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Thread: Early replacement of West Eurasian male Y chromosomes from the east

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    Early replacement of West Eurasian male Y chromosomes from the east

    interesting paper

    https://www.biorxiv.org/content/10.1101/867317v1

    Abstract

    The genomes of humans outside Africa originated almost entirely from a single migration out ~50,000-60,000 years ago1,2, followed closely by mixture with Neanderthals contributing ~2% to all non-Africans3,4. However, the details of this initial migration remain poorly-understood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movements/reshaping5. One locus, however, does retain extensive information from this early period: the Y-chromosome, where a detailed calibrated phylogeny has been constructed6. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations6,7. We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model8,9, and thus informing and constraining models of the initial expansion.
    Fathers mtdna T2b17
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    Sons mtdna K1a4o
    Mum paternal line R1b-S8172
    Grandmum paternal side I1d1-P109
    Wife paternal line R1a-Z282

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    So out of Africa into East Asia, then westward wiping out/replacing all Y-lineages on their path and then much later into Europe? Am I understanding this right?
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    1 members found this post helpful.
    We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants).
    The first human group which migrated out of Africa carried Y-DNA haplogroups C and D. But hg F is a descendant haplogroup of CF and it emerged outside Africa out of the C branch, which occurred after the first human migration out of Africa. Most West Eurasian haplogroups are from its direct descendant haplogroup GHIJK, which came into existence 50,000-55,000 years ago possibly in Asia.

    Haplogroup C historically existed in Europe and a medieval Italian sample (R1285) had C1a2a1 (Antonio et al. 2019). But haplogroup D may have never entered Europe, which can be found only in Tibet and Japan in East Asia today. Interestingly, Haber et al. (2019) discovered haplogroup D0 in Nigeria, meaning that all Asian D subclades are its descendants.

    Present-day humans outside Africa descend mainly from a single expansion out ∼50,000–70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000–100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300–81,000 years ago (latest date for FT lineage expansion outside Africa – earliest date for the D/D0 lineage split inside Africa), and most likely 50,300–59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.
    https://www.genetics.org/content/212/4/1421
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    Quote Originally Posted by ThirdTerm View Post
    The first human group which migrated out of Africa carried Y-DNA haplogroups C and D. But hg F is a descendant haplogroup of CF and it emerged outside Africa out of the C branch, which occurred after the first human migration out of Africa. Most West Eurasian haplogroups are from its direct descendant haplogroup GHIJK, which came into existence 50,000-55,000 years ago possibly in Asia.

    Haplogroup C historically existed in Europe and a medieval Italian sample (R1285) had C1a2a1 (Antonio et al. 2019). But haplogroup D may have never entered Europe, which can be found only in Tibet and Japan in East Asia today. Interestingly, Haber et al. (2019) discovered haplogroup D0 in Nigeria, meaning that all Asian D subclades are its descendants.

    that is correct that D never made it to europe
    in east asia D was found in some remains not so old but
    still

    https://i.imgur.com/GMlwQRn.png

    https://i.imgur.com/IaSN03b.png

    and the Japanese branch is damn old :)

    Recently it was confirmed that the Japanese branch of haplogroup D-M55 is distinct and isolated from other D-branches since more than 53,000 years. The split between D1a probably happened in Central Asia, while some others suggest a instant split during the origin of haplogroup D itself, as the Japanese branch has five unique mutations not found in any other D-branch.[42]

    source : https://link.springer.com/article/10...439-017-1800-0
    Last edited by kingjohn; 07-12-19 at 17:30.

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    Quote Originally Posted by ThirdTerm View Post
    The first human group which migrated out of Africa carried Y-DNA haplogroups C and D. But hg F is a descendant haplogroup of CF and it emerged outside Africa out of the C branch, which occurred after the first human migration out of Africa.
    Perhaps my information is out of date, but I thought hg F was a descendant of CF, not C, and that C and F were sibling clades. Not a big point, but since CF is only inferred can we be certain it is an out-of-Africa haplogroup?

