First Farmers

There’s a new paper (by Iosif Lazaridis and others) out on the genetics of the world’s first farmers in the Middle East. There are a number of interesting points.

They find that early farming populations are about half descended from the somewhat mysterious “Basal Eurasians”, who apparently split off from other Eurasians before they separated from each other. Those Basal Eurasians appear to have little or no Neanderthal admixture, but they are no closer to sub-Saharan Africans than other Eurasians. Which they means that they probably left sub-Saharan Africa a long time ago – but where then did they go? Somewhere without any Neanderthals? North Africa might work: we have no evidence that there were ever any Neanderthals there. But if the Basal Eurasians didn’t mix with Neanderthals, they likely mixed with someone else. Someone lived in North Africa before modern humans: we might see a trace of that in populations with Basal Eurasian ancestry. With luck and some ancient DNA from North Africa (or possibly South Arabia?), we might find the answer.

Genetic differentiation was much stronger back in those days. Fst between Natufians and the hunter-gatherers in the Zagros mountains ( western Iran) was comparable to that between Germans and Chinese today. You can bet that their languages were highly differentiated as well.

The first farmers seem to be descended from the hunter-gatherers that immediately preceded them. All the groups that picked up farming expanded outward: early Anatolian farmers into Europe (LBk and Cardial cultures), Levantine farmers into Africa (so Hamito-Semitic must have originated in the Middle East). it looks as if ur-Georgians mixed with eastern hunter-gatherers that were closely related to ANE (75%) to form the proto-Indo-Europeans, which means that pre-PIE was spoken by those eastern hunter-gatherers, and the similarities between Kartvelian languages like Georgian and Indo-European may boil down to pillow talk and lullabies.

By the Bronze age Natufians and Zagros mountaineers and Anatolian farmers were mixing a lot – but before agriculture, such mixing must have been very rare for a long time, in order to generate that big Fst. There was probably more trade with the advent of agriculture ( more mixing) , and later, technical developments like ships and wheeled vehicles probably favored mixing. Farmers can have specialists, who may make use of exotic materials ( like tin or lapis lazuli) than are imported over long trade routes. Eventually there were empires, some of which seem to have shuffled ethnic groups around the chess board simply because they could. Probably the horrible Ice Age climate played a role in keeping populations isolated before the Holocene.

But back before the Holocene, it seems that, more often than not hunter-gatherers either didn’t mix or exterminated each other. It looks as if there were two waves of replacement ( with little admixture) in Europe after modern humans replaced Neanderthals and before Anatolian farmers largely replaced the last population of European hunter-gatherers!
We see a couple of cases in which new populations are found almost entirely with males from one population and females from another: early Indo-Europeans and Amerindians.

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52 Responses to First Farmers

  1. dearieme says:

    Surely Chinese archaeologists can be trusted to prove that those SW Asian people were not the first farmers after all.

    • spandrell says:

      Has any ancient DNA been coming out from China? They got plenty of interesting questions of their own to answer. It might turn their nation was also the result of a mix between herders and farmers in 3000 BC.

      • dearieme says:

        The answers, I suspect, would need to be entirely to the satisfaction of the Chinese Communist party.

        It’s one of the great strokes of scholarly luck that the archaeology of Egypt, Mesopotamia and so on was all done by Britons, Germans, and so forth, who were not interested parties in the question of who did what to whom there. You can see that very clearly in the contrast with the sub-genre of Biblical Archaeology, where there’s a sudden drop in intellectual standards because investigation was no long disinterested.

        • spandrell says:

          Not really, the sort of data that would come out of prehistoric DNA is not particularly sensitive in China.
          And at any rate the Communist Party is explicitly anti-nationalist; DNA showing how the Han are a mix of this and that race would, if anything, validate the leadership of the Communist Party as the father of the “Great Family of the Chinese Nation”.

          • dearieme says:

            Ask yourself: what if, contrary to your guess and mine, the Chinese turned out to be descendants of the Japanese? Do you really think the CCP would be indifferent?

            • gcochran9 says:

              Or what if the Shang empire were founded by Indo-European charioteers?

              • Peter Lund says:

                I thought you were joking. Then I googled it.

