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Thread: New Paper on Ancient Eurasian DNA

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    New Paper on Ancient Eurasian DNA

    New preprint paper that looks interesting. I don't think it has any new samples, but the methodology they used to point to earlier connections (gene flow) between Anatolian and HG seemed interesting.

    Leo Speidel, Lara Cassidy, Robert W. Davies,Garrett Hellenthal, Pontus Skoglund, Simon R. Myers (2021) preprint entitled "Inferring population histories for ancient genomes 2 using genome-wide genealogies"



    https://www.biorxiv.org/content/10.1...573v1.full.pdf

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    Ancient genomes anchor genealogies in directly observed historical genetic variation, and contextualise ancestral lineages with archaeological insights into their geography and lifestyles. We introduce an extension of the Relate algorithm to incorporate ancient genomes and reconstruct the joint genealogies of 14 previously published high-coverage ancients and 278 present-day individuals of the Simons Genome Diversity Project. As the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies, we additionally present a fast and scalable method, Colate, for inferring coalescence rates between low-coverage genomes without requiring phasing or imputation. Our method leverages sharing patterns of mutations dated using a genealogy to construct a likelihood, which is maximised using an expectation-maximisation algorithm. We apply Colate to 430 ancient human shotgun genomes of >0.5x mean coverage. Using Relate and Colate, we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.

    Fascinating! Good find.

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    3 members found this post helpful.
    They make it even a bit more clear here in the paper I think:

    "The extent to which directional gene-flow occurred from groups related to ancient Anatolia into 317 European HGs predating the spread of farming in Europe has remained controversial. We have provided two 318 further lines of evidence that such gene-flow existed, first using coalescence rates of lineages recently coalesced 319 between Anatolia and HGs. The TCC/TTC mutation rate elevation in all these ancient groups, and its strong 320 correlation to inferred recent shared ancestry with Anatolia, offers complementary support that the shared 321 ancestry detected by Colate indeed reflects recent gene exchange, given the age distribution of samples showing 322 this mutational phenomenon."

    So, whether there was gene from European HGs into Anatolia or not, they're arguing there was also gene flow from Anatolia into European HGs BEFORE the arrival of the Anatolian farmers.

    They maintain that the signal, the increased TCC to TTC mutation arrived in Europe twice from Anatolia, once in the late Paleolithic, and once with the farmers.

    ". We do not observe the signal in Neanderthals (Prüfer et al. 2014; 2017) or 267 Denisovans (Meyer et al. 2012), consistent with (Mathieson and Reich 2017). The signal appears already 268 widespread in the Late Upper Paleolithic, as it is carried by Bichon, a 13,700-year-old Western HG, by Sidelkino, a 269 11,000-year-old Eastern HG, by SATP (Satsurblia), a 13,000 year-old Caucasus HG, and Bon002, a 10,000 year-old 270 Anatolian Pre-Pottery individual (Figure 6c, Supplementary Figure 12).

    Already 10,000 years ago, the signal appears weaker in Western HGs compared to the Anatolian, who is among the 279 strongest carriers of this signal (similar strength to later Neolithic individuals and present-day Sardinians) (Figure 280 6e), suggesting that the driver of this mutation rate change, which may have been of genetic or environmental 281 nature, was already extinct by the Mesolithic. Eastern HGs have a slightly elevated signal compared to Western HGs. 282 Moreover, the strength of the TCC/TTC signal shows a remarkable correlation with recent coalescence rates to this 283 Anatolian individual (96% using AUC for SGDP non-Africans and 13 high-coverage ancients, 71% using TCC/TTC 284 proportion for ancients)(Figure 6b, d), and does not correlate as well with coalescence rates to any other HG group 285 for whom we have data (88% or 58% with Caucasus HGs (SATP), 83% or 53% with Scandinavian HGs (sf12), 76% 286 or 37% with Eastern HGs (Sidelkino), 73% or 53% with Western HGs (Bichon), where first number uses AUC, 287 second number uses TCC/TTC proportion) (Supplementary Figures 13). We therefore hypothesise that the signal 288 spread through ancestors of this Anatolian individual across Europe before the arrival of farming, and subsequently 289 arrived in Europe for a second time with Neolithic farmers. 290

