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Thread: The genetic structure of the world’s first farmers

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    Quote Originally Posted by epoch View Post
    If I understand it all correctly ADMIXTURE takes a whole lot of f3 stats and plots them. If it finds some samples clustering (i.e. a number of instances all with very low different f3 stats) it will consider it a population and measure the "distance" of others towards it as admixture proportions. You can imagine that for very old samples this will not work. They will have contributed for instance to population A as well as population B and C. The old samples will also have their own - lost - drift. This will be calculated as a mixture of A, B and C even if it is not.
    Thanks I have to look into f3 stats to understand better.
    ADMIXTURE will try to find a new cluster each step it takes.

    So as long as Levant_N and Anatolia_N aren't considered different populations 1c is valid. As soon as both are considered separate populations 4b. In other words: 1c means K=11, 4b means K>11.
    Hmmm, in 1c figure 1 they distinguish Iranian N by green colour, as distinct admixture. I think if you enlarge the chart you should see a little squares of green in Anatolian Neolithic. Anyway, Iranian Ch contains both Levant and Iranian N, blue and green. Why wouldn't Anatolian then?
    Check this latest paper:
    http://www.eupedia.com/forum/threads...077#post482077
    Figure C, GD13A represents Iranian Neolithic, Anatolian Neolithic has maybe 5% of it.

    I think there is some disagreement here in calculation of influence of Iranian Neolithic in Anatolia, perhaps in what they call prediction.
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    Quote Originally Posted by LeBrok View Post
    The only squeaky wheel in it is that Anatolian farmers have 34% of autosomal Levant Neolithic in them. I see two possibilities to explain. Either Levant Y and mtDNA got deleted by better fit Iranian and local types uniparental DNA, which is not impossible knowing how fast they can bloom and die due to bottlenecking (8.2k event) and other evolutionary forcings. Second solution is that 34% of what appears to be Levant DNA is actually from a group of very related to them HGs in Central Anatolia, possibly carriers of G2a. Therefore all farmers genes come from Iranian Farmers, the rest from local hunters. That's quite a twist to what we assumed just days ago, but it is what it is. Well, possible by now, till dust settles.
    Admixtures are not as reliable as haplogroups. Admixtures are only simulation based on a researcher's selection and comparison of specific alleles. You should be especially careful about the naming of admixtures, as they can be misleading. If you collect ancient samples haphazardly from various sites in different regions, how are you supposed to know where one admixture originated. In most cases it will be with an ancient population that hasn't been sampled yet.

    In the case of Basal Eurasian admixture, we have no idea if it matches exactly a specific Mesolithic or Early Neolithic population, or if it represents an admixture that was already widely distributed and blended with other admixtures in the Mesolithic or Early Neolithic Near East. It is dangerous to assume that Basal Eurasian necessarily represents the very first farmers. Then how do we know that there was only one ethnic group of original farmer? Wheat, barley, oats, flax, lentils, peas and chickpeas, the so-called Neolithic founder crops, could very well have been domesticated each by a different Mesolithic tribe. That is why we see Early Neolithic farmers belonging to a variety of Y-haplogroups like CT, C1a2, E1b1b, G1, G2a1, G2a2, H2, T, which would most likely have been distinct tribes (i.e. extended families) during the Mesolithic. But farmers doesn't only mean cereal and legume farmers, but also goat, sheep, pig and cattle herders, and all the evidence at present suggest that these were domesticated by yet other tribes - R1b for cattle, J1 or J2 for goats and sheep, and possibly one of the above, like G2a, for pigs.

    The way I see it now is that many independent tribes inhabiting the Fertile Crescent in the Mesolithic domesticated various crops. It took there centuries, or even millennia of trading and intermarriages to progressively merge with one another, but leaving large regional disparities. H2 and T may have been domesticating Emmer wheat and barley in modern Syria, while CT and E1b1b domesticated legumes around modern Israel/Palestine and Jordan, G2a domesticated Einkorn wheat pigs in the Taurus, and R1b rounded up the first cow herds just south of the Taurus. If that kind of scenario took place, which population matches the "pure" Basal Eurasian? Or to phrase it another way, isn't Basal Eurasian the result of the merger of several of these tribes already? Shouldn't we have separate admixtures for each group? After all at first there was only one Mesolithic European admixture, but we now clearly distinguish between WHG and EHG, and there could be a third distinct one in the Balkans or Italy for all we know.


    Well, if we assume that proto IE is actually Iranian Neolithic, which fed Anatolian Neolithic, which fed European Neolithic, it makes European Neolithic proto IE too. Meaning all old Europe spoke proto IE language, plus half of Middle East. It makes irrelevant whichever farmers, Maykop or Cucuteni, taught language to Steppe people via farming and mingling, it was all proto IE. Actually it would make it easier to understand why the steppe invaders were so successful teaching all Europe and half Asia to speak their language. It was already very similar to local languages.
    Well, one of possibilities at the moment.
    That's the point. H2a1, U4 and I1c were not found in the European Neolithic, nor in the Anatolian or Iranian Neolithic. The only pre-Bronze Age samples we have are from Chalcolithic eastern/central Europe, Armenia and Iran.
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    @Gravetto-Danubian

    I have also something like that in my head, the first different tribes involved in agriculture and herdering would have reached a population density high enough as to need more land; there were two solutions left: fight for land agaisnt their farmer neighbours (already with a dense population also), or the easy solution, to occupy lands of the neighbour HG, almost empty.

