      5. Skoglund & Mälstrom, as well as their colleague Dasakali independently, show Gökhem overlapping with modern Basques: http://forwhattheywereweare.blogspot.com/2014/04/diversity-and-legacy-of-ancient.html

      And finally you have the mysterious "ultra-modern" Portuguese early farmers, discussed also in ref. #3, whose data may be old but has not been directly contested ever. Atlantic Europe is demanding more direct research because all we have strongly suggests that this area was crucial in the formation of modern European populations (via Megalithism and maybe also Bell Beaker).

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    11. "PS; Not sure if you are referring to the PCA plot (p.10) but the Chalcolithic_Iberians cluster closer to the modern Sardinians (highest EEF) than to modern Basques".

      Sure and when you trace a straight line between them (or other "Neolithic" samples, including the new West Anatolian ones) and WHGs... it goes right on a distictive grey cluster that we all are familiar with: Basques. This does not happen in other analyses, sure, but that's yet another reason why we should not just rely only on autosomal DNA: because statistical analysis is not rocket science. Much less we should rely only on this or that study, for the very same reason.

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    12. And, continuing my first reply, another piece of info we cannot ignore re. the origins of LCT and "modern" European genetics: massive consumption of milk in Britain continuous between the Neolithic and the Danelaw:

      http://forwhattheywereweare.blogspot.com/2014/02/neolithic-peoples-from-britain-and.html

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    13. But that is hogwash;
      Not a single Neolithic Brit was ever sequenced in that study to conclude they were Lac.PERSISTANT; Reminds me of a tripe study about TRB-Sweden a few years ago when claimed that this Neolithic framers-culture was Lac.Persistant --- than P. Skoglund sequenced several Neolithic Swedes (Farmers AND Hunter-Gatherers) and none were Lac.Persistant at rs4988235;

      But i remember you once had an article featured about several Lac.Persis. mutations across the globe --- maybe the Neolithic farmers had a separate one as well than most modern Europeans; modern day Sardinians are overwhelmingly ancestral at rs4988235 yet have a massive traditional dairy (sheep/goat) industry; Funny and strange at the same time;

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    14. No aDNA from Neolithic Britain is known. We know however that in Sweden and in the Basque Country it already existed, in this last case it was fixated in a subpopulation and absent in another one.

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    15. It already existed? By whom?

      The derived mutation at rs4988235 did not exist in Gök2 nor in Ajv58 also not in Motala12 and mesolithic StoraFörvar11; It also didnt exist in Ötzi or Stuttgart or any of the LBK/Lengyel farmers of Neolithic Hungary nor in CO1 of the late Baden (farmer) culture; In fact it didnt even exist in the Chalcolithic Atapuerca (ATP2/ATP16/ATP12-1420)!

      Im also not familiar with aDNA from Britain, 'a' in this case meaning Neolithic/Chalcolithic, but exited to hear about it; Neolithic folks and Sardinians are most probably Lac.Persist. but not at rs4988235; Otherwise Sardinians couldnt produce and consume so much dairy products;

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    16. 50% of Gokhem people had the T allele, reported by Malstrom 2007 as such without further detail (taken from here). Also 1/20 alleles in Pitted Ware Gotland were T (lower frequency therefore).

      Among Chalcolithic Basques, I discussed the matter extensively HERE. The data of the "military" (mostly adult men) cemeteries clearly indicates two distinct source populations: (a) the main one (n=19) which is CC and (b) a smaller one (n=5) that is TT, only two individuals were CT. My interpretation is that pop. A is mainline EEF/MN peoples, similar to Atapuerca, La Mina, etc. and surely dominant in the Ebro banks and that pop. B is people from further north (piedmont, coast) who represent a phenotype that was already fixated or in accelerated process of fixation among Atlantic farmers.

      The Gökhem data and the British Neolithic strong preference for milk reinforce the idea that the T allele fixation happened in Atlantic Europe first. After all it is precisely in those areas where it is today most common: Britain, Sweden and the Basque Country (as well as a few others not far away from them).

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    17. As for British aDNA, we known nothing before the Bronze Age (save for a couple of Paleolithic mtDNA sequences). It has been strongly neglected in research, even if it should be a quite informative region.

      For British Neolithic (and later up to the Danelaw) strong preference for dairies and dislike of fish, see HERE.

      As for other possible sources of the T allele: Mathieson 2015 clearly finds nothing, even if he's obsessed with ignoring Atlantic ancient DNA. The first T allele in his cherry-picked sample is a German Bell Beaker and its likely that he/she got it from Western or Southern Europe, after all BB expanded from South to North. Neither LBK nor Kurgan peoples can be the source of the lactose tolerance alelle: they just had none of it.