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    Quote Originally Posted by [email protected] View Post
    Perhaps my information is out of date, but I thought hg F was a descendant of CF, not C, and that C and F were sibling clades. Not a big point, but since CF is only inferred can we be certain it is an out-of-Africa haplogroup?

    it goes DE and CF groups
    then C and F split
    F becomes GHIJK

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    1 members found this post helpful.
    buttom line Y haplogroups : A,B, E
    are the only ones who stayed in africa
    ....
    than
    in Mesolithic we see some E branch in natufians levant
    and in the neolithic a branch of E - M78-L618 made it to europe

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    Then what haplogroups would've every male outside of East or Southeast Asia belonged to before 50-55kya? The study seems to argue C, D and F (FT) all arose there, so what remains for all the rest of the primeval out-of-Africa population? If E is supposedly African, and C, D and F arose in the same one region in East Eurasia, then, well, every other lineage arose, expanded and then just disappeared? AFAIK all even oldest aDNA samples belonged to one of those haplogroups (C, D or F), no surprises there. The replacement must've been pretty dramatic and (historically) fast then.

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    I agree with the out of Asia model. I don't think widespread replacement of humans from the east was probable. It's more probable that a small band of modern humans made it out of Africa and went to SE Asia without stopping. Previous and subsequent pulses out of Africa didn't survive, probably due to competition with Neanderthals. The surviving band of humans had contact with them, shown by early admixture. The resulting combo of them were able to survive, but perhaps the reason they moved on to SE Asia was to get out of competition territory of Neanderthals, putting modern humans back into the equatorial zone in which we evolved but Neanderthals were not adapted for.

    I don't think it's a random chance that modern humans were around for 100k years before expanding. Their advance was checked by a force they were unable to overcome. Once a way was found to push the Neanderthals, they were slowly erased from existence. The Neanderthal rollback would be the Y lineage being replaced, rather than humans replacing humans.

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    It makes a lot of sense that humans emerging from Africa would initially expand far faster along the band of climate that they were familiar with, i.e. east through south Asia. I wonder if some minority went north a bit, becoming the Basal Eurasians?

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    Quote Originally Posted by Gnarl View Post
    It makes a lot of sense that humans emerging from Africa would initially expand far faster along the band of climate that they were familiar with, i.e. east through south Asia. I wonder if some minority went north a bit, becoming the Basal Eurasians?
    check this site out ..............they also deal with the asiatic Denisovans

    https://www.eva.mpg.de/genetics/nean...Fsize=0Frickel

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    Quote Originally Posted by Gnarl View Post
    It makes a lot of sense that humans emerging from Africa would initially expand far faster along the band of climate that they were familiar with, i.e. east through south Asia. I wonder if some minority went north a bit, becoming the Basal Eurasians?
    Unlikely as Basal Eurasians never mixed with Neanderthals. I'd rather think Basal Eurasians stayed in the Arabian Peninsula and/or southern Iran whereas other groups moved further to South Asia or even as far as Southeast Asia. But I find that difficult to reconcile with the idea that all the Y-DNA lineages found in all of Eurasia would come only from those who went to S-SE Asia, when the impact of BE ancestry was so large in the Paleolithic and Mesolithic West Eurasia. No trace at all of their paternal lineages? That'd be a bit surprising.

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    There is one sample of IJ* in the world per the FTDNA tree (none on YFull).

    It's in Sri Lanka.

    A look at H distribution is also a clue. Besides H-P96 which came to Europe (tmrca 16,000), it's widespread in India/Pakistan, Sri Lanka, Bangladesh, Nepal, and some in the middle east.

    Haplo G is not really relevant because it's like I-M253, a one lineage survivor of a much older lineage. There's not enough info due to lack of relevant time info. The one surviving lineage was probably in the Caucasus but we have no info prior.

    L is in the far east and middle east but has a 20k year gap in SNP tmrca.

    T is similar. An old formation but a 20k year gap.

    P* sample is from the Andaman islands.


    Once again I think the authors have it right.