    @Maciamo

    If you suggest that R1b was carrying PIE from Iran... it would have similar problems as the IE from Anatolia: what to do then with the hundreds of no-IE languages left in the Caucasus? Why the way what this new R1b guy does is in fact is adding up another signal for a "yellow alarm", in this case one that may give with more data the final game over to R1b / IE; if the paper puts clear that peoples from Iran arrived to the steppes, it was through Armenia / Caucasus, and there we find now (again before any IE expansion) a R1b person, in this case under a stone kurgan from a developed culture that expanded over a region that the first language known in the area was non-IE Hurrian (and then the related Urartian). Once the Urartian kingdom was beaten by the Assyrians the IE Armenians were able to profit the kaos to get in from the west in the VI BC. Other R1b's remained there, as in the sample of 1800 BC (a R1b-ht35 Hurrian) and 1000 BC (a R1b-Z2013 Uratian) as to continue with actual R1b Armenians being of the same R1b clade as their Urartian ancestors. But the worst with that is that the first clade is the same found in 1 Yamnayan and the "son" clade is found in 10 Yamnayans... so what to do? to think that R1b was added up to the northwards expansion with metals and wheels reaching Yamnaya, or to figure out that the same R1b Yamnayans clades came back to where they came? (and only such R1b specific clade among those that is supposed to have Yamnayans). As the new Armenian sample is xM269 it is reasonable to think that he was M73? The case is that M73 are now in the area that spans from Samara to Kabul, peaking in Bashkirs, is so another possible case of a clade carried northwards to add up? So the yellow alarm is that there are enough data to point that a bunch of R1b clades came to the steppe from the south... but it is doubtful that they were speaking IE when settled there.

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    Quote Originally Posted by Angela View Post
    I don't think there's any way of knowing at this stage where the Basal Eurasian was hiding, but one of the points against an Arabian refugia is that Levant Neolithic has less of it than Iranian hunter-gatherer (44% to 64%). On the other hand, both Levant Neolithic and Iranian Neolithic have about the same amount-44%-so the argument could be made that Basal was diluted in the west by something WHG like and in the east by something EHG or maybe ANE like.

    The other alternative often mentioned is a Persian Gulf refugia, which is actually I think what Alan said?

    @Holderlin,
    I've considered that too. It would certainly explain why we haven't stumbled upon it yet, given that we have nothing really old from that region.

    @Alan,
    That makes sense to me, and I think the statements in the paper alluding to perhaps more "proximate" contacts was included. So, not that there wasn't actual steppe movement to India, but that there are older processes which may be inflating the figures.

    My poor old brain.All these simulations! Everyone of them is based upon human choice. No divine revelation helas as always in autosomes evluations.
    I' ve to read and read again before synthetize. But yes I think (it's almost evident) exchanges of genes occurred between CHG ancient people and EHG of Steppes, even before Neolithic without speaking of an ancient common "ANE" or/and "proto-partly-gedrosia" anterior layer of old genes common all over central Asia. What is from deepcommon ancestry, what is from newly admixtures? We are sometimes speaking as if the genes states were a stable and "frozen" thing.
    admixtures simulations are simulations (I repat myself, the age!), we need other tools as IBS, IBD things and what more?...
    Concerning Basal Eurasian, seemingly Arabia is not the best choice; maybe as you say something around Persic Gulf?
    By the way concerning Koweit people and surroundings, Coon said they presented some 'veddoid' traits more than central Arabs. In admixture we have South-Asian (for the worth it has) too. Here too, same problem: Is the ASI found among Near-Eastern Iranian Hindu Kush people the result of recent events linked to Harrapan introgression, or to gradual osmosis after Iranian/South Caucasus introgressions into ex-Harappa (Neolithoc, BA?) or for a part to deep ancestry? Perhaps no links with true (recent it's true) ASI but B-E could be linked to Elamits of Southern Iran (dravidian speaking)? All that is very complicated for me.
    I would like to have the supposed 'basal-eurasian' estimations for Southern India.

    &: apart: diverse papers I red always show a slight but ever present taste of Northern European in Hindu Kush and surroundings regions. WHat depth???

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    Quote Originally Posted by berun View Post
    @Gravetto-Danubian

    I have also something like that in my head, the first different tribes involved in agriculture and herdering would have reached a population density high enough as to need more land; there were two solutions left: fight for land agaisnt their farmer neighbours (already with a dense population also), or the easy solution, to occupy lands of the neighbour HG, almost empty.

    @Maciamo

    If you suggest that R1b was carrying PIE from Iran... it would have similar problems as the IE from Anatolia: what to do then with the hundreds of no-IE languages left in the Caucasus? Why the way what this new R1b guy does is in fact is adding up another signal for a "yellow alarm", in this case one that may give with more data the final game over to R1b / IE; if the paper puts clear that peoples from Iran arrived to the steppes, it was through Armenia / Caucasus, and there we find now (again before any IE expansion) a R1b person, in this case under a stone kurgan from a developed culture that expanded over a region that the first language known in the area was non-IE Hurrian (and then the related Urartian). Once the Urartian kingdom was beaten by the Assyrians the IE Armenians were able to profit the kaos to get in from the west in the VI BC. Other R1b's remained there, as in the sample of 1800 BC (a R1b-ht35 Hurrian) and 1000 BC (a R1b-Z2013 Uratian) as to continue with actual R1b Armenians being of the same R1b clade as their Urartian ancestors. But the worst with that is that the first clade is the same found in 1 Yamnayan and the "son" clade is found in 10 Yamnayans... so what to do? to think that R1b was added up to the northwards expansion with metals and wheels reaching Yamnaya, or to figure out that the same R1b Yamnayans clades came back to where they came? (and only such R1b specific clade among those that is supposed to have Yamnayans). As the new Armenian sample is xM269 it is reasonable to think that he was M73? The case is that M73 are now in the area that spans from Samara to Kabul, peaking in Bashkirs, is so another possible case of a clade carried northwards to add up? So the yellow alarm is that there are enough data to point that a bunch of R1b clades came to the steppe from the south... but it is doubtful that they were speaking IE when settled there.
    Good point, we fall into known shortcomings of Anatolian origin of IE hypothesis, likewise there are too many ancient non-IE languages in the area, Caucasus, Minoans, Etruscans, Sumerians to make Iranian and Anatolian farmers IEs. There is no evidence of IE language till late Bronze Age. It could indeed be a language of Steppe herders/HGs and expended with them in Bronze Age.