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    18. Yes, Malmström 2007 is the tripe study i was referring to;
      The 2 Gökhem farmers that supposedly carried the derived T allele have yet to be confirmed; But Gök2 was def. not one of them (Skoglund et al incl. Mlamström 2014);

      The British data only shows that the Farmers consumed dairy products, it doesnt however suggest a derived mutation at rs4988235; Once they actually sequence a farmer the result will most prob. be like all the other results i.e. ancestral at rs4988235; Sardinians (also the 2014 study you once featured) are living proof that Farmers didnt need a mutation at rs4988235 in order to stomach dairy products they must have had a different mutation for it mostly inherited to South Europeans;

      And rs4988235 is not confined to 'Britain, Sweden and the Basque Country' it is also very prominent in Eastern Europe and Altentoft (fig.7) shows that Steppe cultures brought this mutation to Europe;

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    19. You are not well informed, I fear, Roma, please look at the second map in this entry. Actual lactose tolerance is more common (first map) but what matters here is the European LCT allele (second map, at least regarding Europe) and there it is obvious that the allele is only dominant in Britain, Ireland, West France, Basque Country and some Nordic districts. Eastern Europe is very low on the allele, under 60%, under 50% in many cases, Finland excepted. Hungary is another exception but there's no trace of the allele before the Middle Ages if I recall correctly.

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    20. "they must have had a different mutation for it mostly inherited to South Europeans"...

      That's possible indeed. Actual lactase persistance is not sufficiently explained by known alleles. Anyhow ancient romans considered raw milk a purge and their consumption of dairies was almost only in form of cheese.

      My point is anyhow about the Europe-specific rs4988235-T which is attested among Chalcolithic Basques and Swedes first of all, roughly in the same areas where it is now >80%.

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    21. "My point is anyhow about the Europe-specific rs4988235-T"

      So was mine, throughout;
      Well i guess "prominent" leaves room for interpretation; But i have looked at two other studies (Witas 2015 / Plantinga 2012) and maybe you are correct; Maybe the derived mutation of rs4988235 did originate on the southern Biscaya during the Neolithic (though Witas also suggests a possible different origin);

      But than how is India (Fig.3 Itan 2010) to be explained, this than again pulls towards Indo-European steppe cultures as a place of common origin; Seems like more testing is needed; And the Plantinga data also suggests (along with modern Hungary) an in situ development for modern high concentration spots of inherited T alleles;

      Yes, the Romans considered drinking raw milk as Barbaric, a view they adopted from the Greeks (already Homer alludes to it in his Odyssey); and also correct, Roman dairy industry was Cheese making from raw milk (Cow/Goat/Sheep) - T. Varro explained it in great details;

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    22. Notice please that I'm not saying it originated in the Basque Country but rather within the wider Atlantic Neolithic (~ Dolmenic Megalithism). Maybe the climatic peculiarities of this area (too wet for optimal cereal agriculture maybe) may have favored a greater reliance on pastoralism and particularly on dairies, favoring the fixation of the allele because of the diet of the poor relied heavily on goat milk. Goats are very cheap and hardy and were the main source of milk in Europe until at least the late Middle Ages, and milk provides proteins and calories (fat), plus calcium for the bones.

      If you look at the Gurgy mtDNA data (or also the very similar Paternabidea one, in the Basque piedmont), it is very apparent that their genetic pool represents the future, unlike everyone else. So it's reasonable to imagine that the Upper Ebro-Seine arch, or more flexibly the whole Atlantic region from Portugal to Sweden, was key in the formation of European peoples. This region is very poorly researched however, so we better wait for more data.

      "But than how is India (Fig.3 Itan 2010) to be explained"...

      Not sure which exactly is the issue but notice that all these LCT alleles seem to converge to a NE African or West Asian origin. Do they have the same exact allele as Europeans or rather the Arab one? I'm unfamiliar. It'd be helpful if you included links.

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    23. Not sure about Gurgy, have to look at that again; The way i remember it however, it was a fusion (transition) of Cardial and LBK farmers;

      Itan et al 2010 - p.6 (Fig.3)
      http://www.biomedcentral.com/content/pdf/1471-2148-10-36.pdf
      Shows the global results for rs4988235 derived T only; India sticks out;
      This mutation has to have originated somewhere, but the data is not conclusive;

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    24. Wow, I'm seeing it now (fig. 3)! Sorry to ask for the link without realizing I already had it and was I the one pointing at it. Somehow I missed the obvious.

      Anyhow, it seems to imply that the "European" allele 13,910-T is also found in two clearly unrelated locations: Sindh and South of Lake Chad. Thank you for calling my attention to this bit, really.

      IMO that does not make it original from Europe but probably different branches diverging from the same origin in either West Asiar or NE Africa. The fact that it is found in Tropical Africa only in relation with Y-DNA R1b, even if it is a distant branch from Western European R1b, strongly suggest that the migration of the allele is related to the migration of Y-DNA R1b from West Asia, although it's not (nor can be) a 1:1 relation (we can and do inherit autosomal DNA from all our other lines).

      What is clear from that data (which I had totally forgotten) is that the allele existed already in Neolithic (or older) peoples expanding from West Asia and that they brought it with them in random fashion, creating founder effects here and there.

