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Thread: Massive new paper from Allenthoft and Willerslev

  1. #1
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    Massive new paper from Allenthoft and Willerslev

    Population Genomics of Stone Age Eurasia

    Allenthoft & Willerslev et. al. 2022, Biorxiv.

    Abstract:
    The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.
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  3. #2
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    Excerpts:
    Our study comprises the largest genomic dataset on European hunter-gatherers to date, including
    329 113 imputed hunter-gatherer genomes of which 79 were sequenced in this study. Among them, we
    330 report a 0.83X genome of an Upper Palaeolithic (UP) skeleton from Kotias Klde Cave in Georgia,
    331 Caucasus (NEO283), directly dated to 26,052 - 25,323 cal BP (95%)
    . In the PCA of all non-African
    332 individuals, it occupies a position distinct from other previously sequenced UP individuals, shifted
    333 towards west Eurasians along PC1 (Supplementary Note 3d). Using admixture graph modelling, we
    334 find that this Caucasus UP lineage derives from a mixture of predominantly West Eurasian UP
    335 hunter-gatherer ancestry (76%) with ~24% contribution from a “basal Eurasian” ghost population,
    first observed in West Asian Neolithic individuals29 336 (Extended Data Fig. 5A).
    Models attempting to
    337 reconstruct major post-LGM clusters such as European hunter-gatherers and Anatolian farmers
    338 without contributions from this Caucasus UP lineage provided poor admixture graph fits or were
    339 rejected in qpAdm analyses (Extended Data Fig. 5B,C). These results thus suggest a central role of
    340 the descendants related to this Caucasus UP lineage in the formation of later West Eurasian
    341 populations, consistent with recent genetic data from the nearby Dzudzuana Cave, also in
    Georgia30 342
    .
    We replicate previous results of broadscale genetic structure correlated to geography in European hunter-gatherers after the LGM17 347 , while
    348 also revealing novel insights into their fine-scale structure. Ancestry related to southern European
    349 hunter-gatherers (source: Italy_15000BP_9000 BP) predominates in western Europe.
    This includes
    350 Denmark, where our 28 sequenced and imputed hunter-gatherer genomes derive almost exclusively
    351 from this cluster, with remarkable homogeneity across a 5,000 year transect (Fig. 3A). In contrast,
    352 hunter-gatherer individuals from the eastern and far northern reaches of Europe show the highest
    353 proportions of Russian hunter-gatherer ancestry (source: RussiaNW_11000BP_8000BP; Fig. 2B,
    354 D), with genetic continuity until ~5,000 BP in Russia.
    Ancestry related to Mesolithic hunter355 gatherer populations from Ukraine (source: Ukraine_10000BP_4000BP) is carried in highest
    356 proportions in hunter-gatherers from a geographic corridor extending from south-eastern Europe
    357 towards the Baltic and southern Scandinavia.
    Swedish Mesolithic individuals derive up to 60% of
    358 their ancestry from that source (Fig. 2C). Our results thus indicate northwards migrations of at least
    359 three distinct waves of hunter-gatherer ancestry into Scandinavia: a predominantly southern
    360 European source into Denmark; a source related to Ukrainian and south-eastern European hunter361 gatherers into the Baltic and southern Sweden; and a northwest Russian source into the far north,
    before venturing south along the Atlantic coast of Norway31 362 (Fig. 2).
    These movements are likely to
    represent post glacial expansions from refugia areas shared with many plant and animal species32,33 363 .
    Interestingly, two herein reported ~7,300-year-old imputed
    383 genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa,
    384 NEO113 & NEO212) derive ~20-30% of their ancestry from a source cluster of hunter-gatherers
    385 from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non386 imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from
    387 the European hunter-gatherer cline towards Iran and the Caucasus.
    Our results thus document
    388 genetic contact between populations from the Caucasus and the Steppe region as early as 7,300
    389 years ago...
    From approximately 5,000 BP, an ancestry component appears on the eastern European plains in
    425 Early Bronze Age Steppe pastoralists associated with the Yamnaya culture and it rapidly spreads
    across Europe through the expansion of the Corded Ware complex (CWC) and related cultures20,21 426 .
    427 We demonstrate that this “steppe” ancestry (Steppe_5000BP_4300BP) can be modelled as a
    428 mixture of ~65% ancestry related to herein reported hunter-gatherer genomes from the Middle Don
    429 River region (MiddleDon_7500BP) and ~35% ancestry related to hunter-gatherers from Caucasus
    430 (Caucasus_13000BP_10000BP) (Extended Data Fig. 4).
    Thus, Middle Don hunter-gatherers, who
    431 already carry ancestry related to Caucasus hunter-gatherers (Fig. 2), serve as a hitherto unknown
    432 proximal source
    for the majority ancestry contribution into Yamnaya genomes. The individuals in
    433 question derive from the burial ground Golubaya Krinitsa (Supplementary Note 3). Material culture
    434 and burial practices at this site are similar to the Mariupol-type graves, which are widely found in
    435 neighbouring regions of Ukraine, for instance along the Dnepr River. They belong to the group of
    436 complex pottery-using hunter-gatherers mentioned above, but the genetic composition at Golubaya
    437 Krinitsa is different from the remaining Ukrainian sites (Fig 2A, Extended Data Fig. 4).
    Individuals associated with Neolithic
    470 farming cultures from Denmark show some of the highest overall hunter-gatherer ancestry
    471 proportions (up to ~25%), mostly derived from Western European-related hunter-gatherers
    472 (EuropeW_13500BP_8000BP) supplemented with marginal contribution from local Danish groups
    473 in some individuals (Extended Data Fig. 7D; Supplementary Note 3f). We estimated the timing of
    the admixture using the linkage-disequilibrium-based method DATES48 474 at ~6,000 BP. Both lines of
    475 evidence thus suggest that a significant part of the hunter-gatherer admixture observed in Danish
    476 Neolithic individuals occurred already before the arrival of the incoming Neolithic people in the
    477 region (Extended Data Fig. 7), and further imply Central Europe as a key region in the resurgence
    478 of HG ancestry.
    The second continental-wide and CWC-mediated transition from Neolithic farmer ancestry to
    497 Steppe-related ancestry was found to differ markedly between geographic regions. The contribution
    498 of local Neolithic farmer ancestry to the incoming groups was high in eastern, western and southern
    Europe, reaching >50% on the Iberian Peninsula (“postNeol” set; Extended Data Fig. 4, 6B, C)34 499 .