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by Maciamo View Post
    Admixtures are not as reliable as haplogroups. Admixtures are only simulation based on a researcher's selection and comparison of specific alleles. You should be especially careful about the naming of admixtures, as they can be misleading. If you collect ancient samples haphazardly from various sites in different regions, how are you supposed to know where one admixture originated. In most cases it will be with an ancient population that hasn't been sampled yet.

    In the case of Basal Eurasian admixture, we have no idea if it matches exactly a specific Mesolithic or Early Neolithic population, or if it represents an admixture that was already widely distributed and blended with other admixtures in the Mesolithic or Early Neolithic Near East. It is dangerous to assume that Basal Eurasian necessarily represents the very first farmers. Then how do we know that there was only one ethnic group of original farmer? Wheat, barley, oats, flax, lentils, peas and chickpeas, the so-called Neolithic founder crops, could very well have been domesticated each by a different Mesolithic tribe. That is why we see Early Neolithic farmers belonging to a variety of Y-haplogroups like CT, C1a2, E1b1b, G1, G2a1, G2a2, H2, T, which would most likely have been distinct tribes (i.e. extended families) during the Mesolithic. But farmers doesn't only mean cereal and legume farmers, but also goat, sheep, pig and cattle herders, and all the evidence at present suggest that these were domesticated by yet other tribes - R1b for cattle, J1 or J2 for goats and sheep, and possibly one of the above, like G2a, for pigs.

    The way I see it now is that many independent tribes inhabiting the Fertile Crescent in the Mesolithic domesticated various crops. It took there centuries, or even millennia of trading and intermarriages to progressively merge with one another, but leaving large regional disparities. H2 and T may have been domesticating Emmer wheat and barley in modern Syria, while CT and E1b1b domesticated legumes around modern Israel/Palestine and Jordan, G2a domesticated Einkorn wheat pigs in the Taurus, and R1b rounded up the first cow herds just south of the Taurus. If that kind of scenario took place, which population matches the "pure" Basal Eurasian? Or to phrase it another way, isn't Basal Eurasian the result of the merger of several of these tribes already? Shouldn't we have separate admixtures for each group? After all at first there was only one Mesolithic European admixture, but we now clearly distinguish between WHG and EHG, and there could be a third distinct one in the Balkans or Italy for all we know.
    I'm not sure if I can buy such narrow farming specialization, to make every haplogroup farm or herd something different than others. Once you domesticate one plant or one animal, you understand the concept and develop genetic inclinations to farming, the rest should snowball into domestication whatever grows and walks and is tasty in the area. Having said that, the genetic picture shows that many independent groups survived LGM there and developed farming/herding independently. At least two, Natufians and Iran_N, possibly third one in Anatolia. The picture is still muddy, and as you mentioned at the beginning, we can't trust the admixture calculators too much yet.

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    Quote Originally Posted by LeBrok View Post
    Good point, we fall into known shortcomings of Anatolian origin of IE hypothesis, likewise there are too many ancient non-IE languages in the area, Caucasus, Minoans, Etruscans, Sumerians to make Iranian and Anatolian farmers IEs. There is no evidence of IE language till late Bronze Age. It could indeed be a language of Steppe herders/HGs and expended with them in Bronze Age.


    We don't know what kind of language Sumerians, Elamites etc spoke for that matter all we know it could be isolated, but also Indo European related. Yet what people seem to miss out, Those Steppes were populated by Uralic speaking people too. In fact EHG peaks in Uralic speakers, not Indo European speakers.

    If we believe EHG is simply WHG+ANE, which part of their ancestry brought the PIE language? Was ist WHG or was it ANE? ANE isn't exclusive to Indo Europeans, and I doubt WHG was Indo European.

    So the argument that the Iranian plateau and Mesopotamia had too many non IE languages (well I can't think of any attested Bronze Age language from the Iranian Plateau anyways beside Elamite which imo is more connected to South Mesopotamia than Iranian Plateau). Can be used for the Steppes too.

    The best hypothesis so far is, that one PIE language or culture didn't exist but we deal with several creol languages which emerged out of similar propotions of admixture.

    Having Hittite samples would be great, and could bring all this debate more towards the end. If the Hittites who are the oldest most archaic Indo Europeans turn out with significantly higher percentages EHG than calcolthic/mesolithic Iranian Plateau and West Asian highland samples, and we have pre Neolithic South_Central Asian samples which do not appear EHG like, than we can conclude the Indo European language definitely evolved in the Steppes.

    But I am very convinced as I pointed out in the past that PIE was more of a network of cultures, being all around the Black and Caspian Sea (North, south, East and West of it).

    And something tells me Kura Araxes or Maykop will turn out as the origin of Hittite, since the appearance of Hittites fits with the Kura Araxes collapse.

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    0 out of 1 members found this post helpful.
    Quote Originally Posted by LeBrok View Post
    Nope, all the other Jews in the area, especially the Libyan and Tunisian Jews. Look at modern population PCA in Extended Figure 1. Compare it to PCA Figure 1b
    Yes, if the projected ancient samples from the Levant Neolithic are accurately placed in relationship to the modern samples, the Levant Neolithic clusters right in between the Palestinians and Jordanians to their right, and at the top left corner to the North African Jews.