      I know that the Arabian allele, and others from Africa are also related, so it was part of an expansion process of some sort, even if not all the resulting peoples surely carried the allele. For example is possible that some but not most Neolithic farmers and herders carried it. For the coalescence and initial fixation of the allele itself you don't need selection, just a fluke, selection may be needed to counter the influence of the C allele upon secondary admixture events and even expand in areas initially dominated by the C allele.

      I'm going to see if I can find the African relatives' data. It was very interesting.

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    25. It's this one: http://forwhattheywereweare.blogspot.com/2014/03/lactase-persistence-genetics-in-africa.html

      It seems I was wrong about the carriers of the 13910-T allele in Central Africa: the Bulala are not Chadic but Nilo-Saharan (Central Sudanic) speakers and hence unrelated to general R1b dispersal most likely. On the other hand I have recently argued for a possible Nubian (Eastern Sudanic, possibly also within Nilo-Saharan) partial origin of Basque language via mainline European Neolithic, so the Neolithic connection still stands as possible in my eyes. This variant is also found among the Fulani.

      The T-13910 allele also has other branches one {West Asian + Mozabites} and the other is strictly African {Baggara + Fulani}. Considering everything in full it's plausible that the allele did not originate in Europe but rather in NE Africa or West Asia.

      There are two related alleles: one in Arabia and NE Africa (and also found around Sindh per Itan) and the other in NE Africa only. The node joining them is not LP+, hence the relationship is necessarily pre-selection.

      This study (Ranciaro 2014) is very important in order to understand the origins of LP+ alleles and begin to understand them in the wider global context with a Red Sea core of some sort.

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    26. Yes, for Africa there can be several scenarios; R1b might not be the necessary correlation as also the data from Sweden and Finland show; In my opinion it is India that is the highlight concerning rs4988235 T, hard to make sense of that in the light of the Plantinga 2012 data;

      Thank you for the links;

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    27. I'd point out that the oldest known example 13910-T allele is from an R1b positive Bell Beaker grave. I don't think it's out of line to posit an early link between R1b and lactase persistence.

      Has anyone tested Tocharian mummies for this allele? They had pretty high frequencies of R1b IIRC.

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    28. Ryan: in spite of Mathieson's cherry-picking of the data, what you say is just not true. There are at least 10 older T-positive individuals that are older than that: 7 in the Basque Country (5 are TT) and 3-5 in Sweden (one CT in Gotland's Pitted Ware late "foragers" and 50% of the alleles in the n=4 sample of Megalithic Gökheim).

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    29. What time frame are the Basque samples? Also, I assume the Pitted Ware ones are Y haplogroup I?

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    30. Longar is 4500 BP (uncalibrated, so maybe 2-3 centuries earlier in "real years") and San Juan Ante Porta Latinam is 5000 BP. So they are both several centuries, even close to a whole millenium older in the case of SJAPL, relative to Central European Bell Beaker, which in no case can be older than 2500 BCE and is more likely to be c. 2300 BCE or more recent (not sure which is the exact date of that particular individual).

      This is consistent with the generally accepted notion of Bell Beaker being a phenomenon that expanded from South to North and largely related, although not strictly, to pre-IE Megalithic networks.

      See:
      → http://forwhattheywereweare.blogspot.com/2012/01/caught-in-act-lactose-intolerant-and.html
      → http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1378091/pdf/10364533.pdf (fig. 1 has the dates)

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    31. Ok, well that still presumably supports a common origin for lactase persistence and the Bell beaker phenomenon in Europe. I think Mathieson's early Corded Ware samples are all lactose intolerant. Then the Bell Beakers arrive in Corded Ware lands (as in this part of Germany IE arrived before the Bell Beakers), and they are lactose tolerant, while their Corded Ware are not. Then the Corded Ware people become lactose tolerant over time.

      So my suspicion is that the late Neolithic resurgence in hunter-gatherer ancestry and the spread of lactase persistence are linked, at both of those are linked to both the Bell Beaker phenomenon and the spread of R1b.

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  6. Maju, a minor point of English usage:

    "Not rocket science" means "not very difficult, relatively simple and easy to understand", rather than not precise or replicable. Better would be "not an exact science".

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    1. Ouch, really? For me it has always meant a hard science, because you need everything to be correct so the rockets hit the target or the satellites stay in orbit. Actually space science (sic) scored as the hardest, more self-critical, academic discipline in a 2010 study, while genetics and biology scored very low. And I guess I've been using the term that way ever since - for 5 years already!

      I guess I'll have to correct but it was a cool expression within my logic. Then again what is it worth if people gets you wrong? So, well, thank you for blowing my bubble, I guess.

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  7. Major update: the conclusions of the study about the alleged Eurasian admixture have been recanted (they still stand for East Africa but not for Yoruba and Mbuti). See: http://forwhattheywereweare.blogspot.com/2016/02/most-africans-do-not-have-significant.html

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    1. ^^ This profile has been spamming anthropology blogs recently with generic comments only to put a link to his site. I'm not going to tolerate that kind of stuff. Everybody can make meaningful contributions and link to whatever RELEVANT source but free publicity cammuflaged as a comment is mere spam.

      Delete

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