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Thread: New DNA Papers

  1. #1311
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    A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans

    A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans
    Hugo Zeberg,Michael Dannemann, Kristoffer Sahlholm, Kristin Tsuo, Tomislav Maricic, Victor Wiebe,
    Wulf Hevers, Hugh P.C. Robinson Janet Kelso and Svante Paabo

    SUMMARY
    The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1].
    In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and
    studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination
    of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to
    painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals,
    the three Neanderthal substitutions are found in 0.4% of present-day Britons, where they are associated
    with heightened pain sensitivity.


    Neanderthal gene linked to increased pain sensitivity
    People who have inherited nerve-altering mutations from the ancient hominins tend to experience more pain.
    Ewen Callaway
    YFull: YF14620 (Dante Labs 2018)

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  3. #1312
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    Genetic Consequences of the Transatlantic Slave Trade in the Americas

    Genetic Consequences of the Transatlantic Slave Trade in the Americas
    Steven J. Micheletti
    Kasia Bryc
    Samantha G. Ancona Esselmann
    23andMe Research Team
    Sandra Beleza
    Joanna L. Mountain

    According to historical records of transatlantic slavery, traders forcibly deported an estimated 12.5 million people from ports along the Atlantic coastline of Africa between the 16th and 19th centuries, with global impacts reaching to the present day, more than a century and a half after slavery’s abolition. Such records have fueled a broad understanding of the forced migration from Africa to the Americas yet remain underexplored in concert with genetic data. Here, we analyzed genotype array data from 50,281 research participants, which—combined with historical shipping documents—illustrate that the current genetic landscape of the Americas is largely concordant with expectations derived from documentation of slave voyages. For instance, genetic connections between people in slave trading regions of Africa and disembarkation regions of the Americas generally mirror the proportion of individuals forcibly moved between those regions. While some discordances can be explained by additional records of deportations within the Americas, other discordances yield insights into variable survival rates and timing of arrival of enslaved people from specific regions of Africa. Furthermore, the greater contribution of African women to the gene pool compared to African men varies across the Americas, consistent with literature documenting regional differences in slavery practices. This investigation of the transatlantic slave trade, which is broad in scope in terms of both datasets and analyses, establishes genetic links between individuals in the Americas and populations across Atlantic Africa, yielding a more comprehensive understanding of the African roots of peoples of the Americas.
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  5. #1313
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    Genomic insights into the early peopling of the Caribbean
    Kathrin Nägele1 *†, Cosimo Posth1,2†, Miren Iraeta Orbegozo3, Yadira Chinique de Armas4, Silvia Teresita Hernández Godoy5,6, Ulises M. González Herrera7 , Maria A. Nieves-Colón8, Marcela Sandoval-Velasco3, Dorothea Mylopotamitaki3, Rita Radzeviciute1 , Jason Laffoon9, William J. Pestle10, Jazmin Ramos-Madrigal3, Thiseas C. Lamnidis1 , William C. Schaffer11,12, Robert S. Carr13, Jane S. Day14, Carlos Arredondo Antúnez15, Armando Rangel Rivero15, Antonio J. Martínez-Fuentes15‡, Edwin Crespo-Torres16‡, Ivan Roksandic4, Anne C. Stone8,12, Carles Lalueza-Fox17, Menno Hoogland9,18, Mirjana Roksandic4, Corinne L. Hofman9,18, Johannes Krause1 *, Hannes Schroeder

    Science 24 Jul 2020: Vol. 369, Issue 6502, pp. 456-460
    DOI: 10.1126/science.aba8697
    https://science.sciencemag.org/content/369/6502/456

    A complex dispersal into the Caribbean
    The settlement of the Caribbean and genetic relationships among pre-European Caribbean people remain a mystery. After examining 93 ancient genomes dating to a range from about 3200 to 400 years ago, Nägele et al. suggest that at least three separate colonization events, including a previously unknown wave, were connected to radiation events in North America. The two more ancient lineages coexisted in Cuba but were fully separate genetically, with later movement into the region from a third group from South America. The study not only informs on the settlement of the Caribbean but also lends insights into the broader-scale intercontinental radiation of humans across the American landscape, including across substantial water boundaries.
    Abstract
    The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
    The mtDNA data reveal clear differences in haplogroup frequencies between the individuals from the two contexts (fig. S1). While most of the individuals from Cuba 3200-700
    cal. BP carry haplogroups D1 and C1d (with a frequency of 47% and 30%, respectively), these haplogroups are less common among individuals from Ceramic-related contexts, including those reported in previous studies (11, 12). Overall, mtDNA diversity is higher among Ceramic Age individuals, with haplogroups B2, C1b, and C1c unique to this group (fig.S1).
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
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    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  7. #1314
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    not sure is this paper is new or old or already presented