    The answer as to why is rather unclear to me. I think maybe the more likely scenario is that the Jews of the Bronze Age, like the Canaanites, were probably like ancient Bronze Age Levant samples, and the "Western" Jews are being pulled away by European and North African admixture. The North African ones are closer because they have less of the European gene flow. From my recollection, North African Jews are very structured by area because of endogamy as well as slightly different gene flow, but they all have a segment of ancient Jewish ancestry from colonies that existed along the coast for millennia, a Berber component of converted Jews who would have had a big chunk of Levant Neolithic, and then influx directly from Sephardim from Spain, and European Jews from Italy and other regions.

    An interesting point that is once again made is the incredible variation among the "Jewish" populations. Look at the span from the Ashkenazim to the Libyan Jews, and then beyond that to the Iranian "Eastern" Jews, to the "Southern" Yemenite Jews.

    Or, an alternative would be that their stay in Egypt made them different from the Canaanites, less Iranian Chalcolithic like, and they kept that difference because of all the prophets fulminating against admixture with "foreign" women. :)

    None of this is going to be resolved without ancient samples of Jews from the Levant, imo.

    Exactly what gene flow into the Ashkenazim made them so different is still a mystery to me. There they are again right next to the Sicilians, and yet IBD analysis shows no sharing between them at least from the Classical Era forward, or at least no sharing any higher than with any other group.


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    Quote Originally Posted by Angela View Post
    Exactly what gene flow into the Ashkenazim made them so different is still a mystery to me. There they are again right next to the Sicilians, and yet IBD analysis shows no sharing between them at least from the Classical Era forward, or at least no sharing any higher than with any other group.
    Possible amateurish explanation:
    Askhenaze picked along history, by more than an event, "european" (non-near-eastern) admixtures; that push them closer to Sicilians as global admixture levels, but the shared non-near-eastern genes were not inherited through unique sicilian admixture; their shared ancestry traces back farther in past so the IBD?I think. I red in Middle Ages, massive enough conversion to Judaism took place in Poland (it was no more the case at the dawn of the LMWar, helas)

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    Quote Originally Posted by Angela View Post
    Yes, if the projected ancient samples from the Levant Neolithic are accurately placed in relationship to the modern samples, the Levant Neolithic clusters right in between the Palestinians and Jordanians to their right, and at the top left corner to the North African Jews.

    The answer as to why is rather unclear to me. I think maybe the more likely scenario is that the Jews of the Bronze Age, like the Canaanites, were probably like ancient Bronze Age Levant samples, and the "Western" Jews are being pulled away by European and North African admixture. The North African ones are closer because they have less of the European gene flow. From my recollection, North African Jews are very structured by area because of endogamy as well as slightly different gene flow, but they all have a segment of ancient Jewish ancestry from colonies that existed along the coast for millennia, a Berber component of converted Jews who would have had a big chunk of Levant Neolithic, and then influx directly from Sephardim from Spain, and European Jews from Italy and other regions.

    An interesting point that is once again made is the incredible variation among the "Jewish" populations. Look at the span from the Ashkenazim to the Libyan Jews, and then beyond that to the Iranian "Eastern" Jews, to the "Southern" Yemenite Jews.

    Or, an alternative would be that their stay in Egypt made them different from the Canaanites, less Iranian Chalcolithic like, and they kept that difference because of all the prophets fulminating against admixture with "foreign" women. :)

    None of this is going to be resolved without ancient samples of Jews from the Levant, imo.

    Exactly what gene flow into the Ashkenazim made them so different is still a mystery to me. There they are again right next to the Sicilians, and yet IBD analysis shows no sharing between them at least from the Classical Era forward, or at least no sharing any higher than with any other group.
    This always drives me crazy! Every time a genetic study is done that includes Ashkenazim, Sicilians, and Southern Italians, they are always ganged up with each other! This happens consistantly and reliably; yet Ashkenazim weren't made in Italy so to speak with IBD being low (I'll admit my rudimentary genetics is a bit weak, IBD is when longer segments match, right? Fell asleep in genetics class when I was gettin bored of biology but I digress).

    As mentioned, I'm close to a total novice when it comes to this so bear with me. Now, FST is another way to measure genetic relatedness between populations with lower numbers suggesting higher relatedness, correct? If so, why is it that Southern Italians are about just as close to the anatolian neolithic farmers in the map as ashkenazim and sicilians yet their fst from anatolian neolithic farmers is .030?

    Also, why is it that Southern Italians are insanely far removed from everybody at all? It seems based on that chart that even the English are closer to the Greeks than the Southern Italians.

    Am I misunderstanding what these values are actually telling us?

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    Quote Originally Posted by Angela View Post

    An interesting point that is once again made is the incredible variation among the "Jewish" populations. Look at the span from the Ashkenazim to the Libyan Jews, and then beyond that to the Iranian "Eastern" Jews, to the "Southern" Yemenite Jews.

    Or, an alternative would be that their stay in Egypt made them different from the Canaanites, less Iranian Chalcolithic like, and they kept that difference because of all the prophets fulminating against admixture with "foreign" women. :)
    .
    Might as well be the case. I wonder how close they will relate to Phoenicians once we get their samples?

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    0 out of 1 members found this post helpful.
    Quote Originally Posted by davef View Post
    This always drives me crazy! Every time a genetic study is done that includes Ashkenazim, Sicilians, and Southern Italians, they are always ganged up with each other! This happens consistantly and reliably; yet Ashkenazim weren't made in Italy so to speak with IBD being low (I'll admit my rudimentary genetics is a bit weak, IBD is when longer segments match, right? Fell asleep in genetics class when I was gettin bored of biology but I digress).