    500 Scandinavia, however, portrays a dramatically different picture, with a near-complete replacement
    501 of the local Neolithic farmer population inferred across all sampled individuals (Extended Data Fig.
    502 7B, C). Following the second transition, Neolithic Anatolian-related farmer ancestry remains in
    503 Scandinavia, but the source is now different. It can be modelled as deriving almost exclusively from
    504 a genetic cluster associated with the Late Neolithic Globular Amphora Culture (GAC)
    505 (Poland_5000BP_4700BP; Extended Data Fig. 4).
    Strikingly, after the Steppe-related ancestry was
    506 first introduced into Europe (Steppe_5000BP_4300BP), it expanded together with GAC-related
    507 ancestry across all sampled European regions (Extended Data Fig. 7I).
    This suggests that the spread
    508 of steppe-related ancestry throughout Europe was predominantly mediated through groups that were
    509 already admixed with GAC-related farmer groups of the eastern European plains.
    The Neolithic transition also
    610 marks a considerable rise in frequency of major effect alleles associated with light hair
    pigmentation79 611
    , whereas polygenic score predictions for height are generally low throughout the
    612 first millennium of the Neolithic (Funnel Beaker epoch), echoing previous findings based on a
    smaller set of individuals45,80 613 .
    . The most recent individual
    618 in our Danish dataset with Mesolithic WHG ancestry is “Dragsholm Man” (NEO962), dated to
    619 5,947-5,664 cal. BP (95%) and archaeologically assigned to the Neolithic Funnel Beaker farming
    culture based on his grave goods81,82 620 . Our data confirms a typical Neolithic diet matching the
    621 cultural affinity but contrasting his WHG ancestry. Thus, Dragsholm Man represents a local person
    622 of Mesolithic ancestry who lived in the short Mesolithic-Neolithic transition period
    and adopted a
    623 Neolithic culture and diet.
    Last edited by Ryukendo; 05-05-2022 at 06:58 PM.
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  5. #3
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    Germanic origins:

