Patterns in the Y chromosome and Holocene expansion

I’ve been looking at uniparental lineages recently. That is, direct maternal and paternal lineages. The mtDNA and Y chromosomal phylogenies. Between the late 1990s and 2000s phylogenetic reconstructions of these lineages dominated historical population genetic inference.

Today with ancient DNA and genomewide SNP analysis, and now even whole-genome analysis, there isn’t nearly as much focus on Y and mtDNA. But curiously in some ways, the scaffold of autosomal ancestry through ancient DNA allows for better leveraging of the insights of Y and mtDNA patterns.

We now know that the Austro-Asiatic Munda people of northeast India are about 30% East Asian in their ancestry. But their dominant haplogroup, which connects them to East Asia, is present at 60% frequency. In contrast, their mtDNA is totally indistinguishable from their Indian neighbors.

One sees a similar dynamic among the Finnic people. These populations have high frequencies of a Siberian Y chromosomal haplogroup (~60%), which seems to have arrived within the last 3,000 years. But the mitochondrial lineages are very similar to their neighbors (though there are a few stray East Eurasian mtDNA lineages). In fact, Finns and Sami are enriched for U5, which seems to be the dominant lineage of Mesolithic hunter-gatherers. Additionally, “non-European” (East Asian-like) ancestry in Finns is around in the 5-10% range and ~20% for the Sami. This seems quite lower than the frequency of N1c, the haplogroup in question, but a reasonable hypothesis is that the men who brought N1c were already quite mixed between eastern and western ancestry.

In any case, I want to close out this post with a quote which won’t surprise closer readers, Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences:

Potential correspondences between genetics and archaeology in South and East Asia have received less investigation. In South Asia, we detect eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Figs. 14b, 14d, and 14e). The most striking are expansions within R1a-Z93, ~4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the western steppes into the Indian sub-continent27. There is a notable parallel with events in Europe, and future aDNA evidence may prove to be as informative as it has been in Europe. Finally, East Asia stands out from the rest of the Old World for its paucity of sudden expansions, perhaps reflecting a larger starting population or the coexistence of multiple prehistoric cultures wherein one lineage could rarely dominate. We observed just one notable expansion within each of the O2b-M176 and O3-M122 clades.

In First Farmers: The Origins of Agricultural Societies Peter Bellwood argues that agricultural expansions explain most of the genetic variation in the world. In Europe and South Asia, this needs to be updated and modified. Late Neolithic and Bronze Age migrations clearly had a major impact. But what about East Asia?

Japan, for one, transformed in the recent past with the assimilation of post-Jomon people into the Yayoi 2,000 years ago. And the expansion of the Han entailed recent assimilations. But, perhaps there is no “star-shape” phylogeny because these expansions were fundamentally bottom-up demographic expansions as posited by Bellwood.

18 thoughts on “Patterns in the Y chromosome and Holocene expansion

  1. How do we explain the high frequency of haplogroup I in scandinavia and and C1a, D in japan? The yamnaya and yayoi were the dominant cultures. Yet we see a high frequency of the haplogroups of the ‘losers’.

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  2. Additionally, “non-European” (East Asian-like) ancestry in Finns is around in the 1-5% range, and 5-10% for the Sami.

    That is not true. Finns proper are in the 1-10% range in East Eurasian ancestry, but generally in the 5-10% range. Some eastern Finnic populations such as Vepsians have even more East Eurasian ancestry. Saamis, on the other hand, on average have more than 20% East Eurasian ancestry, that explains the visible East Eurasian features seen in too many Saamis.

    https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1522-1

    https://docs.google.com/spreadsheets/d/1Oz6P5-SVEJciPX1TciGe-zoqA5JtOGIMG7nh-rCOj0c/edit#gid=804264822

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  3. @anonymous

    How do we explain the high frequency of haplogroup I in scandinavia and and C1a, D in japan? The yamnaya and yayoi were the dominant cultures. Yet we see a high frequency of the haplogroups of the ‘losers’.

    Sometimes losers might make a big impact on the Y-DNA haplogroups even when they have a minor impact on the autosomes. A good example is the Neolithic farmers in western and some of the other parts of Europe, they were autosomally overwhelmingly Anatolian Neolithic farmer-like, but their Y-DNA haplogroups were overwhelmingly I2, which comes from the European hunter-gatherers.

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  4. That is not true. Finns proper are in the 1-10% range in East Eurasian ancestry, but generally in the 5-10% range. Some eastern Finnic populations such as Vepsians have even more East Eurasian ancestry. Saamis, on the other hand, on average have more than 20% East Eurasian ancestry, that explains the visible East Eurasian features seen in too many Saamis.

    updated.

    Sometimes losers might make a big impact on the Y-DNA haplogroups even when they have a minor impact on the autosomes.

    I1 is star. clear some HG groups were integrated into R1 IE groups early in east-central europe. so it arrived in scand as part of the battle axe

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  5. @Razib

    I1 is star. clear some HG groups were integrated into R1 IE groups early in east-central europe. so it arrived in scand as part of the battle axe

    Yes, that is also a good example.