    As mentioned, I'm close to a total novice when it comes to this so bear with me. Now, FST is another way to measure genetic relatedness between populations with lower numbers suggesting higher relatedness, correct? If so, why is it that Southern Italians are about just as close to the anatolian neolithic farmers in the map as ashkenazim and sicilians yet their fst from anatolian neolithic farmers is .030?

    Also, why is it that Southern Italians are insanely far removed from everybody at all? It seems based on that chart that even the English are closer to the Greeks than the Southern Italians.

    Am I misunderstanding what these values are actually telling us?
    Whether or not it drives us crazy trying to explain it, the relationship is what it is...:)

    You're right, though, about IBD analysis and what it shows, or doesn't show. So, either there was gene flow from a population similar to the Sicilians that went into the proto-Ashkenazi population very early, too early to be captured by current IBD analysis, or it's just happenstance. This is one of the limitations of PCAs and Admixture. If you take a person who is half Chinese and half British, they're going to plot with Uighers, and probably come out Uigher in Oracle. That doesn't mean they have any relationship in terms of gene flow or history with Uighers at all; it's just the admixture of similar ancient populations. The problem with these programs is that they don't come with a time stamp.

    The South Italians aren't far from everyone else in this PCA. They cluster with the Sicilians, the Ashkenazim, and one is drifting toward the Greeks. That's about where I would expect them to be.

    Where are you getting that .030 figure? I just took a look at Supplementary Data Table 3, and they all seem the same, .000 or .001, if I'm reading it correctly.
    http://biorxiv.org/content/early/201...1.figures-only

    However, you're right in that FST and this PCA don't correlate perfectly because everyone in Europe is very close to Anatolia Neolithic if you use just FST values. Of course, that's just one measure.

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    Accidentally posted this at another thread.

    Anatolia_Neolithic might have some CHG/Iran admixture but it doesn't have a lot. Table S7.8 shows that Anatolia_Neolithic can't be explained as a mixture of our the ancient genomes sampled so far. Modelling it as Iran_N+Levant_N+WHG barely works and the result is probably pretty inaccurate. Instead Anatolia_Neolithic is like a brother to Natufians. They're very closely related and this needs to have a lot of emphasis put on it. Also it's important to notice that Levant_Neolithic is significantly closer to Anatolia_Neolithic than Natufians were, so there was gene flow between the two regions maybe because of the spread of farming.

    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    The most important detail from this paper is that in the Stone age there were two distinct races in the Middle East. One in Iran and Caucasus and one in Levant and Anatolia. Metal Age Middle Easterners can nicely be explained as a mixture of these two races, with minor exotic admixture(EHG in Armenia). Modern Middle Easterns will certainly also come out mostly as a mixture of these two races, but many also have exotic ancestry(African, South Asian, European, and Siberian ancestry).

    Exactly what the relationship between these two races or what they're a mixture of can't be discerned. We need more ancient DNA to find out. Members in each race weren't exactly the same but they were very similar. The two races weren't completed distinct they were both a mix of Basal Eurasian and West Eurasian and shared Middle Eastern-specific ancestry that Paleo North Eurasians did not have, this ancestry includes Basal Eurasian but might include more. Their relationship between Paleo North Eurasians isn't the same. Iran/Caucasus is equally close to MA1/WHG while Levant/Anatolia is significantly closer to WHG than to MA1. Both are closer to WHG than to earlier Europeans.

    Figure S4.10 models Iran_N as 38% Basal, 12.4% brother of WHG, 49.6% pre-K14 split(ANE?) and Natufian as 45% Basal, 55% cousin of WHG. These are similar to the results we've been getting with D-stats for the last 6 months. This model doesn't work though because we lack the right ancient genomes.

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    The highlight of the paper is Table S7.25, where they give a list of qpADM results they got for ancient West Eurasians. Here are results for Metal Age Middle Easterners. They make a lot of sense.


    Iran_Chl: 20.2% South(Levant_N), 79.8% North(63.1% CHG, 16.7% Iran_N)
    Anatolia_ChL: 67.1% South(Anatolia_N), 32,9% Iran_Chl
    Armenia_Chl: 52.5% Anatolia_N, 29.2% Iran_N, 18.3% EHG.


    Armenia_EBA: 60.3% CHG, 39.7% Anatolia_N
    Armenia_MBA: 55.3% CHG, 34.4% Anatolia_N, 10.4% EHG
    Levant_BA: 55.7% Levant_N, 44.3% Iran_Chl.


    For the most part there's population continuum in Iran from Mesolithic to Chalcolithic. There's also lots of population continum in Armenia from Chalcolithic to Middle Bronze age. The Bronze age Armenian genomes we already have are very similar to modern Georgians and I think the news ones are to. IMO, Anatolia_Chl will turn out most similar to modern Cypriots and Turkish. I don't think Iran_Chl will turn out very similar to Iranians though. IMO, Iranians have a lot more "Southern" admixture(Levant_N, Anatolia_N related).


    Once these ancient Middle Eastern genomes are made available and we imitate some of the techniques used in the study we'll learn a lot more about West Eurasian. An important detail I think we'll learn is who the Middle Eastern people who moved into Southern Europe after the Neolithic were. I think they came mostly from around Turkey, so similar to our Chalcolithic Turkish genome.

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    Quote Originally Posted by Angela View Post
    Whether or not it drives us crazy trying to explain it, the relationship is what it is...:)

    You're right, though, about IBD analysis and what it shows, or doesn't show. So, either there was gene flow from a population similar to the Sicilians that went into the proto-Ashkenazi population very early, too early to be captured by current IBD analysis, or it's just happenstance. This is one of the limitations of PCAs and Admixture. If you take a person who is half Chinese and half British, they're going to plot with Uighers, and probably come out Uigher in Oracle. That doesn't mean they have any relationship in terms of gene flow or history with Uighers at all; it's just the admixture of similar ancient populations. The problem with these programs is that they don't come with a time stamp.

