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Haplogroup_R1b_(Y-DNA)

Sometimes results precede an appropriate interpretative framework. I am beginning to think that that was the case with the explosion in analysis of Y and mtDNA phylogenies around the year 2000. This was a research program which took the direct male (Y) and female (mtDNA) lineages of humans, inferred a phylogenetic tree, and drew historical and demographic inferences. Part of the reason that this research program flourished is that these lineages are easy to model as a tree, because there isn’t recombination and sex on these lineages. The genealogy of these markers is actually a straightforward tree. And, in the case of mtDNA it is copious, so extraction was and is relatively easy.

The_Journey_of_Man_-_A_Genetic_Odyssey This period not only resulted in an explosion of research, but also several seminal popularizations, in particular Spencer Wells’ Journey of Man, Bryan Sykes’ Seven Daughters of Eve, and Steve Olson’s Mapping Human History. The way this method worked involved taking the distributions and diversity of particular Y and mtDNA lineages present in the world today, and inferring back to the past routes of human expansions assuming that the tree-like model of genetic fission reflected a serial founder process of human migration. On the largest scale this work did confirm and extend previous research which implied a dominant signal “Out of Africa,” as well as broad geographic racial clusters. But on a finer scale the method likely led us astray, in large part because it seems that the model of human expansion and diversification was just too simple. Empirically, the rise of whole-genome analysis via SNP-chips in the middle years of the 2000s and today ancient DNA has revolutionized and clarified our understanding of the human past. Many of the inferences made from Y and mtDNA turn out to be wrong, even if the original results are broadly robust.

And that is a key point, because the original Y and mtDNA results are correct, and there has been an enormous body of research already in this area, they can be leveraged in understanding the human past when slotted into the framework sculpted on the edges by autosomal SNP data and ancient DNA. A serial founder model where the tree-like phylogeny was recapitulated spatially and temporally always had “anomalies.” In light of new results those anomalies may actually make much more sense. In particular, the common lineages which span Sub-Saharan Africa and western Eurasia (e.g., R1b above) are less perplexing in light of a model of periodic Eurasian back migration after the initial Out of Africa event. Admixture between long distinct lineages resolves issues relating to haplogroups with discordant geographic distributions. As long a the results are correct and methodologically sound, more data is better.

 
• Category: Science • Tags: Historical Population Genetics 
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  1. ohwilleke says: • Website

    1. One kind of study that is striking for its absence (since it has been possible for a long time now), is a study the tries to meaningfully correlate data about the coincidence of language, religion/ethnicity, geography, Y-DNA haplogroups, mtDNA haplogroups, informative markers such as those for pigment and lactose persistance and blood type, and other autosomal data from the same individual into a picture correlated at the individual by individual level, rather than looking at total distributions of each separately at the population level and looking for correlations that way. Multi-dimensional cluster analysis ought to be able to leverage more information out of the data if each data point was linked with all relevant data.

    2(a). I was familiar with the outlier R1b population in Africa, mostly speakers of the Chadic language family, mostly Sahel pastoralists who have converted to Islam, with a smattering in Northeastern Fulani community (a Niger-Congo linguistic group at the fringe of the Niger-Congo range to the immediate south). This is overwhelmingly of the R1b-V88 subhaplogroup, a very basil branch of the R1b clade relative to the European clades that diversify in a star-like manner much more recently. This migration can be dated quite precisely because the archaeology very strongly points to a specific time and place at which the Chadic people came into being (making it a nice archaeological calibration point of mutation rates). Tishkoff (in a paper I have a hyperlink to that has gone bad) states:

    “A proposed migration of proto-Chadic Afroasiatic speakers ~7,000 ya [5000 B.C.E.] from the central Sahara into the Lake Chad Basin may have caused many western Nilo-Saharans to shift to Chadic languages. Our data suggest that this shift was not accompanied by large amounts of Afroasiatic gene flow. Analyses of mtDNA provide evidence for divergence ~8,000 ya [6,000 B.C.E.] of a distinct mtDNA lineage present at high frequency in the Chadic populations and suggest an East African origin for most mtDNA lineages in these populations.”

    2(b). I was not aware of the cluster of R1b in the mid-Urals of Russia which appears to be some combination of Bashkir people and Komi people. The Bashkir people are Sunni Muslim people who speak a language in the Turkic family and had an ethnogenesis in the early Middle Ages that may have also incorporated people who previously spoke languages in the same macrolanguage family as Finnish (i.e. Uralic) who were probably close kin of the modern Komi people. The Komi people speak a Uralic language and are located nearby.

    One would not expect R1b in people who spoke a Turkic language (a language family with roots in the Altai Mountains until the historic era that was followed by an expansion of the nearby Mongolian people where R1b is rare). But, apparently, they made their way to their current home via the Danubian Plain and Southern Urals, and picked up R1b on the way. Founder effects in one or more of the seven clans of this people (probably organized patrilineally) probably account for the exaggerated R1b fractions in the Northern Ural Bashkirs relative to their source populations in this thinly populated area.