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  6. “the visible East Eurasian features seen in too many Saamis”
    What is the proper number of Saamis who should have visible East Asian features? 🙂

    I find it ironic that such Y-explosions are said to be rare in East Asia, when the most famous example of one such that we can trace back to a historical person is Genghis Khan.

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  7. @TGGP

    What is the proper number of Saamis who should have visible East Asian features?

    I do not like to get into the numbers when it comes to the visible features as sources too often give conflicting numbers in such cases. Still, there are also too many Saamis who have no visible East Eurasian features, but I do not know how much Saami ancestry such individuals have in their known genealogy as some people might claim to be Saami when they have non-Saami recent ancestors.

    I find it ironic that such Y-explosions are said to be rare in East Asia, when the most famous example of one such that we can trace back to a historical person is Genghis Khan.

    But that specific C2 lineage did not expand much in East Asia proper, it expanded mostly in the Mongolic lands, the Central Asian steppe and some of the adjacent areas to their north and south.

    https://images.ctfassets.net/cnu0m8re1exe/RtLz5xzw2BHi7mBCVeLHh/dfb9ebeac4d0aecee87362409ad88ad4/star2.png

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  8. Onur: You still didn’t specify in which way “too many” Saami-people look or do not look like … something?

    What I have myself seen, there are very diverse types of faces among the people who identify as Saami up there in North (Utsjoki and Finnmark, for example), and the hair colour also varies a lot.

    For example, these ladies are sisters:
    https://www.last.fm/music/Angelin+tyt%C3%B6t/+images/4db196f198234e3491c79f799217c716

    The blonde sister would pass as a standard Finn on the streets of Helsinki, while about the brunette many might start thinking from where her roots are (definitely not from Southern or Western Finland).

    https://fi.wikipedia.org/wiki/Arja_Koriseva is from a small place in “Eastern Central Finland”. Previously I thought (also because of the surname) that the family is from somewhere in Karelia, but after reading about it now, it’s not necessarily so. In any case it’s not from Lapland.

    And finally: https://www.youtube.com/watch?v=46WW3D5a_TU
    She’s from Kautokeino, Finnmark. The song is nice.

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  9. Razib: Do you know how near the modern Latvians are to Finns genetically? The Livonian people (Livs) merged with them, also bringing some Finnic vocabulary and other influences to their IE-language.
    (“Latvian is essentially Lithuanian spoken by Estonians.” See http://vrici.lojban.org/~cowan/essential.html for more jokes)

    On the other hand, we have a lots of Baltic loans in our language, and nowadays there is a strong hypothesis that even for the toponyms “Suomi” (originally meaning just the south-west corner, still called “Finland proper”) and “Häme” (the large inland province in southern and western Finland) is that they both originate from Baltic “zeme” = “land”, cognates of which can be found in Russian, and also in Persian and Avestan.

    See e.g.: https://www.academia.edu/36858309/De_Vanitate_Etymologiae._On_the_origins_of_Suomi_H%C3%A4me_S%C3%A1pmi

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  10. @A. Karhumaa

    Onur: You still didn’t specify in which way “too many” Saami-people look or do not look like … something?

    Sorry for not being specific on that. It was based on both my observations of the Saami faces and my readings on the Saami physical anthropology. Also the East Eurasian visible physical influence is mild in many cases, so I do not mean to say a strong influence in all cases.

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  11. @A.Karhumaa
    Balts have 30-40% N1c but no Siberian admixture in your average ADMIXTURE/STRUCTURE test because they had extended contact with early Finnic people who mostly lacked the Siberian ancestry from recent Saami admixture of modern Finns. I assume Livonians were similar to modern Latvians and southern Estonians.

    Saami admixture within the last 2000 years makes Finnic people living on formerly Saamic land (Finns, Karelians) easily distinguishable from southern Finnic peoples like Estonians and also from more eastern Volga Uralic people.
    See: http://www.elisanet.fi/mauri_my/pcam2h.pdf
    http://terheninenmaa.blogspot.com/2017/02/rare-alleles-show-baltic-finnic-people.html

    Latvians and Lithuanians are still quite closely related to Finns, more closely than Saamis, most Russians and any Volga-Uralic people at any rate.
    https://evolbio.ut.ee/CGgenomes_analyses/OutgroupF3/ModernSamples/ranked/ranked_f3_Finnish.pdf

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  12. Looking at “Punctuated bursts…” we’d probably infer an Upper Paleolithic continuous demographic expansion of the y in East Asia (if we reasoned from the Os being East Asian and appearing to show a funnel shaped expansion).

    But “A recent bottleneck of Y chromosome diversity coincides with a global change in culture” (the other famous paper from 2015-2016), Bayesian skyline plots tend to suggest a reduction in y diversity in East Asia at 10kya which is proportionately similar to counterparts in West Eurasia, but from a much higher base of y-dna size through Upper Paleolithic.

    How to reconcile what might be apparently different findings of these?

    Though “Punctuated bursts…” not completely in disagreement as notes that different patterns “perhaps reflecting a larger starting population (in East Asia) or the coexistence of multiple prehistoric cultures wherein one lineage could rarely dominate”.