    The South Italians aren't far from everyone else in this PCA. They cluster with the Sicilians, the Ashkenazim, and one is drifting toward the Greeks. That's about where I would expect them to be.

    Where are you getting that .030 figure? I just took a look at Supplementary Data Table 3, and they all seem the same, .000 or .001, if I'm reading it correctly.


    However, you're right in that FST and this PCA don't correlate perfectly because everyone in Europe is very close to Anatolia Neolithic if you use just FST values. Of course, that's just one measure.
    That's right, it drives us crazy but at least it isn't bent to make people happy.

    I agree with you in that ashkenazim likely formed from populations similar to Sicilians and any connection is ancient and old. Was the Mid-East itself more "Sicilian" like during this time?

    Weird that a half n' half Brit/Chinese would come out that way, but I have read quite a few results from customers who used gedmatch calculators and I have seen half East Asian half North Euro get Uigher as a top match, but luckily there is a value after each item in the single population sharing list which tells how far apart you actually are from that population, and most of whom I seen with that admixture (note I've only seen a few) get a really really high value (like 15 or over) which means that that person isn't anywhere near that population genetically. I think under 5 means you're pretty warm.

    As for South Italy getting .030, you'll find it in the row marked "Italian_South", column "Anatolia_N". Those are the coordinates where you'll find it. And because of that, its possible that either the PCA is wrong or the fst chart is wrong; but then again this could be due to a lack of knowledge of genetics and/or the article on my part.

    Here's the link so you won't have to run back to your post and click it. I'm not allowed to post links yet due to not having enough posts.
    biorxiv.org/content/early/2016/06/16/059311.figures-only

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    Quote Originally Posted by LeBrok View Post
    I'm not sure if I can buy such narrow farming specialization, to make every haplogroup farm or herd something different than others. Once you domesticate one plant or one animal, you understand the concept and develop genetic inclinations to farming, the rest should snowball into domestication whatever grows and walks and is tasty in the area. Having said that, the genetic picture shows that many independent groups survived LGM there and developed farming/herding independently. At least two, Natufians and Iran_N, possibly third one in Anatolia. The picture is still muddy, and as you mentioned at the beginning, we can't trust the admixture calculators too much yet.
    I am pretty sure that plant or animal domestication were not concept that came easily to the mind of these prehistoric people. If, as you said, there was a snowballing effect from one crop to another, then how comes it took many millennia to domesticate plants beyond the three Neolithic founder crops? It is also pretty clear from what we know from both archaeology and population genetics that cereal farmers, goat herders and cow herders were distinct peoples in the Early Neolithic. Steppe PIE were cow herders; they practically didn't cultivate cereals, nor herd goats or pigs (although they had sheep) despite being in contact with farmers who did.

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    0 out of 1 members found this post helpful.
    Quote Originally Posted by davef View Post
    That's right, it drives us crazy but at least it isn't bent to make people happy.

    I agree with you in that ashkenazim likely formed from populations similar to Sicilians and any connection is ancient and old. Was the Mid-East itself more "Sicilian" like during this time?

    Weird that a half n' half Brit/Chinese would come out that way, but I have read quite a few results from customers who used gedmatch calculators and I have seen half East Asian half North Euro get Uigher as a top match, but luckily there is a value after each item in the single population sharing list which tells how far apart you actually are from that population, and most of whom I seen with that admixture (note I've only seen a few) get a really really high value (like 15 or over) which means that that person isn't anywhere near that population genetically. I think under 5 means you're pretty warm.

    As for South Italy getting .030, you'll find it in the row marked "Italian_South", column "Anatolia_N". Those are the coordinates where you'll find it. And because of that, its possible that either the PCA is wrong or the fst chart is wrong; but then again this could be due to a lack of knowledge of genetics and/or the article on my part.

    Here's the link so you won't have to run back to your post and click it. I'm not allowed to post links yet due to not having enough posts.
    biorxiv.org/content/early/2016/06/16/059311.figures-only
    Thanks for your courtesy but I have an excel spreadsheet open for it...

    I think you should check again:

    Anatolia N is row 8 and Southern Italians get .001 for it, just like practically everyone else.

    Levant Bronze, for which they get .031 is row 61.

    The .030 they get is for Steppe Middle/Late Bronze from what I can see, which is row 86.

    By the way, the "South Italian" here is not the Calabria sample that some people use. This is a different data set altogether, a more balanced one from the reputation, than some of the others being used out there.

    As you can see from the PCA, the Southern Italians and the Sicilians land right next to each other.


    The "bending" of the results, in so far as I can tell, is being done by people on forums like theapricity who are virtually certifiable, in my opinion. It seems to be their mission in life to make Sicilians, and now, lately, southern Italians, non-European and Jews in disguise. It appears to be the result of a weird amalgam of the nordicist Spanish perspective on southern Europeans with unresolved family issues and virulent anti-semitism. Indeed, the prime proponent has a history of anti-Jewish activity, from what I've been told. Also, from what I've heard, some of the examples he uses are fraudulent, even extending to mislabeling people's identity and photo-shopping pictures.

    Much better for your mental health if you stay away. There's nothing of value being posted there anyway.

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    Quote Originally Posted by Angela View Post
    Thanks for your courtesy but I have an excel spreadsheet open for it...

    I think you should check again:

    Anatolia N is row 8 and Southern Italians get .001 for it, just like practically everyone else.

    Levant Bronze, for which they get .031 is row 61.

    The .030 they get is for Steppe Middle/Late Bronze from what I can see, which is row 86.

    By the way, the "South Italian" here is not the Calabria sample that some people use. This is a different data set altogether, a more balanced one from the reputation, than some of the others being used out there.