              • spandrell says:

                Later the mighty Zhou kicked Shang ass and restored the supremacy of good old SIno-Tibetans.
                How much Indo-European Y chromosomes exist today in China? Surely we know that?

              • Bob says:

                The Shang have a somewhat exotic and foreign aspect in traditional Chinese historiography compared to the Zhou. Classical Chinese literature tends to cite the Zhou as being connected and related to subsequent dynasties and Chinese history, and the Shang are culturally distinguished as being more warlike and militaristic and having different religious beliefs. Also the character for Shang is the same for merchant, which may relate to them having been mobile warriors and merchants. So the Chinese literature is not inconsistent with the Shang having been Indo-European or some other foreign group.

                The Shang may have been Indo-European charioteers who were warriors and merchants that would invade and trade with the settled peripheries of the steppe and impose elite dominance where possible. They may not have ended up imposing IE Y chromosomes like they did elsewhere in the settled peripheries of the Eurasian steppe because they were so far east and thus fewer in number or because they were defeated by the Zhou. Or they may have been some other group.

              • rkr says:

                It seems that the chariot became adopted by the Shang only at the very end.
                Let’s not forget that there’s also Seima-Turbinos roaming about in those days and while their ethnic identity is unknown and point of origin(Altai or Volga) controversial there’s at least some connections between them and China(Qijia) which might demonstrate western influence on China.

              • Tom Y says:

                The character Shang “商“ also means merchant in Chinese, and as far as I know the later meaning is derived from the first.

                An even more interesting character is ”敵“ (simpl. Chinese 敌) though, meaning “enemy” , “hostile”, “to be against”, the left half is exactly Shang “商” in older written forms.

                Well, if the Shang is almost literally “the enemy”, whose enemy is that? Zhous?
                Looking at the number of human sacrifices (mostly POWs) at Shang sites, one should not be surprised if they were hated by everyone around them.


            • spandrell says:

              The Japanese didn’t exist until at least 300 AD, so that’s hardly plausible. They’d be rather more angry about being descended from the Koreans, though.
              But as for more DNA from the Northeast; many already know that the Hongshan culture was fairly influential, it would be no surprise if it turned out those had Altaic influences.

              At any rate the real ancestors of the Chinese nation, the Zhou, came from the West, so no chance of that. And those weren’t Indo-Europeans, period.

          • gcochran9 says:

            Which is why there are no nonsense-generating political influences on the study of Tocharian mummies.

            • Bob says:

              Incidentally, it’s not just the Chinese government – the Sinologist who led the study of the Tocharian mummies, Victor Mair, is a liberal who’s obsessed with developing a multicultural historiography against traditional Chinese insularity.

      • says:

        The Chinese Zhou dynasty was formed from the alliance of the Ji (姬) and
        Jiang (姜) people in 1046 BC

        The word Jiang (姜) is one of the eight oldest surname in China. It has
        the word radical of sheep (羊) in it, i.e. they were ancient sheperds.
        The word Jiang (姜) is also used to describe people with red hair.

        The Ji people was originally elites of the Shang people but was exiled
        to the north west to defend the border.

        The above two groups of people had extensive intermarriages with people
        further north, the “Demon Territory” people which include people from
        Atai, Lake baikal, etc.

        The Zhou dynasty lasted more than 700 years and most Chinese surnames
        were derived from these two group of people.

        The Chinese Miao (苗) people

        The word Miao (苗) has the word radical rice field (田) in it.

        “””According to André-Georges Haudricourt and David Strecker’s
        claims based on limited secondary data, the Miao were among the
        first people to settle in present-day China.[4] They claim that
        the Han borrowed a lot of words from the Miao in regard to rice
        farming. This indicated that the Miao were among the first rice
        farmers in China.”””

  2. sprfls says:

    I think the Basals were hiding in Southern Arabia, by the Gulf. Or in the Gulf. 😉 Look at mtDNA R0a.

  3. Greying Wanderer says:

    For anyone who always wondered what happened before history this whole process has been great.

  4. epoch2013 says:

    “It looks as if there were two waves of replacement ( with little admixture) in Europe after modern humans replaced Neanderthals and before Anatolian farmers largely replaced the last population of European hunter-gatherers!”