    2(c). In Europe, most R1b appears to have arrived when an Eastern R1b population migrated there and expanded out of Iberia to most of the current range, although the source and route are unclear. The best fit to the archaeological culture that was the source of that rapid Western European expansion in light of ancient DNA appears to be the Bell Beaker culture in the Copper Age (a people whose language family was shared with modern day Basque and has left a substrate in subsequent Indo-European languages such as words for base twenty numbers), although this isn’t universally accepted. The Bell Beaker archaeological range and the R1b distribution in Europe are very similar and the timing is right in light of ancient DNA data — older farmers tend to be Y-DNA haplogroup G; older hunter-gatherers tend to be Y-DNA haplogroup I. The Y-DNA mix of Europe in ancient DNA is pretty stable from that point onward.

    Increasingly, it looks like the Bell Beaker genetic source stock (at least for men) was somewhere South of the Black and/or Caspian Sea and the Caucasus mountains, but no further south than the Northern Fertile Crescent and the Iranian highlands. There are many similarities in ancient Minoan DNA and the Minoans probably made their way to Crete from Anatolia. The Bell Beaker people were known for the pottery (obviously), their metalworking, and their archery. Northern migrants of this culture acquired lactose tolerance and then back migrated to modern Basque Country.

    This culture maintained a more or less unchanging border with the Indo-European Corded Ware affiliated people to the east of them within Europe (a predominantly Y-DNA R1a people that exploded demographically at the same time with similar technologies) for about 1,000 years, although the Western R1b side collapsed and was eventually overrun by Indo-Europeans (especially Celts and linguistically Germanic people) ca. 1300 BCE.

    2(d). The ultimate source of the most basal branches of R1a, R1b and R2 extant today appears to have been in Iran, although the diversification of the various branches happened elsewhere to a great extent.

    2(e). I recall reading somewhere in the last few days that a division of R1 that is a sister branch to R1a and R1b with equal footing that was recently discovered in Bhutan.

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  2. Kosmatka says:

    I see the Udmurts are popping out again, north and east of the Caspian Sea. (An island of redheads in a sea of brunettes)

    I’d wondered if the Udmurts’ were actually connected to more western populations, or if they’d simply derived their unusual hair color frequencies locally through some parallel process, but this seems to seal the matter.

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  3. Ebizur says:

    Kosmatka,

    The blob of high R1b frequency in that area should be ascribable to the Bashkirs, a Turkic-speaking people, and not to the Permic-speaking Udmurts. The Udmurts instead have been noted for their exhibiting Y-DNA haplogroup N with extremely high frequency.

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  4. Kosmatka says:

    Ebizur, I’ll have to bow to your superior knowledge of haplogroup frequencies on this one. The R1B map had reminded me of this map I’d seen or red hair, with the Udmurts being the center of the outliar population in question. That’s an interesting coincidence then that both maps put an odd eastern bullseye in roughly the same place, but with apparently different populations.

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    • Replies: @Shaikorth
    Udmurts and Bashkirs live right next to each other, and both have peculiarities (high frequency of red hair and R1b respectively) but little genetic overlap, so their distinctive qualities are most likely unrelated.

    Yunusbayev et al in their pre-print "The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia" had quite a bit of populations from that area in their ADMIXTURE run. Udmurts at no point show the South China-centric component that appears at K=3 or the Buryat-Mongol centric orange component appearing at K=9. Bashkirs show both and these could be taken as some sort of indicator of Turkic expansion in West and Central Eurasia.

    http://biorxiv.org/content/biorxiv/suppl/2014/08/13/005850.DC2/005850-1.pdf
  5. Shaikorth says:
    @Kosmatka
    Ebizur, I'll have to bow to your superior knowledge of haplogroup frequencies on this one. The R1B map had reminded me of this map I'd seen or red hair, with the Udmurts being the center of the outliar population in question. That's an interesting coincidence then that both maps put an odd eastern bullseye in roughly the same place, but with apparently different populations. https://4.bp.blogspot.com/-yoWjfATvC5g/VGIW8hocYEI/AAAAAAAAazk/LbYbMueR7Yg/s1600/redmap.png

    Udmurts and Bashkirs live right next to each other, and both have peculiarities (high frequency of red hair and R1b respectively) but little genetic overlap, so their distinctive qualities are most likely unrelated.

    Yunusbayev et al in their pre-print “The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia” had quite a bit of populations from that area in their ADMIXTURE run. Udmurts at no point show the South China-centric component that appears at K=3 or the Buryat-Mongol centric orange component appearing at K=9. Bashkirs show both and these could be taken as some sort of indicator of Turkic expansion in West and Central Eurasia.

    http://biorxiv.org/content/biorxiv/suppl/2014/08/13/005850.DC2/005850-1.pdf

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  6. Anonymous says: • Disclaimer

    L23′s highest diversity is in Romania, then Bulgaria. It is less than 6300 years old. Too young for any migrations from West Asia, but fits Cernavoda. The expansion of Pontic Kurgans into the Balkans. And a good lead to Ezero, and Troy as an introduction of L23 into Anatolia.