    https://www.cell.com/cell/pdf/S0092-...showall%3Dtrue


    Genomic History of Neolithic to Bronze Age Anatolia,Northern Levant, and Southern Caucasus ............................ analysis of 110 ancient individuals from the Near East Gene pools of Anatolia and Caucasus were biologically connected6500 BCEdGene flow from neighboring populations in Northern Levant during
    Authors....Eirini Skourtanioti, Yilmaz S. Erdal

    Skourtanioti et al., 2020, Cell181, 1158–1175May 28, 2020

    Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the LateNeolithic to Late Bronze Age, a period characterized by intense interregional interactions for the NearEast. We find that 6thmillennium BCE populations of North/Central Anatolia and the Southern Caucasusshared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and re-gions in today’s Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, morethan half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the SouthernCaucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a geneticallydistinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales ofpopulation dynamics through time, from extensive admixture during the Neolithic period to long-distancemobility within the globalized societies of the Late Bronze Age.


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483 )


    Grandfather via paternal grandmother = I1-L22 ydna
    Great grandmother paternal side = T1a1e mtdna

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  9. #1315
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    ... micro-inversions provides clues for population genetic analysis of humans

    The landscape of micro-inversions provides clues for population genetic analysis of humans
    Li Qu, Luotong Wang, Feifei He, Yilun Han, Longshu Yang, May D. Wang, Huaiqiu Zhu

    Abstract
    Background: Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (<100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases. Results: In this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6,968 MIs among the 1,937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the Out of Africa hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages. Conclusions: We propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to constructing human population relationships and have a potential effect on human health.
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  11. #1316
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    Genetic-substructure and complex demographic history of South African Bantu speakers

    Genetic-substructure and complex demographic history of South African Bantu speakers
    Dhriti Sengupta, Ananyo Choudhury, Cesar Fortes-Lima, Shaun Aron, Gavin Whitelaw, Koen Bostoen, Hilde Gunnink, Natalia Chousou-Polydouri, Peter Delius, Stephen Tollman, F Gomez-Olive Casas, Shane Norris, Felistas Mashinya, Marianne Alberts, Scott Hazelhurst, Carina M. Schlebusch, Michèle Ramsay, as members and collaborators of AWI-Gen and the H3Africa Consortium
    Abstract
    South Eastern Bantu-speaking (SEB ) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ∼400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.
    Last edited by pmokeefe; Yesterday at 01:28 AM.
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  13. #1317
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    Genome Diversity in Ukraine

    Genome Diversity in Ukraine
    Taras K. Oleksyk, Walter W. Wolfsberger, Alexandra Weber, Khrystyna Shchubelka, Olga T. Oleksyk, Olga Levchuk, Alla Patrus, Nelya Lazar, Stephanie O. Castro-Marquez, Patricia Boldyzhar, Alina Urbanovych, Viktoriya Stakhovska, Kateryna Malyar, Svitlana Chervyakova, Olena Podoroha, Natalia Kovalchuk, Yaroslava Hasynets, Juan L. Rodriguez-Flores, Sarah Medley, Fabia Battistuzzi, Ryan Liu, Yong Hou, Siru Chen, Huanming Yang, Meredith Yeager, Michael Dean, Ryan E. Mills, Volodymyr Smolanka

    Abstract

    The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for the public data release. DNBSEQ-G50 sequences, and genotypes by an Illumina GWAS chip were cross-validated on multiple samples, and additionally referenced to a sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. The genome data has been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, CNVs, SNPs and microsatellites. This study is providing the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for historic and medical research in a large understudied population. While most of the common variation is shared with other European populations, this survey of population variation contributes a number of novel SNPs and structural variants that have not been reported in the gnomAD/1KG databases representing global distribution of genomic variation. These endemic variants will become a valuable resource for designing future population and clinical studies, help address questions about ancestry and admixture, and will fill a missing place in the puzzle characterizing human population diversity in Eastern Europe. Our results indicate that genetic diversity of the Ukrainian population is uniquely shaped by the evolutionary and demographic forces, and cannot be ignored in the future genetic and biomedical studies. This data will contribute a wealth of new information bringing forth different risk and/or protective alleles. The newly discovered low frequency and local variants can be added to the current genotyping arrays for genome wide association studies, clinical trials, and in genome assessment of proliferating cancer cells.
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  15. #1318
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    Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial..

    Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes

    Stanislav V. Dryomov, Elena B. Starikovskaya, Azhar M. Nazhmidenova, Igor V. Morozov & Rem I. Sukernik

    Abstract
    Background

    We have described the diversity of complete mtDNA sequences from ‘relic’ groups of the Russian Far East, primarily the Nivkhi (who speak a language isolate with no clear relatedness to any others) and Oroki of Sakhalin, as well as the sedentary Koryak from Kamchatka and the Udegey of Primorye. Previous studies have shown that most of their traditional territory was dramatically reshaped by the expansion of Tungusic-speaking groups.
    Results

    Overall, 285 complete mitochondrial sequences were selected for phylogenetic analyses of published, revised and new mitogenomes. To highlight the likely role of Neolithic expansions in shaping the phylogeographical landscape of the Russian Far East, we focus on the major East Eurasian maternal lineages (Y1a, G1b, D4m2, D4e5, M7a2, and N9b) that are restricted to the coastal area. To obtain more insight into autochthonous populations, we removed from the phylogeographic analysis the G2a, G3a2, M8a1, M9a1, and C4b1 lineages, also found within our samples, likely resulting from admixture between the expanding proto-Tungus and the indigenous Paleoasiatic groups with whom they assimilated. Phylogenetic analysis reveals that unlike the relatively diverse lineage spectrum observed in the Amur estuary and northwestern Sakhalin, the present-day subpopulation on the northeastern coast of the island is relatively homogenous: a sole Y1a sublineage, conspicuous for its nodal mutation at m.16189 T > C!, includes different haplotypes. Sharing of the Y1a-m.16189 T > C! sublineages and haplotypes among the Nivkhi, Ulchi and sedentary Koryak is also evident. Aside from Y1a, the entire tree approach expands our understanding of the evolutionary history of haplogroups G1, D4m, N9b, and M7a2. Specifically, we identified the novel haplogroup N9b1 in Primorye, which implies a link between a component of the Udegey ancestry and the Hokkaido Jomon.

    Conclusions

    Through a comprehensive dataset of mitochondrial genomes retained in autochthonous populations along the coast between Primorye and the Bering Strait, we considerably extended the sequence diversity of these populations to provide new features based on the number and timing of founding lineages. We emphasize the value of integrating genealogical information with genetic data for reconstructing the population history of indigenous groups dramatically impacted by twentieth century resettlement and social upheavals.
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  17. #1319
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    ... Origin of Fujian Tanka from Ancient Indigenous Daic Populations

    Uniparental Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic Populations

    Xiao-Qin Luo, Pan-Xin Du, Ling-Xiang Wang, Bo-Yan Zhou, Yu-Chun Li, Hong-Xiang Zheng, Lan-Hai Wei, Jun-Jian Liu, Chang Sun, Hai-Liang Meng, Jing-Ze Tan, Wen-Jing Su, Shao-Qing Wen, Hui Li

    Abstract

    The Fujian Tanka people are officially classified as a southern Han ethnic group, whereas they have customs similar to Daic and Austronesion people. Whether they originated in Han or Daic people, there is no consensus. Three hypotheses have been proposed to explain the origin of this group: (1) the Han Chinese origin, (2) the ancient Daic origin, (3) and the admixture between Daic and Han. This study addressed this issue by analyzing the paternal Y chromosome and maternal mtDNA variation of 62 Fujian Tanka and 25 neighboring Han in Fujian. The southern East Asian predominant haplogroups (e.g., Y-chromosome O1a1a-P203 and O1b1a1a-M95, and mtDNA F2a, M7c1, and F1a1) had relatively high frequencies in Tanka. The interpopulation comparison revealed that the Tanka have a closer affinity with Daic populations than with Han Chinese in paternal lineages but are closely clustered with southern Han populations such as Hakka and Chaoshanese in maternal lineages. Network and haplotype-sharing analyses also support the admixture hypothesis. The Fujian Tanka mainly originate from the ancient indigenous Daic people and have only limited gene flows from Han Chinese populations. Notably, the divergence time inferred by the Tanka-specific haplotypes indicates that the formation of Fujian Tanka was a least 1033.8-1050.6 years before present (the early Northern Song dynasty), indicating that they are an indigenous population, not late Daic migrants from southwestern China.
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