    As you can see from the PCA, the Southern Italians and the Sicilians land right next to each other.


    The "bending" of the results, in so far as I can tell, is being done by people on forums like theapricity who are virtually certifiable, in my opinion. It seems to be their mission in life to make Sicilians, and now, lately, southern Italians, non-European and Jews in disguise. It appears to be the result of a weird amalgam of the nordicist Spanish perspective on southern Europeans with unresolved family issues and virulent anti-semitism. Indeed, the prime proponent has a history of anti-Jewish activity, from what I've been told. Also, from what I've heard, some of the examples he uses are fraudulent, even extending to mislabeling people's identity and photo-shopping pictures.

    Much better for your mental health if you stay away. There's nothing of value being posted there anyway.

    You're very welcome!

    Sorry, but you'll have to navigate back to supplement 3 and check out row 46 (Italian_South) column E (Anatolia_N) and you'll see the .030 value. I'll bet my soul you'll find it using those coordinates. Then again, I do have macular degeneration and my eyes are weakening by the minute even though I'm a young buck.

    Look at how much closer the Poles and the Scots are to the neolithics in comparison to the South Italians. Something is wrong here!! This is what kills me when it comes to reading about population genetics! There's too much contradiction. Luckily my expertise is software programming with my background being computer science. I only need to deal with pure logic as opposed to uncertainty and chaos. That Lazaridis fellow is on my team. He's another programmer with a background in computer science. Wonder how he feels about all of this.

    And LOL to their "mission in life". So their "mission in life" is to desperately claim that sicilians and ("now lately"-as you claimed, aka a NEW BREAKTHROUGH in BIGOTRY) South Italians non-European and JEWS in disguise. I don't care. If they want to label South Italians like myself as non-European then go ahead. South Italians in these United States as well as Ashkenazy Jews are making a ton of money. I'm not saying that they are the "Master Race" I'm just pointing out that success doesn't require one to be be related to Brits or Germans.

    I don't take bigots seriously. If bigots want to attack South Italians, or anyone else who score high "east med" in gedmatch I digest their insults. The KKK is still active in America and I'm lynching material. My background is south italian, jewish and irish (italians, jews, and irish fell prety to the kkk, not just Aftrican Americans) and I'll tell that to their faces. Then again, they aren't as violent. TBH I take bigots as seriously as some random guy who lets out a rancid fart just to annoy me. I don't take offense, I just know that he's just an idiot being an idiot.

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    I wonder how these ancient groups in Iran compared to the people of the Indus Valley Civilizations of Harrapa and Mohenjo Daro. People are always claiming a connection, yet I haven't heard of any ancient genetic material from the region being examined.

    Does anyone know of any past genetic tests from the area or tests still underway?

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    Quote Originally Posted by Promenade View Post
    I wonder how these ancient groups in Iran compared to the people of the Indus Valley Civilizations of Harrapa and Mohenjo Daro. People are always claiming a connection, yet I haven't heard of any ancient genetic material from the region being examined.

    Does anyone know of any past genetic tests from the area or tests still underway?
    no, but check this

    http://www.eupedia.com/forum/threads...he-Zagros-Iran

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    just thinking loud ..

    Basal Eurasian had virtualy no Neanderthal admixture ..
    Natufians and Levant Neo and Iran Neo have the most Basal Eurasian .. , it was absent in pre-Neo Europe
    did Basal Eurasian get into Anatolian Neo (and EEF) via Levant Neo and Iran Neo ?
    Natufians is a mixture of African E1b1 and Basal Eurasian which was allready present in the southern Levant before arrival of E1b1 ?
    There were at least 3 neolithic populations in SW Asia : Natufian, Iran Neolithic and the common ancestor of Anatolian and European Neolithic (based on mainly G2a2)
    Natufian spread to African Neo, Iran Neo spread to Central and South Asia Neo.

    Figure 4a
    Iran Chl is 63 % CHG, 20 % Levant Neo and 17 % Iran Neo
    The Iran Chl spread into Anatolia, the Levant and the steppe
    Armenia Chl and Europe Chl seem independent from Iran Chl, but Armenia EBA seems CHG
    so CHG is the source of both Iran Chl and Armenia EBA ?
    steppe EMBA (R1a/R1b) is EHG (R1a/R1b) and Iran Chl (Maykop?)
    steppe MLBA is 68 % steppe EMBA + 32 % Europe MNChl : admixture of Old Europe through Cucuteni into the steppe IE ?

    the spread of metallurgy in SW Asia (and Maykop?) seems heavily related with haplo J coming from Iran or Georgia (CHG)

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Alan View Post
    We don't know what kind of language Sumerians, Elamites etc spoke for that matter all we know it could be isolated, but also Indo European related. Yet what people seem to miss out, Those Steppes were populated by Uralic speaking people too. In fact EHG peaks in Uralic speakers, not Indo European speakers.
    Proto-Uralic has had a large influence on PIE and vice versa. A large number of linguistics think it is possibly of the same origin as PIE. Take a look at what exactly is related, it seems very deep.

    Quote Originally Posted by Alan View Post
    If we believe EHG is simply WHG+ANE, which part of their ancestry brought the PIE language? Was ist WHG or was it ANE? ANE isn't exclusive to Indo Europeans
    First, ANE brought forth a number of languages, some of which were isolates: The American-Indian languages. Secondly, we don't know how languages originated. Take for instance New Guinea where Papua's speak over 850 languages, with large families as well as dozens (!) of isolates. Some larger families have ties with the world around them.

    Quote Originally Posted by Alan View Post
    and I doubt WHG was Indo European.
    On the basis of what exactly do you exclude WHG as source?