    Maybe the difference is the Ice Age and the Mesolithic, and not so much the Neolithic or metal ages…? (E.g. East Asians from the south, where they evolved through most of Upper Paleolithic, and where populations maintained at a high level due to more stable climatic optima over large area, then experienced population increase due to invention of agriculture).

    Different sampling in each panel – note “A recent bottleneck…” uses many Agta, Aeta, to represent its East and Southeast Asian, who may be (probably are) quite atypical.

    Switching topic to ancient y-dna more generally should be very useful. It’s worth noting the current limitations of y-dna through ancient dna though:

    1) Capture based y-dna analysis of ancients, even when it has enough data, will only capture certain mutations that are ascertained on modern variation. So you may not be able to distinguish that a set of samples are all on a subclade that no longer exists of a particular y tree. You may not be able to distinguish between a sample that is basal on tree for a mutation that happened at 14kya or whether it is immediately imminent to an actual star expansion 10kya later. Particularly a problem with star-expansions that replaced majority of close relatives.

    2) Y-dna is still susceptible to founder effects. You may find a group with 80% Y1, 20% Y2, and another with 100% Y1… but actually these groups may have gone through the same process of formation and diverged due to a smaller population size and subsequent expansion of Y1 in the latter set.

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  13. @first comment anonymous, another example of interest is within Sardinia there is star-like expansion under I2a1a1, calibrated to occur at about the same time as the R1b-M269 Western European expansion – https://science.sciencemag.org/content/341/6145/565/tab-figures-data

    Accordingly in Marcus’s 2019 biorxiv preprint this subclade first make an appearance about this time (though their sample set older than this is *fairly* limited) – https://www.biorxiv.org/content/10.1101/583104v1.full

    (No R1b-M269 in ancient Sardinia through 4000-1000 BCE… but plenty of “R1b-V88” that is found in neolithic SW Europe with basal subclades and also appears to undergo its own star expansion in the Sahara).

    I still suspect it may be possible that in regions which look like they have continuous old growth there may be true patterns of old growth+more localized star-like expansions during Bronze Age+lots of admixture following classical era empires which obscures the pattern. Not sure if this is totally investigated yet or not.

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  14. @ Matt: “Though “Punctuated bursts…” not completely in disagreement as notes that different patterns “perhaps reflecting a larger starting population (in East Asia) or the coexistence of multiple prehistoric cultures wherein one lineage could rarely dominate”.

    Isn’t this argument about East Eurasians having a large starting population contradicted by the fact that they are also more inbred than West Eurasians?

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  15. @Mick, that is an solid point; the autosomal dna does not show a pattern of long term larger populations size in East Asia. There’s also a contradition of mtdna, which again does seem to show larger long term population size in East Asia with more basal diversity. The only way I can square these is that autosomal diversity in West Eurasian must have been preserved in structured different groups who ultimately did not contribute as much on mtdna / y-dna side?

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  16. Isn’t this argument about East Eurasians having a large starting population contradicted by the fact that they are also more inbred than West Eurasians?

    this is due to a bottleneck outside of africa. it isn’t due to long-term inbreeding.

    fwiw, i think east asia had a larger Ne than much of northwest eurasia during the holocene beacuse east asia in general had more ‘fall-back’ zones for retreating megafauna.

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  17. East Asia shows a clear pattern of a rapid expansion from a very limited number of population centers. So the difference between Europe and East Asia is that Europe was re-populated by different populations. One by one, they were not much more diverse, but the East Asian main population replaced most of the other groups living in East and South East Asia before. In Europe both Neolithics and steppe people were mixtures already and incorporated additional hunter gatherer ancestry.
    East Asians are like one two way admixture (Northern, core Mongoloid and Southern population) with little other admixture.

    The river populations of the Yellow and Yangtze river were presumably fairly large and diverse before starting to move South and there was additional backflow. But the sheer power and numbers of the river populations overwhelmed the much smaller groups further South. This resulted in a fairly homogeneous genetic landscape in East Asia because with every wave (only mentioning the known ones from prehistoric-historic eras here like Austro-Asiatic, Tai-Kadai, Sino-Tibetan, Old Chinese) the river populations dominance was increased and East Asia homogenised.

    The pre-LGM and pre-expansion genetic landscape was for sure much different and the whole macro-region more diverse.

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  18. Another difference to Europe was, that the fairly large late forager populations of the major river habitats adopted new technologies successfully by themselves with little population replacement. It seems fairly large communities with a clear common base, so relatively homogenous, but not small, adopted new innovations. These already bigger and fairly homogeneous groups moved Southward, instead of like with the European Neolithics or steppe people, which seems to have been really small groups initially which adopted a new way of life and expanded drastically from this small starting point.

    Also, if they write:
    “We observed just one notable expansion within each of the O2b-M176 and O3-M122 clades.”

    By distribution and frequency, it parallels the expansions of R1a+b, so one cannot speak of a drastically different picture in East Asia at all. We can hope for ancient DNA to make things clear and reconstruct what really happened. Because one thing is for sure, its no one way expansion North, definitely not.

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