    Basal R1b is not found in Iran. It is found in Central Asia. As well as much more M-335, that was once thought to only be in Anatolia. It is an obvious transplant by Central Asian Turks, as is the M-73 in Turkey. M-343 is most common in Kazakhstan. You will not find a migration out of Anatolia or Iran/Caucasus to match the ages of R1b subclades.

    Descendants of Cernavoda, in Ezero and Cotafeni did not reach the Carpathian basin before 3000 BCE. Getting to Iberia in less than two-hundred years?… Very, very doubtful. Beakers and R1b were not dominated by Corded Ware. It was Bell Beaker that went in and took over most of the area. It expanded clear into Belarus and down the Adriatic. Hardly a conquered people. Those Indo-European cultures of later years, are dominated by R1b. Why would a people that did the dominating and moving around, also introduced Bronze to Corded Ware, be inferior? It makes more sense that R1b was always Centum speaking. Proto-Celtic dates to 3000BCE. A perfect time for a launching time out of the Carpathian Basin. It sure as hell wasn’t Corded Ware there, but descendants of Cotafeni and Ezero.

    The ANE and WHG in BR1, in Hungary, excludes West Asia as a source of R1b. It’s over a 20% increase in WHG, with 12%ANE. Doesn’t sound very Neolithic or West Asian. Bell Beaker doesn’t have West Asian and Caucasus mtDNA, but Corded does. R1b was either too far North, or in Ukraine, already mixed with Balkan Neolithic peoples, avoiding West Asian mixture.

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  7. Plenty of speculation on R1b. Looking at very extensive HLA haplotype data [n= >10,000,000], the data suggests that all regions characterised by notable R1b Y DNA frequencies today [all clades], coincidentally appear to have experienced gene flow from Northern Africa &/or West Asia within the last 20kya. These HLA haplotypes found at high frequency in high R1b populations reach peak frequencies and diversities within N.Afr/W.Asia and nowhere else. While in Iberia, Caucasus, Urals, etc. the haplotypes are in very strong linkage dis-equilibrium indicating more recent entry. My money is on R1b origins in the Nile Valley or proximal regions. I realise that the majority of people will strongly disagree with my opinion. I say give it another few years and let’s see,

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  8. ohwilleke says: • Website

    @5

    “Udmurts and Bashkirs live right next to each other, and both have peculiarities (high frequency of red hair and R1b respectively) but little genetic overlap, so their distinctive qualities are most likely unrelated.”

    Unrelated perhaps, but probably not coincidental precisely either. Mountains tend to be genetic sinks that act as refuges for relict populations that get wiped out in less hostile terrain. Both the Udmurts and Bashkir communities probably ended up surviving in a remote part of the Ural Mountains while not in surrounding areas for this reason.

    Red hair might be from a Finnish migration which would be unlikely to bring much R1b.

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  9. Ebizur says:

    ohwilleke wrote,

    “Red hair might be from a Finnish migration which would be unlikely to bring much R1b.”

    The Permians (i.e. Udmurts and Komis) vie with the Finns of Finland for the maximal frequency of Y-DNA haplogroup N in Europe and pretty much in the world except perhaps the Northern Samoyeds and the Siberian Turkic-speaking Yakuts (cf. Tambets et al. 2004, Mirabal et al. 2009).

    However, the portion of the Y-chromosome gene pool that does not belong to haplogroup N differs between the Permians and the Finns; the remainder of the former being mostly R1a, and the remainder of the latter being mostly I1. Of course, some R1a (and R1b) has been found among Finns, and some I (and R1b) has been found among Permians, but the difference is quite stark. The Y-DNA pool of the Permians can effectively be summarized as N + R1a, whereas the Y-DNA pool of the Finns can be summarized as N + I1. Any hypothesis of a migration from Finland to Bjarmaland (Permia) needs to explain why the modern Finns have so much I1 whereas the modern Permians have so much R1a. Is it really ascribable to mere Swedish (or other Germanic) influence in Finland and Russian (or other Balto-Slavic or even other satem Indo-European) influence in Bjarmaland subsequent to a prehistoric migration of people from Finland to Bjarmaland or vice versa?

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  10. Shaikorth says:

    Bjarmaland is associated with the southern coast of the White Sea and regions of modern Archangelsk Oblast, the Permians there were most likely Komi-related. Udmurts live in the the Volga-Kama region and any Baltic Finnic influence there is unlikely. It’s actually visible from the graphic I linked too, as components are differentiated Udmurts’ result overlaps more with Russians and Mordvins than with Karelians and Vepsians who belong to the Baltic Finnic group alongside Finns of Finland, and Udmurts also share the minor West Asian component with IE-speaking Europeans when it is present.

    The red hair could just be a founder effect though, its distribution in Eastern Europe outside Udmurts doesn’t follow ethnolinguistic borders.

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  11. Ebizur says:

    I have used “Bjarmaland”/”Permia” as shorthand for the unwieldy “homeland of the speakers of the proto-Permic language, i.e. the territory inhabited by the most recent common ethnolinguistic ancestors of the modern Udmurts and Komis,” which may or may not overlap to any degree with the historical Bjarmaland. I apologize if this has caused any confusion.

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