    667 Finally, we investigated the fine-scale genetic structure in southern Scandinavia after the
    668 introduction of Steppe-related ancestry
    using a temporal transect of 38 Late Neolithic and Early
    669 Bronze Age Danish and southern Swedish individuals. Although the overall population genomic
    670 signatures suggest genetic stability, patterns of pairwise IBD-sharing and Y-chromosome
    671 haplogroup distributions indicate at least three distinct ancestry phases during a ~1,000-year time
    672 span:
    i) An early stage between ~4,600 BP and 4,300 BP, where Scandinavians cluster with early
    673 CWC individuals from Eastern Europe, rich in Steppe-related ancestry and males with an R1a Y674 chromosomal haplotype (Extended Data Fig. 8A, ; ii) an intermediate stage until c. 3,800 BP,
    675 where they cluster with central and western Europeans dominated by males with distinct sub676 lineages of R1b-L51 (Extended Data Fig. 8C, D; Supplementary Note 3b) and includes Danish
    677 individuals from Borreby (NEO735, 737) and Mades° (NEO752) with distinct cranial features
    678 (Supplementary Note 6); and iii) a final stage from c. 3,800 BP onwards, where a distinct cluster of
    679 Scandinavian individuals dominated by males with I1 Y-haplogroups appears (Extended Data Fig.
    680 8E). Using individuals associated with this cluster (Scandinavia_4000BP_3000BP) as sources in
    681 supervised ancestry modelling (see “postBA”, Extended Data Fig. 4), we find that it forms the
    682 predominant source for later Iron- and Viking Age Scandinavians, as well as ancient European
    683 groups outside Scandinavia who have a documented Scandinavian or Germanic association (e.g.,
    684 Anglo-Saxons, Goths; Extended Data Fig. 4).
    Y-chromosome haplogroup I1 is one of the dominant
    685 haplogroups in present-day Scandinavians,s, and we document its earliest occurrence in a ~4,000-
    686 year-old individual from Falk÷ping in southern Sweden (NEO220). The rapid expansion of this
    687 haplogroup and associated genome-wide ancestry in the early Nordic Bronze Age indicates a
    688 considerable reproductive advantage of individuals associated with this cluster over the preceding
    689 groups across large parts of Scandinavia.
    Last edited by Ryukendo; 05-05-2022 at 06:59 PM.
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    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

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  7. #4
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    Ethnicity
    LebaGermish
    aDNA Match (1st)
    Levant_LBN_MA_o4:SI-53 (Sidon Crusader's Pit-mixed)
    aDNA Match (2nd)
    [Mom] Levant_Beirut_ERoman:SFI-33
    aDNA Match (3rd)
    [Dad] VK2020_DNK_Langeland_VA:VK363
    Y-DNA (P)
    P312>DF19>DF88
    mtDNA (M)
    J2a1a1e
    Y-DNA (M)
    J2a1 Z6065>Y7702>M47
    mtDNA (P)
    H1j

    United States of America Lebanon Germany United Kingdom Belgium Switzerland
    Finally, we investigated the fine-scale genetic structure in southern Scandinavia after the 667 introduction of Steppe-related ancestry using a temporal transect of 38 Late Neolithic and Early 668 Bronze Age Danish and southern Swedish individuals. Although the overall population genomic 669 signatures suggest genetic stability, patterns of pairwise IBD-sharing and Y-chromosome 670 haplogroup distributions indicate at least three distinct ancestry phases during a ~1,000-year time 671 span: i) An early stage between ~4,600 BP and 4,300 BP, where Scandinavians cluster with early 672 CWC individuals from Eastern Europe, rich in Steppe-related ancestry and males with an R1a Y-673 chromosomal haplotype (Extended Data Fig. 8A, ; ii) an intermediate stage until c. 3,800 BP, 674 where they cluster with central and western Europeans dominated by males with distinct sub-675 lineages of R1b-L51 (Extended Data Fig. 8C, D; Supplementary Note 3b) and includes Danish 676 individuals from Borreby (NEO735, 737) and Mades° (NEO752) with distinct cranial features 677 (Supplementary Note 6); and iii) a final stage from c. 3,800 BP onwards, where a distinct cluster of 678 Scandinavian individuals dominated by males with I1 Y-haplogroups appears (Extended Data Fig. 679 8E). Using individuals associated with this cluster (Scandinavia_4000BP_3000BP) as sources in 680 supervised ancestry modelling (see ôpostBAö, Extended Data Fig. 4), we find that it forms the 681 predominant source for later Iron- and Viking Age Scandinavians, as well as ancient European 682 groups outside Scandinavia who have a documented Scandinavian or Germanic association (e.g., 683 Anglo-Saxons, Goths; Extended Data Fig. 4). Y-chromosome haplogroup I1 is one of the dominant 684 haplogroups in present-day Scandinavians,s, and we document its earliest occurrence in a ~4,000-685 year-old individual from Falk÷ping in southern Sweden (NEO220). The rapid expansion of this 686 haplogroup and associated genome-wide ancestry in the early Nordic Bronze Age indicates a 687 considerable reproductive advantage of individuals associated with this cluster over the preceding 688 groups across large parts of Scandinavia.
    ^^ at p. 17.
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>FT354149