    The genetic relationship among West Eurasian HG groups in the Late Paleolithic is not fully understood and, to the 291 best of our knowledge, current models do not include a clear source group contributing widely across these HG 292 groups, while able to explain the strong correlation to ancestry from Anatolia. One potential source are ancestors 293 of the Dzudzuana, a group inhabiting the Caucasus ~26k years ago (Lazaridis et al. 2018). This group is closely 294 related to ancient Anatolians, and to a lesser extend to Caucasus HGs and may have contributed ancestry to Eastern 295 and Scandinavian HGs before the spread of farming. The Dzudzuana have a pre-LGM common ancestor with 296 Western HGs, including Bichon, however, placing the signal on this common ancestor lineage would not explain 297 their signal strength difference and correlation to shared ancestry with Anatolia. Instead, one possibility is that the 298 signal spread during the Bølling-Allerød interstadial, a brief warming following the last glacial maximum, during perpetuity. "

    Huge questions remain. First, what caused this spike in mutation rate change in this triplet. Second, what were the consequences? We know many mutations are deleterious, but for it to have spread so far and wide there must have been mutations which were beneficial, yes?


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    Jovialis/Angela: Thanks and I agree, very interesting. Related to your questions Angela, I kind of wonder if this method can be shown to show how quick other mutations can occur and become fixed in a given population, etc vs. deleterious.

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    So now we know European HGs have Anatolian geneflow into them dating back to the Paleolithic! This is pretty big.

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    2 members found this post helpful.
    Quote Originally Posted by Jovialis View Post
    So now we know European HGs have Anatolian geneflow into them dating back to the Paleolithic! This is pretty big.
    It could also explain how EHG and SHG (which has EHG) got their skin depigmentation alleles, which were much more helpful in the far north than in the Caucasus or the plateaus of Anatolia. It's nice to know one of my more speculative ideas has some data to support it.

    I have to say I've been hoping for something like this; wish it hadn't been such a long time coming. It would have been helpful in those long debates where, to continual disparagement from some quarters, I insisted the gene flow could at least have been mutual between Europe and ancient Anatolia.


    Thinking some more about this, to have spread so far, perhaps it had some really large scale beneficial effect leading to some major change in the human genome.

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    I remember reading that the Villabuna Western Hunter Gatherers had ancestry from the Near East, and that these HGs replaced the Hunter Gatherers in the rest of Europe who had Magdenalian culture.

    I also, from scanning the pdf that the researchers stated that Northern Europeans have more SGH, and WHG ancestry. I have always assumed they had very little, and more of EHG. I am still unconvinced that the level of WHG ancestry in Northern Europeans is more that other Europeans. It is obvious that Northern European have a stronger affinity to both East Eurasians and especially Native Americans that EHG ancestry is involved.

    Regarding the Neolithic farmers, the farmers of Germany and Hungary were LBK culture, and the ones in the Mediterranean were Cardial culture. Usually different cultures mean different genetic groups.

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    Quote Originally Posted by Jovialis View Post
    So now we know European HGs have Anatolian geneflow into them dating back to the Paleolithic! This is pretty big.
    Jovialis: I agree, I noticed the Dzudzuana Samples were suggested as a major player in all this as the quote Angela put in her post clearly suggest. I think you have been making some predications about this before. There is that Lazaradis, Reich, etc analyzing the Dzudzuana samples that I think is still in pre-print. If it has been published, I haven't seen it, but I doubt as I think one of you would have posted it here. I think you and Angela have both been suggesting earlier Anatolian ancestry into Europe before Neolithic. Also, maybe some, not all of this CHG_Iran_NEO that shows up in the Neolithic period in Lazio (say in the Antonio et al 2019 paper) may in fact have already been in Italy. Need some other WHG samples from the period they indicate the admixture happened. So the Neolithic is not the first signal of Anatolian type ancestry it was in areas where WHG lived dating back before 14K years ago.

    So it is pretty big and this indicates Anatolian type ancestry predates any Steppe ancestry entering Europe by an even larger time period.

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    2 members found this post helpful.
    [QUOTE=Ozzie;619834]I remember reading that the Villabuna Western Hunter Gatherers had ancestry from the Near East, and that these HGs replaced the Hunter Gatherers in the rest of Europe who had Magdenalian culture.

    I also, from scanning the pdf that the researchers stated that Northern Europeans have more SGH, and WHG ancestry. I have always assumed they had very little, and more of EHG. I am still unconvinced that the level of WHG ancestry in Northern Europeans is more that other Europeans. It is obvious that Northern European have a stronger affinity to both East Eurasians and especially Native Americans that EHG ancestry is involved.