    1. Small pulse out of Africa
    2. That small pulse populated the entire rest of the world from SE Asia
    3. There was subsequent back and forth with Africa such as exit of E-V13 and intro of R1b-V88

    There could have been a small pocket of basal Eurasian but that probably isn't a good descriptive term because they were not basal to existing groups to the east. They were probably a different pulse out of Africa. If so, they were wiped out prior to the expansion from the east or were completely erased by it. I doubt that a hunter/gatherer culture wiped any human populations out, just my opinion.

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    Quote Originally Posted by I1a3_Young View Post
    There is one sample of IJ* in the world per the FTDNA tree (none on YFull).

    It's in Sri Lanka.

    A look at H distribution is also a clue. Besides H-P96 which came to Europe (tmrca 16,000), it's widespread in India/Pakistan, Sri Lanka, Bangladesh, Nepal, and some in the middle east.

    Haplo G is not really relevant because it's like I-M253, a one lineage survivor of a much older lineage. There's not enough info due to lack of relevant time info. The one surviving lineage was probably in the Caucasus but we have no info prior.

    L is in the far east and middle east but has a 20k year gap in SNP tmrca.

    T is similar. An old formation but a 20k year gap.

    P* sample is from the Andaman islands.


    Once again I think the authors have it right.

    1. Small pulse out of Africa
    2. That small pulse populated the entire rest of the world from SE Asia
    3. There was subsequent back and forth with Africa such as exit of E-V13 and intro of R1b-V88

    There could have been a small pocket of basal Eurasian but that probably isn't a good descriptive term because they were not basal to existing groups to the east. They were probably a different pulse out of Africa. If so, they were wiped out prior to the expansion from the east or were completely erased by it. I doubt that a hunter/gatherer culture wiped any human populations out, just my opinion.

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    Also the only modern sample of F on YFull is in China with a very old formation and tmrca.

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    2 members found this post helpful.
    Quote Originally Posted by I1a3_Young View Post
    There is one sample of IJ* in the world per the FTDNA tree (none on YFull).

    It's in Sri Lanka.

    A look at H distribution is also a clue. Besides H-P96 which came to Europe (tmrca 16,000), it's widespread in India/Pakistan, Sri Lanka, Bangladesh, Nepal, and some in the middle east.

    Haplo G is not really relevant because it's like I-M253, a one lineage survivor of a much older lineage. There's not enough info due to lack of relevant time info. The one surviving lineage was probably in the Caucasus but we have no info prior.

    L is in the far east and middle east but has a 20k year gap in SNP tmrca.

    T is similar. An old formation but a 20k year gap.

    P* sample is from the Andaman islands.


    Once again I think the authors have it right.

    1. Small pulse out of Africa
    2. That small pulse populated the entire rest of the world from SE Asia
    3. There was subsequent back and forth with Africa such as exit of E-V13 and intro of R1b-V88

    There could have been a small pocket of basal Eurasian but that probably isn't a good descriptive term because they were not basal to existing groups to the east. They were probably a different pulse out of Africa. If so, they were wiped out prior to the expansion from the east or were completely erased by it. I doubt that a hunter/gatherer culture wiped any human populations out, just my opinion.

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    there is IJ* in 32 ka Vestonice, the Sri Lanka sample, it is very odd

    indeed H2 is a split off from H in India, just like G, a one lineage survivor of a much older lineage.
    I wouldn't be surprised if G also originated in India.

    IMO the main expansion happened from India/Pakistan, not the far east

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    Check this out:
    https://www.livescience.com/10340-lo...sian-gulf.html
    https://www.ancient-origins.net/huma...-forced-021390

    I have posted some of this before but unreadable due to a big mistake: What arguments exist for basal eurasians not to be this population of the Persian gulf/oasis surrounded by deserts and isolated from Neanderthals, (Neanderthals only reached the headwaters of the tiger and euphrates rivers), which perhaps even reduced to slavery where they sought refuge in Iran, Levant and Egypt, (archaic agriculture and grinding require a lot of labor and are very painful ), saw their y chromosomes replaced (or almost replaced) by those of the already settled populations there , as is normally the case for disadvantaged populations. The origin of agriculture in the Persian Gulf with a radiation to the Levant populations independent of radiation to the Iran populations may explain both being farmers without having mixed their genes.This Persian gulf population may also help explain some of the questions that still remain about the initial diversification of human haplogroups. The Bible states that the garden of Eden was in Mesopotamia, phaps this prolongation by the gulf was the truly paradisiacal part.