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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  9. #5
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    New methods:

    757 To investigate the distribution of Stone Age and Early Bronze Age ancestry components in modern
    populations, we used ChromoPainter 100 758 to “paint” the chromosomes of individuals in the UK
    759 Biobank (https://www.ukbiobank.ac.uk) using a panel of 10 ancient donor populations

    (Supplementary Note 3h). Painting was done following the pipeline of Margaryan et al. 101 760 based on
    GLOBETROTTER 102 761 , and admixture proportions were estimated using Non-Negative Least
    762 squares. Haplotypes in the modern genomes are assigned to the genetically closest ancient
    763 population as measured by meiosis events, which favours more recent matches in time. Therefore,
    764 ancestry proportions assigned to the oldest groups (e.g. WHG) should be interpreted as an excess of
    765 this ancestry, which cannot be explained by simply travelling through more recent ancient
    766 populations [RK: e.g. small % WHG in Yamnaya] up to present times....


    ...774 The various hunter-gatherer ancestries are not homogeneously distributed amongst modern
    775 populations (Fig. 5). WHG-related ancestry is highest in present-day individuals from the Baltic
    776 States, Belarus, Poland, and Russia; EHG-related ancestry is highest in Mongolia, Finland, Estonia
    777 and Central Asia; and CHG-related ancestry is maximised in countries east of the Caucasus, in
    Pakistan, India, Afghanistan and Iran, in accordance with previous results 103 778 . The CHG-related
    779 ancestry likely reflects both Caucasus hunter-gatherer and Iranian Neolithic signals, explaining the
    relatively high levels in south Asia 104. Consistent with expectations 105,106 780 , Neolithic Anatolian781 related farmer ancestry is concentrated around the Mediterranean basin, with high levels in southern
    782 Europe, the Near East, and North Africa, including the Horn of Africa, but is less frequent in
    783 Northern Europe. This is in direct contrast to the Steppe-related ancestry, which is found in high
    784 levels in northern Europe, peaking in Ireland, Iceland, Norway, and Sweden, but decreases further
    785 south.
    There is also evidence for its spread into southern Asia. Overall, these results refine global
    786 patterns of spatial distributions of ancient ancestries amongst modern populations.
    The proportion of
    794 Neolithic farmer ancestry is highest in southern and eastern England today and lower in Scotland,
    795 Wales, and Cornwall. Steppe-related ancestry is inversely distributed, peaking in the Outer
    Hebrides and Ireland, a pattern only previously described for Scotland 108 796 . This regional pattern was
    797 already evident in the Pre-Roman Iron Age and persists to the present day even though immigrating
    798 Anglo-Saxons had relatively less Neolithic farmer ancestry than the Iron-Age population of
    799 southwest Briton (Extended Data Fig. 4). Although this Neolithic farmer/steppe-related dichotomy
    800 mirrors the modern ‘Anglo-Saxon’/‘Celtic’ ethnic divide, its origins are older, resulting from
    801 continuous migration from a continental population relatively enhanced in Neolithic farmer
    ancestry, starting as early as the Late Bronze Age 109 802 ... We also found higher levels of WHG-related ancestry
    805 in central and Northern England. These results demonstrate clear ancestry differences within an
    806 ‘ethnic group’ (white British) traditionally considered relatively homogenous, which highlights the
    807 need to account for subtle population structure when using resources such as the UK Biobank
    808 genomes.
    Last edited by Ryukendo; 05-05-2022 at 07:00 PM.
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  11. #6
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    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>FT354149

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

  12. #7
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    Quote Originally Posted by Ryukendo View Post
    Germanic origins:
    This quote deserves to be forwarded to the proto-Germanic topic, it's very interesting and I can't wait to see these post 3800BP samples (and how poorly they'll fit my data )
    YDNA E-Y31991>PF4428>Y134097>Y134104>Y168273>FT17866 (TMRCA ~1100AD) - Domingos Rodrigues, b. circa 1690 Hidden Content , Viana do Castelo, Portugal - Stonemason, miller.
    mtDNA H20 - Monica Vieira, b. circa 1700 Hidden Content , Porto, Portugal

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    [1] "distance%=1.497"
    Ruderico

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    RY'N NI YMA O HYD!