    Regarding the Neolithic farmers, the farmers of Germany and Hungary were LBK culture, and the ones in the Mediterranean were Cardial culture. Usually different cultures mean different genetic groups.[/QUOTE]

    Yet when compared genetically, they're remarkably similar.

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    The point is that WHG and EHG, who were quite different from each other as seen on PCA plots, and SHG who were a mix, also plotted away from the other two hunter gathers, seem to not be distinguished by the programs used by the researchers. They end up lumped together. Considering their genetic differences, and their geographical locations and genesis in different refugia, separating the two hunter gatherers should be easy.

    With Neolithic farmers, Anatolia is a large landmass, it is unreasonable that every group acquiring farming in Anatolia to be exactly the same. And as I said previously in another thread, the Neolithic package of plants and animals undergoing domestication came from different parts of the Near East. All I am saying is that Neolithic farmers were not some monolithic group from one tiny part of Anatolia.

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    1 members found this post helpful.
    You're confusing things, I'm afraid. Let's say that in Anatolia there were three groups of farmers. How does that change the fact that only the members of group "A" went into Europe, which seems to be the case? Why should the genetics of the other two groups matter?

    Plus, genetics doesn't lie. When farmers from the Danubian trail are compared to farmers from the Cardial trail, there are only minor differences.

    Unless/until new data is found reversing that conclusion, it is what it is.

    The farmers who went into Europe came from northwestern Anatolia, and so they had a bit of Iran Neo, and a bit of Levant Neo, but were mostly of "Anatolian" descent.

    The papers are all there. You really should read them. This isn't a hobby where you can be lazy.

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    Quote Originally Posted by Ozzie View Post
    The point is that WHG and EHG, who were quite different from each other as seen on PCA plots, and SHG who were a mix, also plotted away from the other two hunter gathers, seem to not be distinguished by the programs used by the researchers. They end up lumped together. Considering their genetic differences, and their geographical locations and genesis in different refugia, separating the two hunter gatherers should be easy.

    With Neolithic farmers, Anatolia is a large landmass, it is unreasonable that every group acquiring farming in Anatolia to be exactly the same. And as I said previously in another thread, the Neolithic package of plants and animals undergoing domestication came from different parts of the Near East. All I am saying is that Neolithic farmers were not some monolithic group from one tiny part of Anatolia.
    My take away from this paper (and I think the point of the paper) is that some signal from Anatolia, closely related to the Later Neolithic Anatolian Farmers, and somewhat related to CHG, entered into the areas where the various WHG, SHG (Scandinavian) and EHG lived well before the Neolithic Farmers actually brought farming to what we call Europe today (which of course was first defined by the Greeks "Europa").

    And several studies have shown the Anatolian Farmers from various sites are genetically similar (form a cluster). Yes they have some genetic variability, but still similar as evidence by the plots in the 2 papers.

    Lazaridis et al 2016 (See Figure 1)

    https://www.nature.com/articles/nature19310

    Kilinc et al 2016 (See Figure 2)
    https://www.cell.com/current-biology...822(16)30850-8

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    Quote Originally Posted by Jovialis View Post
    So now we know European HGs have Anatolian geneflow into them dating back to the Paleolithic! This is pretty big.
    Is it different from result in ice age paper that an affinity to near easterners begins with the villabruna cluster and another east asians?:

    http://abload.de/img/asgjb6.png

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    1 members found this post helpful.
    I find curious all these new papers about Europea HG's and so called "Near Eastern" input.
    1- I shall be obliged to read all this stuff less lazzily and more deeply.
    2- It's important to distinguish between more or less old affinities and new introgressions by pop's after the drifts and selection occurred after separation of common ancestors.
    3- Concerning European HG's I don't see anything amazing in the fact they share affinities with Near-Eastern or South Caucasus paleo people; all depends on the dates of the origins: the more they are ancient, the less it's surprising, for people (Sapiens) coming from Africa! If not Near-East, it would be Caucasus or Indus, as I already said.


    &: Secndarily: typology and metrics seemed to me (layman) showing southeastern inputs in Western Europe since the Late Paleolithic (in Laugerie-Chancelade BI). I know this is unsure but...? Mediated by females exchanges between western and eastern Mediterranea?

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