    GoyetQ166 appeared wiped away by Gravettians but returns with Magdalenians. WHG appeared to have been wiped away by EEF but we see an increase in WHG admixture over time. That had to come from somewhere. Furthermore, an increase of WHG in the late Neolithic is needed to explain Europeans.

    • Matt says:

      The models in the Fu et al paper had around about 16-20% survival of the GoyetQ166 ancestry in WHG from Western Europe – La Brana, Loschbour – though not in Hungary near where it seems likely the WHG expanded from, or the most Paleolithic WHG in Western Europe, Bichon. (Page 54 of their supplement, at

      Since that ancestry is 63-80% in Magdalenians, could imply low end 20% (16/0.8) to 30% Magdalenian type ancestry in Mesolithic Western WHG.

      “Little admixture” after a fashion I guess.

      (These level of admixture may possibly had more to do with one region being more climatically favourable than the other, after the end of the Ice Age. Or possibly “extermination”, I guess, if you really must have this as a strongly held hypothesis for whatever reason).

      Of course, these Western WHG were probably not the WHG who contributed much of the additional 20-25% WHG that the European Middle Neolithic farmers seem to have over the European Early Neolithic farmers.

    • Anon says:

      There are no known paleolithic population replacements in Europe. The only difference between older samples like Kostenki14, Goyet, Vestonice and WHGs like Loshbour, La Brana, KO1, Villabruna is the older ones still had leftover OoA(or out of wherever) archaic human/Eurasian DNA, while by the time of the WHGs, they had genetically drifted away from it. People like Kostenki14, Goyet samples, etc may still have been genetic dead ends, but their y-dna/mtDNA haplogroups are 100% right for being ancestral to WHGs, so at the very least, they were close cousins of the ancestors of WHGs and those ancestors would’ve been autosomally extremely similar to them. It’s amazing to me how the people who release these studies like Lazaridis don’t point this out. If you take out the archaic human DNA from paleolithic Europeans(that archaic human DNA seems to show up mostly as SSA and what peaks in South Indian tribals/Tamils, ASI basically), you get a full WHG.

      The increase in WHG admixture over time after the neolithic farmer migrations came from EHG/Indo-Europeans. If we go by Yamnaya as being the PIEs, even they had heavy outside admixture(CHG) but as time went on each successive IE group got more European. Yamnaya>Corded Ware>Bell Beaker/Unetice, Yamnaya being closest to Tatars while Bell Beakers/Unetice/Sintashta/Srubna were already looking like modern northern Europeans. Genetic drift in that short amount of time is unlikely so maybe western WHGs did have a role to play in further increasing WHG admixture.

  5. rashomon says:

    Interesting theory on timing of agriculture’s beginning. Opinions?

    • Frank says:

      Well… if you want opinions…

      I think it is way to simplistic. Show me actual data that the plants that were later domesticated were actually struggling to survive before this time. It sounds like these theories we get from conspiracy theorists. I could come up with a hundred of these every day (if someone paid me). It’s like writing greeting cards.

  6. Anon says:

    I think the biggest news from this is

    Neolithic Levantines/Natufians had little to no SSA admixture(nor European admixture), despite Natufians being described as a SSA-admixed populace by anthropologists
    Neolithic Iranians were 23% of the stuff that peaks in South Indian tribals(N. Levantines had none)
    ANE admixture was already in mesolithic Iran, which explains the R2 found(Ma’lta boy was R*) in an ancient Iranian and modern Central/South Asians
    The farmers that migrated from Anatolia/the Balkans into the rest of Europe during the neolithic were very different from Natufians/Neolithic Levantines, closest to Sardinians while the former look very much like modern Levantines/Saudis with no SSA or Euro, which means the whole Middle-Eastern migration to Europe is a farce, especially given there’s no evidence of WHG even being native to the south Balkans(early mesolithic Greek mtDNA was similar to Anatolian farmers), it was more like a SE Europe migration into the rest of Europe. These Balkan/Anatolian farmers also had some shared common admixture with WHGs unexplained by WHG admixture(missing other key WHG admixture), meaning Balkan/Anatolian farmers are likely descended from paleolithic Europeans, who also had components that were present in Anatolian farmers.
    We see an increase of Euro/WHG/steppe admixture by the copper age/bronze age Middle-East, including the bronze age Levant, and at ridiculous amounts in copper age Armenians(looks about 5 times more than what modern Armenians have) and odd amounts of light hair/eyes in these areas(although not anywhere near a majority, but much more than these populations have today).