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    Interesting paper but I already noticed one mistake lol....They have Kotias Klde listed as J2b yet we know he is actually J2a.

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  16. #9
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    Selective sweeps on different autosomal backgrounds:

    907 Our analysis identified no genome-wide significant (p < 5e-8) selective sweeps when using
    908 genomes from present-day individuals alone
    (1000 Genomes Project populations GBR, FIN and
    909 TSI), although trait-associated variants were enriched for signatures of selection compared to the
    910 control group (p < 2.2e-16, Wilcoxon signed-rank test).
    In contrast, when using imputed aDNA
    911 genotype probabilities, we identified 11 genome-wide significant selective sweeps in the GWAS
    912 variants, and none in the control group, consistent with selection acting on trait-associated variants
    913 (Supplementary Note 4a, Supplementary Figs. S4a.4 to S4a.14).
    However, when conditioned on
    914 one of our four ancestral histories—genomic regions arriving in present day genomes through
    915 Western hunter-gatherers (WHG), Eastern hunter-gatherers (EHG), Caucasus hunter-gatherers
    916 (CHG) or Anatolian farmers (ANA)
    —we identified 21 genome-wide significant selection peaks
    917 (including the 11 from the pan-ancestry analysis)
    (Fig. 7). This suggests that admixture between
    918 ancestral populations has masked evidence of selection at many trait associated loci in modern
    919 populations.
    I.e., there has been a lot of selection but in different directions in different populations. So when all the populations mix, some of those signals are lost.

    We find strong changes in selection associated with lactose digestion after the introduction of
    939 farming, but prior to the expansion of the Yamnaya pastoralists into Europe around 5,000 years ago
    20,21, settling controversies regarding the timing of this selection 129–132 940 . The strongest overall signal
    941 of selection in the pan-ancestry analysis is observed at the MCM6 / LCT locus (rs4988235; p=9.86e31; s=0.020), where the derived allele results in lactase persistence 133,134 942 (Supplementary Note 4a).
    943 The trajectory inferred from the pan-ancestry analysis indicates that the lactase persistence allele
    944 began increasing in frequency only c. 7,000 years ago, and has continued to increase up to present
    945 times (Fig. 7).
    Our ancestry-stratified analysis shows, however, that selection at the MCM6/LCT
    946 locus is much more complex than previously thought. In the pan-ancestry analysis, this sweep is led
    947 by the lactase persistence SNP rs4988235, whereas in the ancestry-stratified analysis, this signal is
    948 primarily driven by sweeps in two of the ancestral backgrounds (EHG and CHG), each of which
    949 differ in their most significant SNPs (Fig. 7).
    Conversely, in the WHG background, we find no
    950 evidence for selection at rs4988235, but strong selection at rs12465802 within the last c. 2,000
    951 years.
    Overall, our results suggest that there were multiple, asynchronous selective sweeps in this
    952 genomic region in recent human history, and possibly targeting different loci.
    079 Additionally, our results provide unprecedentedly detailed information about the duration and
    1080 geographic spread of these processes (Fig. 7) suggesting that an allele associated with lighter skin
    1081 was selected for repeatedly, probably as a consequence of similar environmental pressures
    1082 occurring at different times in different regions.
    In the ancestry-stratified analysis, all marginal
    1083 ancestries show broad agreement at the SLC45A2 locus (Fig. 7) but differ in the timing of their
    1084 frequency shifts. The ANA ancestry background shows the earliest evidence for selection, followed
    1085 by EHG and WHG around c. 10,000 years ago, and CHG c. 2,000 years later.
    In all ancestry
    1086 backgrounds except WHG, the selected haplotypes reach near fixation by c. 3,000 years ago, whilst
    1087 the WHG haplotype background contains the majority of ancestral alleles still segregating in
    1088 present-day Europeans.
    This finding suggests that selection on this allele was much weaker in
    1089 ancient western hunter-gatherer groups during the Holocene compared to elsewhere.
    I.e., most of the dark alleles in SLC45A2 in present-day Europeans are carried on segments contributed by WHG populations.

