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Thread: New DNA Papers

  1. #1371
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    High-depth African genomes inform human migration and health

    High-depth African genomes inform human migration and health
    Ananyo Choudhury, Shaun Aron, Laura R. Botigué, Dhriti Sengupta, Gerrit Botha, Taoufik Bensellak, Gordon Wells, Judit Kumuthini, Daniel Shriner, Yasmina J. Fakim, Anisah W. Ghoorah, Eileen Dareng, Trust Odia, Oluwadamilare Falola, Ezekiel Adebiyi, Scott Hazelhurst, Gaston Mazandu, Oscar A. Nyangiri, Mamana Mbiyavanga, Alia Benkahla, Samar K. Kassim, Nicola Mulder, Sally N. Adebamowo, Emile R. Chimusa, Donna Muzny, Ginger Metcalf, Richard A. Gibbs, TrypanoGEN Research Group, Charles Rotimi, Michèle Ramsay, H3Africa Consortium, Adebowale A. Adeyemo, Zané Lombard & Neil A. Hanchard

    Abstract
    The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

    Africa.PCA.png

    a, Geographical regions and populations of origin for H3Africa WGS data. The size of the circles indicates the relative number of sequenced samples from each population group (before quality control; Supplementary Methods Table 1). Samples with WGS data from the 1000 Genomes Project and the African Genome Variation Project are included for comparison (grey circles). CAM includes 25 individuals who are homozygous for the sickle mutation (HbSS); MAL includes unaffected individuals with a family history of neurological disease; BOT comprises children who are HIV-positive; BRN included only female participants. 1000G, 1000 Genome Project; AGVP, African Genome Variation Project. Maps were created using R43. b, Principal component analysis of African WGS data showing the first two principal components. New populations used in this study are indicated by crosses. Population abbreviations are as described in the 1000 Genomes and H3Africa Projects as provided in Supplementary Methods Table 1 and Supplementary Table 22. Shaded background elipses relate to the geographical regions as shown in a.

    Last edited by pmokeefe; 10-28-2020 at 05:41 PM.
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  3. #1372
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    Exome sequencing of Finnish isolates enhances rare-variant association power
    Adam E. Locke, Karyn Meltz Steinberg, […]Nelson B. Freimer
    Abstract
    Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.

    Extended Data Fig. 7: Population structure of the FinMetSeq dataset, by region.

    Extended Data Fig. 8: Hierarchical clustering tree produced by fineSTRUCTURE.

    Thread for paper here:
    https://anthrogenica.com/showthread....ociation-power
    Last edited by pmokeefe; 10-28-2020 at 11:10 PM.
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  5. #1373
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    Effects of Evolutionary History and Substructure on Modern Populations- ASHG 2020

    Selected abstracts from the session Effects of Evolutionary History and Substructure on Modern Populations at ASHG 2020

    Neanderthal Homologous Regions in African Populations Arose Predominantly through Ancient African to Neanderthal Admixture
    Harris et al.
    Abstract
    There is strong evidence that anatomically modern humans (AMH) and Neanderthals admixed after the Out-of-Africa expansion. Most of this admixture is identified in non-African AMH populations. However, recent analyses suggest that there was an early AMH migration from Africa that led to gene flow into Neanderthals, and back migrations of West Eurasians that introduced Neanderthal ancestry to sub-Saharan Africans. To further investigate admixture between Neanderthals and AMH, we used a recently published method called IBDmix to identify Neanderthal homologous regions (NHR) in 180 AMH African individuals from Botswana, Cameroon, Ethiopia, and Tanzania. We discovered NHR in all individuals, totaling from 7 to 22 megabases (MB ) per individual. The average size of an NHR ranges from 75 to 110 kilobases per individual. These distributions of NHR are likely impacted by recent gene flow from non-sub-Saharan African sources primarily into East Africa; we identified a strong positive correlation between an individual’s non-sub-Saharan African ancestry and both their cumulative size of NHR (R2 = 0.8582), and their average NHR size (R2 = 0.6174). The distribution of the cumulative NHR size in individuals without non-sub-Saharan African admixture is narrow (sd = 1.01 MB ), and most of these NHR are shared between populations, which likely reflects AMH to Neanderthal admixture. Based on analyses of genetic distance between AMH and Neanderthals at NHR, we estimated that 93-100% of NHR in populations without non-sub-Saharan African admixture are likely due to AMH to Neanderthal admixture. However, for populations with non-sub-Saharan African admixture we estimated that 10-64% of their NHR are likely due to Neanderthal to AMH admixture. Interestingly, the Amhara and Fulani populations, which are from Ethiopia and Cameroon, respectively, are estimated to have substantial non-sub-Saharan African admixture, but share few NHR. Local ancestry analysis revealed that the NHR in the Fulani are primarily from North African populations, and the NHR in the Amhara have a large contribution from Levant populations. Through the analysis of NHR in African AMH populations, we provided additional support for ancient gene flow from AMH to Neanderthals, and identified different sources of Neanderthal ancestry in the Fulani compared to East African populations.