    • Frank says:

      These are definitely some highlights.

      The shared ancestry between the Anatolian Neolithic and the WHG groups seems to indicate another population buffering them from each other. If they were living side by side, you might expect some Basal Eurasian in WHG, and there is none at all. Some genomes from Southeast Europe will be very interesting.

      The abundance of light skin alleles, as far back as the Natufians, and that they were so far separated genetically from the Anatolians, suggests that these alleles were very old.

      • Anon says:

        Actually, interestingly enough, none of the Natufian samples had neither of SLC24A5 or SLC45A2, everyone else did including the neolithic Levant so your point still stands. It goes along with more southern Middle-Eastern pops lacking them today as well.

        • Frank says:

          Sorry, I meant as far back as until the Natufians (but not including them).

          It is still very interesting that we have now hundreds of ancient genomes that have various pigmentation alleles, but the actual selection mechanism is a mystery.

          It almost looks as if, during the Bronze Age, different skin, hair, and eye pigmentation boosted a person’s status, and made it more likely that they would have many more children. Especially in certain cultures in Northern Europe, but also elsewhere.

      • Matt says:

        Adna from pre-Neolithic SE Europe would be a thing to see.

        Estimating Basal Eurasian seems not what is was though – they have a model in Figure 2 of their paper which fits the Scandinavian Hunter Gatherers as on the order of 10% Basal Eurasian. So zero contact South->North along that boundary between Anatolia and the WHG “urheimat”, or very low?

        • Frank says:

          The Scandinavian Hunter Gatherers are very interesting. They were in a very remote place, yet got admixture from East Asians, ANE, Basal Eurasians, EDAR alleles, light pigmentation alleles, etc.

          What’s the deal… with the Scandinavian Hunter Gatherers?

          • Anon says:

            Remember that only a few thousand years before their time, the SHGs wouldn’t have been in Scandinavia because it would’ve been covered in ice sheets, so them being in a remote area yet having outside admixture isn’t really that surprising. I’m not aware of any East Asian admixture in them, only ANE(and plenty of it).

            My guess is SHGs are EHGs(who are just a mix of WHG/ANE as well, but more ANE than SHGs) that went west as the ice melted, picked up more WHG admixture on the way there in Poland/Germany/Denmark(EHGs going through Karelia/Finland into Sweden via the Alands is also another option and meeting an already existing WHG population who got there first or later faced a WHG migration once they got there, but I guess it doesn’t matter how they got there) , although you’d think they’d have more EHG y-DNA/mtDNA, they were all the typical WHG I2/U5. Also a possibility that they’re another totally isolated population descendant from the paleolithic(again, paleolithic Europeans like Kostenki14 and Goyet all had WHG/ANE/Anatolian farmer components, they were like the start of a branch for many populations, but already shifting towards WHG), but that seems much less likely.

            Either way, it explains the DNA of SHGs as well as their light pigmentation(although of course it doesn’t explain why EHGs were light and WHGs weren’t).

            The EDAR alleles definitely come from ANE, even though the actual ANE samples we have themselves didn’t have it. ANE are definitely a distinct, seperate population but they seem to be halfway inbetween Europids and Amerindians, if that makes sense. Amerindians have EDAR, so it’s reasonable to assume.

        • Anon says:

          Two K1c’s rather than the typical U WHG mtDNA in two Thessaly Greeks one thousand years before the Barcin Neolithic Anatolian samples is good enough for me(7500 BC, btw). I think the WHG/ENF territory cut off is around anywhere from Bosnia to Macedonia and the rest of Europe(the rest of southern Europe like Spain/Italy was definitely WHG territory), not the Aegean Sea.

