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Thread: New DNA Papers - General Discussion Thread

  1. #2201
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    Quote Originally Posted by rozenfeld View Post
    The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
    It's pretty much what the other paper said, it's just a shame they limited the Portuguese samples to two coastal cities with no geographical barriers in between them, I'd much rather they had picked a city in the interior north instead of Porto.
    YDNA - E-Y31991>PF4428>Y134097>Y168273 Domingos Rodrigues, b. circa 1680 Hidden Content , Viana do Castelo, Portugal
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  3. #2202
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    Quote Originally Posted by pmokeefe View Post
    Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism
    [INDENT]CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1, strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, attenuating its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22's role in metabolism and have potential to differentially influence the human insulin response.
    ...

    rs1061325 was the main SNP discussed in the paper. It was present in both my 23andMe and Ancestry DNA tests. I was mixed (CT) for rs1061325. If I interpreted the paper correctly C should be the allele associated with farmers and T is the allele associated with hunter-gatherers. I tried to figure that out by looking at dbSNP https://www.ncbi.nlm.nih.gov/snp/rs1061325. It would would be great if anyone would be kind enough to confirm that. Anyone else willing to share their test results for rs1061325?
    The allelic variation reported here for CLTCL1 in human and bear populations further supports the hypothesis that CLTCL1 has undergone continued selection during vertebrate evolution in relation to diet. While purifying selection appears to be operating on CLTCL1 in those species that retain it, CLTCL1 is far more variable than CLTC in these species.
    In humans, we find two major and functionally distinct alleles at remarkably similar frequencies in all populations studied. Statistical analysis comparing early farmer and hunter-gatherer populations shows an apparent increase of the V1316 variant, suggesting a correlation with regular consumption of digestible carbohydrate.
    Notably, the SNP distinguishing these alleles is human-specific and likely arose 550-50 KYA (i.e. post-Neanderthal, pre-Neolithic).
    Other dramatic increases in digestible carbohydrate utilization have been inferred for humans in this timeframe; in particular the advent of cooking (which gelatinizes crystalized starch, making it much easier to digest), salivary amylase gene copy number increase (allowing increased starch digestion capacity) and accelerated brain size increase (which would increase demands for blood glucose) (Hardy et al., 2015).
    Fascinating that glucose changes such as cooking, clathrin changes and amylase copy number increase long ago all helped to make us human.
    But that very recently, sugar excess may be causing health problems.
    Last edited by Saetro; 05-25-2019 at 05:02 AM.

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  5. #2203
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    Quote Originally Posted by J1 DYS388=13 View Post
    EXPLOSION FROM THE STEPPE?
    THE DISTRIBUTION AND ORIGINS OF THE Y-HAPLOGROUP R1a
    Dr. Joe Flood
    DRAFT May 28 2019
    SUMMARY: The Y-haplogroup R1a is found in quantity over a vast area stretching east-west across
    the Eurasian steppe from Scandinavia to China, and north-south from the Urals to Sri Lanka, then
    west to Arabia. The subclade distribution of R1a is spatially differentiated, showing that the
    mainstream R1a1a1 of the steppe expanded in different directions from only two men who lived
    after 3000 BC. The initial expansions are extreme founder effects in the early Bronze Age, probably a
    bottleneck 'Event', while later expansions occurred in part through the control of key resources and
    strategic access to food technology.
    R1a may have originally travelled to the steppe via the Middle East and Central Europe in the early
    Holocene with other subclades of archaic R1, leaving small early trace branches behind. The main
    R1a1a line is found in ancient DNA as a minority of about 20 per cent within ‘Europoid’ Neolithic
    populations on the Dnieper and Volga basins. As associates of Yamna traders they supplied Urals and
    Altai minerals to settled early Bronze Age cultures around the Caucasus, gaining early access to the
    package of Bronze Age technologies. Two R1a men living around 3000 BC and carrying the Z283 and
    Z93 mutations survived an extreme bottleneck event that destroyed the Cucuteni-Trypillia and
    Maykop cultures. R1a subsequently expanded very rapidly into almost empty space, often taking on
    the characteristics of the cultures with whom they came in contact. Today at least 150 million men
    are descended from these two founders.
    Employing their skills with overland and river trading, metalworking and mining, the wheel, herding,
    the axe and the plough, the western branch R1a-Z283 formed the Corded Ware/Battle
    Axe/Catacomb culture of the South Baltic and Scandinavia, supported by the amber and salt trade.
    To the east R1a-Z93 gained control of the trade in metals from the Urals, continuing to mine and
    ship copper for the southern civilisations, and expanding with R1b as the Poltavka kurgan culture
    along the Volga and Don rivers. As well as gaining the benefits of trade, they were probably assisted
    by improvements in herding technology, and spread east and south on the steppe.
    From about 2200 BC, R1a-Z94 tribespeople displaced by the 4.2 kiloyear drying event founded the
    Sintashta fortified settlements near the Ural River and east to the Altai. They followed the southern
    trade routes through the proto-urban Bactria-Margiana complex on the Amu Darya river, gaining
    control of key mineral resources in Bactria and the Punjab and along the Silk Road, and moving as far
    east as the Tarim basin in China.
    Almost immediately they settled within the dispersed remnants of the advanced Indus civilization,
    bringing the Indo-Aryan language of the Avestas and the Vedas into South Asia, and forming the late
    Indus culture as a group of R1a-dominated Aryan tribes. By the middle Bronze Age these tribes
    consolidated into the urban kingdoms of North India and the Ganges plain; codifying the Vedas and
    creating the Hindu caste system in which they held the highest ranks.
    The wandering R1a tribes proceeded simultaneously through Iran to Arabia. In all this rapid
    movement and expansion, they continued to employ the tented bullock wagon to move and settle
    over vast distances. They were probably also assisted by river transport and the newly-invented
    chariot.
    ii
    The R1a expansion concluded at the end of the Bronze Age when the civilizations of Eurasia no
    longer required exotic minerals. Although the steppe mastered mounted archery, leading to the
    military successes of the Scythians and Sarmatians, R1a probably lost ground to tribes from further
    east, and was challenged to the west and south.
    In mediaeval times, the Slavic and Ashkenazi expansions occurred in East-central Europe, creating
    friction with the expanding Germanic tribes. The ramifications have extended almost to the present.
    The last expansion of R1a took place in the New World as a 'massive migration'.
    The theory underlying this narrative is that Y-distributions in established populations maintain a selfsimilar subclade distribution and remain largely unchanged in proportion unless subjected to specific
    shocks or forces. These may include bottlenecks, selective improvements in acquisition of food due
    to improved technology or trade, and large migrations. R1a has been subject to all of these changes
    during its five-thousand-year history as a substantial haplogroup.
    Considerable improvements in testing of modern and ancient Y-DNA will be necessary to confirm the
    details of this outline.