    We reconstructed polygenic scores for phenotypes in
    1123 ancient individuals, using effect size estimates obtained from GWASs performed using the
    124 > 400000 UK Biobank cohort (http://www.nealelab.is/uk-biobank) and looked for
    1125 overdispersion among these scores across ancient populations, beyond what would be expected
    under a null model of genetic drift 194 1126 (Supplementary Note 4c).
    We stress that polygenic scores and
    1127 QX statistic may both be affected by population stratification, so these results should be interpreted
    with caution 195–198 1128 . The most significantly overdispersed scores are for variants associated with
    1129 pigmentation, anthropometric differences and disorders related to diet and sugar levels, including
    1130 diabetes (Fig. 9). We also find psychological trait scores with evidence for overdispersion related to
    1131 mood instability and irritability, with Western Hunter-gatherers generally showing smaller genetic
    1132 scores for these traits than Neolithic Farmers.
    Intriguingly, we find highly inconsistent predictions
    1133 of height based on polygenic scores in western hunter-gatherer and Siberian groups computed using
    1134 effect sizes estimated from two different - yet largely overlapping - GWAS cohorts (Supplementary
    1135 Note 4c), highlighting how sensitive polygenic score predictions are to the choice of cohort,
    1136 particularly when ancient populations are genetically divergent from the reference GWAS cohort
    198 1137 . Taking this into account, we do observe that the Eastern hunter-gatherer and individuals
    1138 associated with the Yamnaya culture have consistently high genetic values for height, which in turn
    1139 contribute to stature increases in Bronze Age Europe,
    relative to the earlier Neolithic populations
    45,80,199 1140 .
    142 We performed an additional analysis to examine the data for strong alignments between axes of
    trait-association 200 1143 and ancestry gradients, rather than relying on particular choices for population
    1144 clusters (Supplementary Note 4e).... Along the axis separating Mesolithic hunter1148 gatherers from Anatolian and Neolithic farmer individuals, we find significant correlations with
    1149 trait-association components related to skin disorders, diet and lifestyle traits, mental health status,
    1150 and spirometry-related traits (Fig. 9). Our findings show that these phenotypes were genetically
    1151 different among ancient groups with very different lifestyles....
    1181 Taken together, these analyses help to settle the famous discussion of selection in Europe relating to
    height 45,80,203 1182 . The finding that steppe individuals have consistently high genetic values for height
    1183 (Supplementary Note 4c), is mirrored by the UK Biobank results, which find that the ‘Steppe’
    1184 ancestral components (Yamnaya/EHG) contributed to increased height in present-day populations
    1185 (Supplementary Note 4h). This shows that the height differences in Europe between north and south
    1186 may not be due to selection, as claimed in many previous studies, but may be a consequence of
    1187 differential ancestry.

    1188
    1189 Likewise, European hunter gatherers are genetically predicted to have dark skin pigmentation and
    dark brown hair 11,20,21,79,83,168,204,205 1190 , and indeed we see that the WHG, EHG and CHG components
    1191 contributed to these phenotypes in present-day individuals whereas the Yamnaya and Anatolian
    1192 farmer ancestry contributed to light brown/blonde hair pigmentation (Supplementary Note 4h).

    1193 Interestingly, loci associated with overdispersed mood-related polygenic phenotypes recorded
    1194 among the UK Biobank individuals (like increased anxiety, guilty feelings, and irritability) showed
    1195 an overrepresentation of the Anatolian farmer ancestry component; and the WHG component
    1196 showed a strikingly high contribution to traits related to diabetes.
    We also found that the ApoE4
    1197 effect allele is preferentially found on a WHG/EHG haplotypic background
    , suggesting it likely was
    1198 brought to western Europe by early hunter-gatherers (Supplementary Note 4h)....
    "I contain multitudes." WHG leading to diabetes and high cholesterol/heart disease (the ApoE4 allele) is interesting--I guess if you have too much WHG ancestry, you're less adapted to a carb-rich diet and can blame at least part of your poor health outcomes on the hunter-gatherer ancestors that are especially represented within you.
    Last edited by Ryukendo; 05-06-2022 at 03:45 AM.
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    " A Basal Eurasian and an Aurignacian walk into a bar... "

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  18. #10
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    Quote Originally Posted by J Man View Post
    Interesting paper but I already noticed one mistake lol....They have Kotias Klde listed as J2b yet we know he is actually J2a.
    It should be a different sample, as this one appears to be dated to Neolithic - Chalcolithic period.

    NEO281*, -7773, Kotias Klde, Georgia: J2b

    Can't wait to see the raw data, but if so, this is more likely to be a J2b-L283 or an "ancestor”.
    Last edited by Trojet; 05-05-2022 at 07:08 PM.

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