          Me personally, I’m dieing for mesolithic samples from the northern Black Sea area around Ukraine. I’m betting on light skin, as well as less ANE than EHGs(I just can’t believe the light features of EHGs come from their ANE, solely going based on where ANE peaks today, that being the Urals and the Sami) and the source of light hair being there. More EHGs overall would be nice too(there’s like what, 2?) or other pre-Yamnaya Pontic steppe populations. Ancient civilization aDNA would be nice too, not sure how we still don’t have Roman aDNA.

          Also, y-dna indicates WHG/Anatolia contact(some I2, but still a majority of G2a, and I’m unaware of the specific clades so it could be two completely unrelated I2 clades), but not autosomal. The first time we can forsure say a farmer actually had direct admixture with a Loshbour-type WHG rather than having WHG affinity is NE1 in Hungary, and then of course WHG admixture looks a lot more common into LBK in Germany/etc, with Spanish/Swedish farmers were the most admixed.

        • Frank says:

          If you read the supplements, I think that figure 2 is misleading. These are not really hard numbers on the amount of Basal Eurasian or Neanderthal ancestry.

          Each of these is estimated statistically, and without any 100% Basal Eurasian genomes, those statistics are extremely noisy for those estimates.

          The overall trend, though, indicates that ‘Crown Eurasians’ had a certain base level of Neanderthal ancestry, and Basal Eurasians had none.

          Since SHG had one of the highest levels of Neanderthal (without clear recent admixture), then they probably had no Basal Eurasian at all.

  7. Ilya says:

    (Sorry: put the question, erroneously, under previous topic.)

    To make sure I understand the timeline correctly: Basal Eurasians branched out around 60KYA and then diversified, circa 20KYA, into 3 branches: Anatolian, Natufian, and Iranian?

    • gcochran9 says:

      Those three populations have a fair amount of Basal Eurasian ancestry, on the order of half or a bit more in the case of the Iranians, but they’re not entirely or close-to-entirely descended from the Basal Eurasians, so they’re not really the result of a simple split.

      I don’t think we’re sure about the split time between Basal Eurasians and other Eurasians, either: probably early than 60 K, maybe as early as the Eemian.

      • Ilya says:

        Thanks! I’ve also been trying to find records on what the climate of Arabia and North Africa was from 130K to this day. If anyone has sources, I’d welcome a link.

      • Ilya says:

        I surmise, your last “Morocco” post was almost a direct response to my question. Thanks again.

    • Anon says:

      Anatolian farmers descend atleast partially from paleolithic Europeans. All the older paleolithic Europeans had Basal Eurasian ancestry and SNPs that were absent from WHGs but present in Anatolian farmers. I also don’t think the term Basal Eurasian is as meaningful as people think, given there seems to be no obvious link between it and racial/ethnic components, other than it seems have a link with MENA populations but the highest person with Basal Eurasian was still only 65%, Natufians were 45% yet have no admixture from “Crown Eurasian” populations, etc.

      • Frank says:

        How are you measuring to determine that the older paleolithic Europeans had Basal Eurasian ancestry?

        • Anon says:

          All the new paleolithic European samples from the recent study 2 months ago also had this. Actually, the only paleolithic samples without Basal Eurasian are Ust-Ishim and Tianyuan, which are mostly considered proto-Mongoloids but still had a plethora of other common ancestry.

          Why I think specifically Anatolian Farmers are descended from paleolithic Europeans:

          From the Eurogenes K15 calc on GEDMatch:

          Vestonice16(100k+ SNPs) 30k BC

          North_Sea – 18.17%
          Atlantic – 24.01%
          Baltic – 10.05%
          Eastern_Euro – 9.44%
          West_Med – 11.18%
          West_Asian –
          East_Med –
          Red_Sea – 0.37%
          South_Asian – 10.69%
          Southeast_Asian –
          Siberian – 2.19%
          Amerindian – 3.72%
          Oceanian – 4.44%
          Northeast_African – 1.47%
          Sub-Saharan – 4.28%

          (all the paleolithic Eurasians were extremely similar, and the older ones had more exotic ancestry, peaking in Kostenki, which indicates clear genetic drift, the newer ones looked more WHG-like, WHG was all North Sea, Atlantic, Baltic, while Neolithic Levantines had no Atlantic, which is the main WHG-Anatolian affinity, and Natufians had no West Med)

          Anatolian farmer:

          North_Sea –
          Atlantic 16.72
          Baltic –
          Eastern_Euro –
          West_Med 44.34
          West_Asian –
          East_Med 34.14
          Red_Sea 4.80
          South_Asian –
          Southeast_Asian –
          Siberian –
          Amerindian –
          Oceanian –
          Northeast_African –
          Sub-Saharan –

          If you’re familiar with GEDMatch you can see similar results on other calcs too. We’ll need paleolithic Middle-Eastern samples to know forsure where Anatolian farmers come from, but yes, paleolithic Europeans had Basal Eurasian.