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    Quote Originally Posted by bicicleur View Post
    there is IJ* in 32 ka Vestonice, the Sri Lanka sample, it is very odd

    indeed H2 is a split off from H in India, just like G, a one lineage survivor of a much older lineage.
    I wouldn't be surprised if G also originated in India.

    IMO the main expansion happened from India/Pakistan, not the far east
    It also strikes me as more likely that what happened is that virtually all non-Africans, except BE, migrated very switfly through the coast of Arabia and from the Levant to the Gulf, leaving few people along the way, and through the Iranian coast they reached South Asia and started to thrive there. It would also make sense of the early division between West Eurasians and East Eurasians, since South Asia is just to the south of a massive barrier dividing West Eurasia from East Eurasia. It'd make sense people split by moving northwestward and northeastward from there.

    Moreiver, I have sometimes wondered if the very big gap between the origin of G and its TMRCA could be a signal of the Basal Eurasians, having separated early from the other non-Africans. It's basically restricted to where BE made a difference in the local gene pool beginning even before the LGM. Or is its dating to 48.5 ybp too late for that possibility?

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    2 members found this post helpful.
    Quote Originally Posted by jose luis View Post
    Check this out:
    https://www.livescience.com/10340-lo...sian-gulf.html
    https://www.ancient-origins.net/huma...-forced-021390

    I have posted some of this before but unreadable due to a big mistake: What arguments exist for basal eurasians not to be this population of the Persian gulf/oasis surrounded by deserts and isolated from Neanderthals, (Neanderthals only reached the headwaters of the tiger and euphrates rivers), which perhaps even reduced to slavery where they sought refuge in Iran, Levant and Egypt, (archaic agriculture and grinding require a lot of labor and are very painful ), saw their y chromosomes replaced (or almost replaced) by those of the already settled populations there , as is normally the case for disadvantaged populations. The origin of agriculture in the Persian Gulf with a radiation to the Levant populations independent of radiation to the Iran populations may explain both being farmers without having mixed their genes.This Persian gulf population may also help explain some of the questions that still remain about the initial diversification of human haplogroups. The Bible states that the garden of Eden was in Mesopotamia, phaps this prolongation by the gulf was the truly paradisiacal part.
    As far as I know the Persian Gulf region, including even Sumer, was a surprising latecomer in the practice of agriculture (at least in an intensive way) in the Middle East, well after evidences of agriculture appear in the Levant, Anatolia and Iran (and even parts of Europe, South Asia and the Caucasus).

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    1 members found this post helpful.
    Ancient DNA confirm human paternal roots in Asia

    https://www.biorxiv.org/content/10.1...042v1.abstract



    Analyses of Y chromosome variations of extant people have resulted in two models for the paternal phylogenetic tree of modern humans with roots either in Africa or East Asia. These two trees are differentiated mainly by when and where their mega-haplogroups branched apart. This paper examines previously published Y chromosome sequencing data of 17 ancient samples to compare these two competing models. As ancient samples have had less time to evolve, they are expected to have mutated in some, but not all, of the sites that define present day haplogroups to which they belong. Indeed, most of the ancient DNAs here showed that expected pattern for both the terminal and the basal haplogroups to which they belong, all of the ones which are non-controversial or considered real by both of the two competing models followed that pattern. However, for basal haplogroups not shared by the two models, such expected pattern could be observed only if the haplogroups specific to the Asia rather than the Africa model are real, including ABCDE, ABDE, AB, A00-A1b. Another important point is that, if the mega-haplogroups of the Africa model were real, including BT, CT, CF and F, it would mean that numerous alleles would be shared between these haplogroups and several ancient A1b1b2 samples, which is unexpected and unseen in present day samples. Sharing alleles like this would also violate the infinite site assumption that makes the Africa rooting possible in the first place. Therefore, the data from ancient Y chromosomes confirm the actual existence of the haplogroups specific to the Asia model.

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