    https://www.academia.edu/39342899/EX...jaZZYXutS3pQuc
    Dude sounds crazy.

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  7. #2204
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    Quote Originally Posted by Generalissimo View Post
    Dude sounds crazy.
    Not his first work, was peddling some nonsense about L21 a little while back.

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  9. #2205
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    Sounds like an Anti-Out of Africa paper. Good luck countering current consensus.

  10. #2206
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    Quote Originally Posted by pmokeefe View Post
    And now for something completely different ...

    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

    Abstract
    The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
    Finally!

  11. #2207
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    Quote Originally Posted by pmokeefe View Post
    And now for something completely different ...

    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

    Abstract
    The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
    I was interested by this tentative paper by these Chineses partisans of the multiregionalism theory . I was not able to understand their classifications of mutations and relative calculations, although I guessed a possible lack of coherence in the development of their arguments.
    But when they want to change the phylogenic tree of the Y and mt DNA , I abandonned quickly . their modification of the trees with F* for Y-tree and M* for mt-tree beginning the basis of their trees with an East and South Asiatic origin as that seemed me the aim of their discourse. That seems me impossible to be related to the nowadays archeological , genetical and anthropological knowledges, specially statistical genetic relations between the populations.

    Describe the A00, A0 , A1 .. and B* as derived branches of F* chocked me, and also the branches of L from M* because of the well-established anthropological correspondences.

    the date of about 1.8M for the divergence of present human branches is absurd, the present human species is relatively too homogeneous to have a so old divergence as enough divergent to talk against the exaggerate homogeneity of the politically correct .A datation of the first divergence at least < 200.000 years is the more acceptable. In fact I read quickly but I don't see neither any coherence in their ideas, nor a relatively acceptable explanation of their views.

    Anyway, the old main basis of the multiregionalism could be explained by the introgression of the mutated EDAR gene (which created multiple phenotypic traits of East Asians) from Denisovans to Modern Humans in East Asia which creates an enough selective advantage to diffuse thru the whole East Asian population during selective glacial episodes. I saw a documentation about the frequency of the mutated EDAR gene in modern populations, but I don't remind the reference.
    Last edited by palamede; 06-13-2019 at 08:51 AM.

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  13. #2208
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    Quote Originally Posted by palamede View Post
    Anyway, the old main basis of the multiregionalism could be explained by the introgression of the mutated EDAR gene (which created multiple phenotypic traits of East Asians) from Denisovans to Modern Humans in East Asia which creates an enough selective advantage to diffuse thru the whole East Asian population during selective glacial episodes. I saw a documentation about the frequency of the mutated EDAR gene in modern populations, but I don't remind the reference.
    Not sure which paper you had in mind, this seems to be one of the earlier papers on the EDAR gene and East Asians, but there have been numerous other papers on the topic.
    Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
    Summary
    An adaptive variant of the human Ectodysplasin receptor, EDARV370A, is one of the strongest candidates of recent positive selection from genome-wide scans. We have modeled EDAR370A in mice and characterized its phenotype and evolutionary origins in humans. Our computational analysis suggests the allele arose in central China approximately 30,000 years ago. Although EDAR370A has been associated with increased scalp hair thickness and changed tooth morphology in humans, its direct biological significance and potential adaptive role remain unclear. We generated a knockin mouse model and find that, as in humans, hair thickness is increased in EDAR370A mice. We identify new biological targets affected by the mutation, including mammary and eccrine glands. Building on these results, we find that EDAR370A is associated with an increased number of active eccrine glands in the Han Chinese. This interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.
    ...
    Results
    Single Origin of 370A in Central China
    Using both newly generated and publicly available data, we examined 280 SNPs flanking the 370A SNP in 51 worldwide populations in order to assess the origin of 370A. Haplotype analysis supports a single origin of the derived allele (Figure 1A), with the mutation lying on a unique, nearly unbroken haplotype extending more than 100 kb among both East Asians and Native Americans.
    YFull: YF14620 (Dante Labs 2018)

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  15. #2209
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    Quote Originally Posted by pmokeefe View Post
    And now for something completely different ...

    Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

    Abstract
    The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.
    Sounds like a right load of twaddle

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  17. #2210
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    Quote Originally Posted by jdean View Post
    Sounds like a right load of twaddle
    Reminds me of Professor Wolpoff's Regional Continuity Theory.

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