Dataset Information

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

ABSTRACT: We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.

SUBMITTER: Fan S

PROVIDER: S-EPMC10568978 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

Fan Shaohua S Spence Jeffrey P JP Feng Yuanqing Y Hansen Matthew E B MEB Terhorst Jonathan J Beltrame Marcia H MH Ranciaro Alessia A Hirbo Jibril J Beggs William W Thomas Neil N Nyambo Thomas T Mpoloka Sununguko Wata SW Mokone Gaonyadiwe George GG Njamnshi Alfred A Folkunang Charles C Meskel Dawit Wolde DW Belay Gurja G Song Yun S YS Tishkoff Sarah A SA

Cell 20230301 5

We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression ev ...[more]

PMID: 36868214

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Project description:High-latitude ocean basins are the most productive on earth, supporting high diversity and biomass of economically and socially important species. A long tradition of responsible fisheries management has sustained these species for generations, but modern threats from climate change, habitat loss, and new fishing technologies threaten their ecosystems and the human communities that depend on them. Among these species, Alaska's most charismatic megafaunal invertebrate, the red king crab, faces all three of these threats and has declined substantially in many parts of its distribution. Managers have identified stock structure and local adaptation as crucial information to help understand biomass declines and how to potentially reverse them, with regulation and possible stock enhancement. We generated low-coverage whole genome sequencing (lcWGS) data on red king crabs from five regions: The Aleutian Islands, eastern Bering Sea, northern Bering Sea, Gulf of Alaska, and Southeast Alaska. We used data from millions of genetic markers generated from lcWGS to build on previous studies of population structure in Alaska that used < 100 markers and to investigate local adaptation. We found each of the regions formed their own distinct genetic clusters, some containing subpopulation structure. Most notably, we found that the Gulf of Alaska and eastern Bering Sea were significantly differentiated, something that had not been previously documented. Inbreeding in each region was low and not a concern for fisheries management. We found genetic patterns consistent with local adaptation on several chromosomes and one particularly strong signal on chromosome 100. At this locus, the Gulf of Alaska harbors distinct genetic variation that could facilitate local adaptation to their environment. Our findings support the current practice of managing red king crab at a regional scale, and they strongly favor sourcing broodstock from the target population if stock enhancement is considered to avoid genetic mismatch.

Dataset Information

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

Publications

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

Similar Datasets

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