    Genetic-substructure and complex demographic history of South African Bantu speakers.
    Sengupta et al
    Abstract
    More than 40 million South Africans speak at least one of the languages belonging to the South-Eastern Bantu (SEB ) language family. Most of these SEB-speaking groups have a very specific geographic distribution within the country. Genetically, the SEB-speakers are distinct from other Bantu-speakers as they are known to have admixed with the indigenous Khoe-San (K-S) people. Despite having clear linguistic, ancestral and geographic diversity, the genetic differences between South African SEB groups have not been investigated systematically, often leading to the consideration of SEB groups as a single genetic unit.
    Based on genome-wide SNP data from over 5000 individuals, representing eight major SEB groups (Tsonga, Venda, Pedi, Sotho, Tswana, Zulu, Swazi and Xhosa), genotyped on the novel H3A-genotyping array (2.3M variants), we report the first comprehensive genetic study of SEB groups. Principle component analysis (PCA) provides strong evidence for a fine-scale population structure that broadly aligns to the geographic distribution of SEB groups in the country. Both, PCA and genetic distance-based trees concurs with linguistic phylogenies showing separation of the three major SEB linguistic groups: Tsonga, Sotho-Tswana (Sotho, Pedi and Tswana) and Nguni (Zulu and Xhosa) speakers. Differential K-S gene flow, ranging from ~2% in Tsonga to ~20% in Tswana, plays a key role in the differentiation of the SEB groups. The observed population sub-structure persists even after K-S ancestry masking, although reduced. In accordance with the observed structure, dates of K-S admixture and effective population size (Ne) fluctuations correspond to differences in demographic histories of SEB groups. Together, the convergence of earliest dates of K-S admixture and the differentiation of Ne profiles around 40 generations ago likely reflect the initiation of migration events that gradually separated the demographic history of these populations. The comparisons with five Iron-Age Bantu-related genomes supported genetic continuity since last 300-500 years ago in certain regions of the country. Finally, based on simulated trait genome-wide association studies (GWAS), we demonstrated that the detected fine-scale population structure have major implications for biomedical and genomics research in Southern Africa.
    Overall, our study significantly enhances our understanding of the complex demographic history of SEB groups from South Africa, and highlights the necessity for nuanced study designs in population genetics and GWAS, especially candidate gene-based studies where correction for population structure and admixture is not possible.

    Native American gene flow into Polynesia predating the settlement of Easter Island confirms voyaging contact between the Americas and Oceania.
    Ioannidis et al
    Abstract
    The possibility of voyaging contact between prehistoric Polynesians and Native Americans has long intrigued researchers. Proponents have pointed to New World crops, such as the sweet potato and bottle gourd, found in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas, while critics have argued that these botanical dispersals need not have been human mediated. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South Americans played an important role in the settlement of east Polynesia and particularly Easter Island (Rapa Nui). Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested. Here, for the first time, we analyze genome-wide variation in individuals from islands spanning Polynesia for signs of Native American admixture, analyzing over eight hundred individuals from seventeen island populations and fifteen Pacific coast Native American groups. We introduce new methods for localizing the origin of small ancestry components with only small sample sizes, having applications to personalized genomics, and we demonstrate the use of a technique for unraveling genetic bottlenecking and directionality for the first time in humans. Using these and traditional methods, we find conclusive evidence for prehistoric contact of Polynesians with Native Americans (ca. 1200 CE) contemporaneous with the stepwise settlement of these remote Oceanian islands. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, prior to the settlement of Easter Island (Rapa Nui), between Polynesians and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.
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