    Quote Originally Posted by Alan View Post
    So the argument that the Iranian plateau and Mesopotamia had too many non IE languages (well I can't think of any attested Bronze Age language from the Iranian Plateau anyways beside Elamite which imo is more connected to South Mesopotamia than Iranian Plateau). Can be used for the Steppes too.
    But the relation between PIE and proto-Uralic runs very, very deep. Read about it.

    Quote Originally Posted by Alan View Post
    The best hypothesis so far is, that one PIE language or culture didn't exist but we deal with several creol languages which emerged out of similar propotions of admixture.
    No, the best hypothesis is a language originating between proto-Uralic and the Caucasus. And not just because influences of those, also because PIE roots for animals and certain trees limit its possible places or origin. So the steppe origins is independently derived from archaeology, language roots and language contacts. As we now have seen DNA supports that.

    Apart from that: PIE was not a creole language, as these are simplified languages: i.e. non-speakers adapt a simplified version and make it their own. PIE was highly complicated indicating it originated from native speakers.

    Quote Originally Posted by Alan View Post
    Having Hittite samples would be great, and could bring all this debate more towards the end. If the Hittites who are the oldest most archaic Indo Europeans turn out with significantly higher percentages EHG than calcolthic/mesolithic Iranian Plateau and West Asian highland samples, and we have pre Neolithic South_Central Asian samples which do not appear EHG like, than we can conclude the Indo European language definitely evolved in the Steppes.

    But I am very convinced as I pointed out in the past that PIE was more of a network of cultures, being all around the Black and Caspian Sea (North, south, East and West of it).

    And something tells me Kura Araxes or Maykop will turn out as the origin of Hittite, since the appearance of Hittites fits with the Kura Araxes collapse.

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    1 out of 1 members found this post helpful.
    something else : 'Anatolian' is actually NW Anatolian, 'Sea of Marmara' would be a better label
    we are missing the 'central Anatolian' DNA, i.e. DNA from Asikli Hoyuk or Catal Hoyuk, which I think is different from 'Anatolian' and from Levantine
    Asikli Hoyuk Neolithic was very early, ca 11 ka and allready before it was the most important source of obsidian for the Natufians
    https://en.wikipedia.org/wiki/A%C5%9...%C3%B6y%C3%BCk
    furthermore central Anatolians were one of the early adopters of metallurgy

    'Anatolian' and European neolithic are just ca 8.4 ka (starting ca 9 ka with some few settlements, but ca 8.4 ka new farmers arrived who were responsible for start of the expansion)

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    Quote Originally Posted by bicicleur View Post
    something else : 'Anatolian' is actually NW Anatolian, 'Sea of Marmara' would be a better label
    we are missing the 'central Anatolian' DNA, i.e. DNA from Asikli Hoyuk or Catal Hoyuk, which I think is different from 'Anatolian' and from Levantine
    Asikli Hoyuk Neolithic was very early, ca 11 ka and allready before it was the most important source of obsidian for the Natufians
    https://en.wikipedia.org/wiki/A%C5%9...%C3%B6y%C3%BCk
    furthermore central Anatolians were one of the early adopters of metallurgy

    'Anatolian' and European neolithic are just ca 8.4 ka (starting ca 9 ka with some few settlements, but ca 8.4 ka new farmers arrived who were responsible for start of the expansion)
    Is it possible it's an admixture of Levantine Neolithic and some Iranian Neolithic and that's how the CHG starting reaching Northwest Anatolia?

    As we discussed on another thread, the archaeology does point to influences on northwest Anatolia from Central Anatolia.

    Basal Eurasian had virtualy no Neanderthal admixture ..
    Natufians and Levant Neo and Iran Neo have the most Basal Eurasian .. , it was absent in pre-Neo Europe
    did Basal Eurasian get into Anatolian Neo (and EEF) via Levant Neo and Iran Neo ?
    I think the Iranian hunter-gatherer had the most; I think it was something close to 66%. I think Basal did get into NWAnatolia and then EEF via the other two Neolithic groups. The question, as we've been discussing, is where is the source? It would seem it diffused from the south, but given there's more to the east, perhaps not from Arabia.

    Natufians is a mixture of African E1b1 and Basal Eurasian which was allready present in the southern Levant before arrival of E1b1 ?

    I'm not sure about this one. At first I thought E1b1 might be the Basal lineage, but it is an African lineage and there seems to be no connection between Basal and SSA, contrary to what was vociferously championed by a lot of people. If "E" were actually Eurasian and all that "E" in Africa were the result of a back migration, that would solve that problem, but the authors of the paper maintain that basal "E" is African. Of course, the Natufians carry it and there's no SSA in them, which just goes to show again how disconnected yDna can become from autosomal signatures. If this is correct, so much for all those videos showing "African" looking people as Natufians. :)

    So, I don't know...maybe G2a? Or could it be "H"?

    Natufian spread to African Neo
    According to the authors, not precisely Natufian, but rather Levant Neolithic, yes?


    • ran Chl is 63 % CHG, 20 % Levant Neo and 17 % Iran Neo
      The Iran Chl spread into Anatolia, the Levant and the steppe
      Armenia Chl and Europe Chl seem independent from Iran Chl, but Armenia EBA seems CHG
      so CHG is the source of both Iran Chl and Armenia EBA ?
      steppe EMBA (R1a/R1b) is EHG (R1a/R1b) and Iran Chl (Maykop?)
      steppe MLBA is 68 % steppe EMBA + 32 % Europe MNChl : admixture of Old Europe through Cucuteni into the steppe IE ?

      the spread of metallurgy in SW Asia (and Maykop?) seems heavily related with haplo J coming from Iran or Georgia (CHG)



    • It seems like it to me, except I'm not sure about the bolded part. That's where you get into direction of movement across the Caucasus. It certainly doesn't seem like a barrier to migration...and I think the migration did go both ways.



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