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Thread: "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chr"

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    "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chr"

    Similar to preceding papers on Y chromosome, a new paper by Poznik et al. provides more perspectives and resolutions of some of the big Y haplogroup lineages.

    We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
    image.jpg


    In addition to again looking at European haplogroups like I1, it has delved into South Asia also, including a look at R1a-Z93 expansion.

    In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring 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 Steppe into the Indian subcontinent 27. 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
    Link
    Unfortunately, behind a Pay-Wall
    Last edited by Gravetto-Danubian; 04-26-2016 at 02:34 AM.

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  3. #2
    J Man
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    Any news about Y-DNA haplogroup J2a from this new study?

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    Quote Originally Posted by J Man View Post
    Any news about Y-DNA haplogroup J2a from this new study?
    yes, apparently there is. But Im still trying to obtain access

    ADD: ok look at Suppl material; eg page 21 & 82
    Last edited by Gravetto-Danubian; 04-26-2016 at 02:47 AM.

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    There is a lot of information in the Supplementary Information

    http://www.nature.com/ng/journal/vao...ry-information

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    Ok so some more :

    ""First, in the Americas, we observed expansion of Q1a-M3 (Supplementary Figs. 14e and 17) at ~15 kya, the time of the ini- tial colonization of the hemisphere. This correspondence, based on one of the most thoroughly examined dates in human prehistory, attests to the suitability of the calibration we have chosen.

    Second, in sub-Saharan Africa, two independent E1b-M180 lineages expanded ~5 kya (Supplementary Fig. 14a), in a period before the numerical and geographical expansions of Bantu speakers, in whom E1b-M180 now predominates22. The presence of these lineages in non-Bantu speakers (for example, Yoruba and Esan) indicates an expansion predating the Bantu migrations, perhaps triggered by the develop- ment of ironworking.

    Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe"

    Most of the money is in Suppl data available freely
    Last edited by Gravetto-Danubian; 04-26-2016 at 02:44 AM.

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    From the paper:

    As the haplogroup expansions we report are among the most extreme yet observed in humans, we think it more likely than not that such events correspond to historical processes that have also left archaeological footprints. Therefore, in what follows, we propose links between genetic and historical or archaeological data. We caution that, especially in light of as yet imperfect calibration, these connections remain unproven. But they are testable, for example, using aDNA. First, in the Americas, we observed expansion of Q1a-M3 (Supplementary Figs. 14e and 17) at ~15 kya, the time of the initial colonization of the hemisphere21. This correspondence, based on one of the most thoroughly examined dates in human prehistory, attests to the suitability of the calibration we have chosen. Second, in sub-Saharan Africa, two independent E1b-M180 lineages expanded ~5 kya (Supplementary Fig. 14a), in a period before the numerical and geographical expansions of Bantu speakers, in whom E1b-M180 now predominates22. The presence of these lineages in non-Bantu speakers (for example, Yoruba and Esan) indicates an expansion predating the Bantu migrations, perhaps triggered by the development of ironworking23. Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe26. Potential correspondences between genetics and archeology in South and East Asia have not been investigated as extensively. In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring ~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 Steppe into the Indian subcontinent27. 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 (Supplementary Fig. 14d).

    [...]

    Present day geographical distributions provide strong support for the correspondences we proposed for the initial peopling of most of Eurasia by fully modern humans ~50–55 kya and for the first colonization of the Americas ~15 kya. For later male-specific expansions, we should consider the consequences of alternative mutation rate estimates, as pedigree-based methods relying on variation from the most recent several centuries8,10,28 may be more relevant. The pedigree-based estimate from the largest set of mutations8 would lead to a ~15% decrease in expansion times, increasing the precision of the correspondences proposed for E1b and R1a. For R1b, a 15% decrease would suggest an expansion postdating the Yamnaya migration. Using either mutation rate estimate, the lineage expansions seem to have followed innovations that may have elicited increased variance in male reproductive success29, innovations such as metallurgy, wheeled transport, or social stratification and organized warfare. In each case, privileged male lineages could undergo preferential amplification for generations. We find that rapid expansions are not confined to extraordinary circumstances30,31 and that the Y chromosome resulting from these rapid expansions can predominate on a continental scale and do so in some of the populations most studied by medical geneticists. Inferences incorporating demography may benefit from taking these male–female differences into account.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    It appears to be a follow up of the Wei, Xue, Jobling, Tyler Smith.. paper from 2013
    A calibrated human Y-chromosomal phylogeny based on resequencing

    http://www.ncbi.nlm.nih.gov/pmc/arti...9/#!po=30.8824

    This article has several quotes from the authors

    "Dr Yali Xue, lead author from the Wellcome Trust Sanger Institute, explained: "This pattern tells us that there was an explosive increase in the number of men carrying a certain type of Y chromosome, within just a few generations. We only observed this phenomenon in males, and only in a few groups of men."

    The earliest explosive increases of male numbers occurred 50,000-55,000 years ago, across Asia and Europe, and 15,000 years ago in the Americas. There were also later expansions in sub-Saharan Africa, Western Europe, South Asia and East Asia, at times between 4,000 and 8,000 years ago. The team believes the earlier population increases resulted from the first peopling by modern humans of vast continents, where plenty of resources were available.

    The later expansions are more enigmatic.

    Dr Chris Tyler-Smith, from the Sanger Institute, added: "The best explanation is that they may have resulted from advances in technology that could be controlled by small groups of men. Wheeled transport, metal working and organised warfare are all candidate explanations that can now be investigated further."

    https://www.sciencedaily.com/release...0425141808.htm
    Last edited by Heber; 04-26-2016 at 04:10 PM. Reason: Science Daily
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    The Bantu expansion, whatever the exact timeframe, seems to have not involved R-V88.
    YDNA: R1b-BY50830 Stepney, London, UK George Wood b. 1782 English <-> Bavarian cluster
    m gf YDNA: ?? Gurr, James ~1740, Smarden, Kent, England.
    m gm YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    m ggf YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    p ggf YDNA: R1b-Z17901. Gould, John Somerset England 1800s.
    p ggf YDNA: R1b-L48. Scott, William Hamilton Ireland(?) 1800s

    other:
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    Welch: early 1800s E-M84 Kent, England.

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    "Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe26"

    They seem to imply that the expansion of R1b-L11 is due to the Bell-Beaker culture in Western Europe.

    image.jpeg

    image.jpeg
    Last edited by Heber; 04-26-2016 at 05:27 PM.
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    Nothing or not much about R1a-Z283.

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