          • Frank says:

            Well I think this has been covered extensively in the supplements of a couple of papers. I believe the consensus of the experts is that the pre-Neolithic Europeans did NOT have any Basal Eurasian ancestry.

            In “The genetic history of Ice Age Europe” Fu et al., the supplement 8, titled “No evidence of Basal Eurasian ancestry in pre-Neolithic Europeans” covered it pretty well, and concluded “Here, we present compelling evidence against this hypothesis.”

            Also, in “The genetic structure of the world’s first farmers” Lazaridis et al., the supplement 4, titled “Pervasive Basal Eurasian ancestry in the ancient Near East” also shows convincingly that the previous assumption that Kostenki14 and other early pre-Neolithic samples from Europe do not actually have Basal Eurasian ancestry. They say, “European hunter-gatherers (EHG, WHG, SHG, Kostenki14, Switzerland_HG show no evidence of Basal Eurasian ancestry, but populations of Near Eastern or partial Near Eastern ancestry do.”

            • Matt says:

              The original Lazaridis paper back in 2013 modeled Basal Eurasian ancestry in EEF (European Early Farmers) on the basis of a greater shared drift with ENA in WHG and MA1 than EEF, and exactly the same in WHG and MA1, thought to be unlikely by admixture from East Asians.

              With the publishing of the sample from Ust Ishim and new Upper Paleolithic Europeans, that’s been modified to gene flow from East Asians to WHG and MA1, and EEF, and not to Paleolithic Europeans, and Basal Eurasian gene flow to EEF as well. This is as UP Europeans are as related to Ust Ishim as WHG, MA and East Asians, but EEF is less related to Ust Ishim.

              The other alternative is simply admixture from an Ust Ishim like population into Upper Paleolithic Europeans, WHG, and East Asians, and not to EEF’s ancestors (that they don’t share with WHG), and no actual Basal Eurasian. Time will tell what actually happened! At some point the Basal Eurasians may (or may not) be found…. The sort of extensive tree modeling that served to postulate that Basal Eurasians actually were the most parsimonious solution is elusive in Lazaridis, Reich and Patterson’s new work, which seems instead to tweak the model initially decided as most parsimonious in 2013.

              • Frank says:

                Despite the complications, the existence of genuine Basal Eurasian populations does greatly simplify the explanation of how the various modern and ancient populations with ‘extra’ Neanderthal admixture happen to be exactly the ones that are more closely related to Ust-Ishim.

                Saying that they all had extra admixture very late while in East Asia seems a bit of a stretch.

              • Matt says:

                Although by Fu et al, Upper Paleolithic Europeans, Mesolithic Europeans and East Asians do vary in relatedness to Neanderthal, so to some extent some form of process (whatever it is – population admixture or selection) independent of Basal Eurasian ancestry is already needed to account for this (Basal Eurasian as the only mediator of reduced affinity to Neanderthal != parsimonious)..

  8. Frank says:

    This paper definitely gives good reason to doubt the strength of the conclusions of another recent paper that showed that Neanderthal ancestry was being lost due to selection.

    If the Basal Eurasian component has low to no Neanderthal, and this component has been entering Europe increasingly through time, then Neanderthal ancestry was being lost largely due to admixture with populations higher in Basal Eurasian.

    This could be selection for functional genes from early farmers, not selection against deleterious Neanderthal genes.

    Until we get a lot more ancient genomes, from various time points, from Eastern populations lacking Basal Eurasian, we should definitely be skeptical of those conclusions.

  9. spandrell says:

    Hey, there is some ancient DNA from China, and it’s not being suppressed.

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