8
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      The fine-scale genetic structure and evolution of the Japanese population

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

          Related collections

          Most cited references42

          • Record: found
          • Abstract: found
          • Article: not found

          The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

          There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the 'hard sweep' model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field. Copyright 2010 Elsevier Ltd. All rights reserved.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Estimating and interpreting F ST: The impact of rare variants

            In a pair of seminal papers, Sewall Wright and Gustave Malécot introduced F ST as a measure of structure in natural populations. In the decades that followed, a number of papers provided differing definitions, estimation methods, and interpretations beyond Wright's. While this diversity in methods has enabled many studies in genetics, it has also introduced confusion regarding how to estimate F ST from available data. Considering this confusion, wide variation in published estimates of F ST for pairs of HapMap populations is a cause for concern. These estimates changed—in some cases more than twofold—when comparing estimates from genotyping arrays to those from sequence data. Indeed, changes in F ST from sequencing data might be expected due to population genetic factors affecting rare variants. While rare variants do influence the result, we show that this is largely through differences in estimation methods. Correcting for this yields estimates of F ST that are much more concordant between sequence and genotype data. These differences relate to three specific issues: (1) estimating F ST for a single SNP, (2) combining estimates of F ST across multiple SNPs, and (3) selecting the set of SNPs used in the computation. Changes in each of these aspects of estimation may result in F ST estimates that are highly divergent from one another. Here, we clarify these issues and propose solutions.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Mapping human genetic diversity in Asia.

              Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.
                Bookmark

                Author and article information

                Contributors
                Role: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                1 November 2017
                2017
                : 12
                : 11
                : e0185487
                Affiliations
                [1 ] Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
                [2 ] Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
                [3 ] Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
                [4 ] Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
                [5 ] Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
                [6 ] Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
                [7 ] Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
                [8 ] Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
                [9 ] Saw Swee Hock School of Public Health, National University of Singapore, Singapore
                [10 ] NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
                [11 ] Life Sciences Institute, National University of Singapore, Singapore, Singapore
                [12 ] College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
                [13 ] Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, Yinchuan, Ningxia, China
                [14 ] Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China
                [15 ] School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
                [16 ] Collaborative Innovation Center of Genetics and Development, Shanghai, China
                [17 ] Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
                [18 ] Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
                Universitat Pompeu Fabra, SPAIN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                ¶ Membership of the Japanese Genome Variation Consortium is provided in the Acknowledgments.

                Author information
                http://orcid.org/0000-0003-3185-5661
                Article
                PONE-D-16-50035
                10.1371/journal.pone.0185487
                5665431
                29091727
                e3828090-437a-488d-a9cf-b0931395d715
                © 2017 Takeuchi et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 December 2016
                : 13 September 2017
                Page count
                Figures: 6, Tables: 1, Pages: 28
                Funding
                N.K. acknowledges support from the grants (26S-111 and 26S-115) of National Center for Global Health and Medicine; a grant-in-aid from the MEXT/JSPS KAKENHI (Grant Number 26290067); and grants from SENSHIN Medical Research Foundation. W.Y.S. and Y.Y.T. acknowledge support from the Saw Swee Hock School of Public Health, and Life Sciences Institute from the National University of Singapore. Y.Y.T. also acknowledges support from the National Research Foundation Singapore (NRF-RF-2010-05). S.X. gratefully acknowledges the support of the National Natural Science Foundation of China (NSFC) grants (91331204), the National Science Fund for Distinguished Young Scholars (31525014) and Program of Shanghai Subject Chief Scientist (16XD1404700). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Genetic Loci
                People and Places
                Geographical Locations
                Asia
                Japan
                People and places
                Population groupings
                Ethnicities
                Chinese people
                Han Chinese people
                Computer and Information Sciences
                Computer Software
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Genetic Drift
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Genetic Drift
                Biology and Life Sciences
                Genetics
                Population Genetics
                Genetic Drift
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Genetic Drift
                Earth Sciences
                Geomorphology
                Topography
                Landforms
                Islands
                Custom metadata
                The Asian Diversity Project data have been deposited at the European Genome-phenome Archive under the accession number EGAS00001002100. The URLs for data and software presented herein are as follows: European Genome-phenome Archive, https://ega-archive.org; FigTree program, http://tree.bio.ed.ac.uk/software/; HapMap project, http://hapmap.ncbi.nlm.nih.gov/; Human Genome Diversity Project, http://www.hagsc.org/hgdp/files.html; Jorde Lab, http://jorde-lab.genetics.utah.edu/?page_id=23; R software, http://www.r-project.org/. All additional relevant data are within the paper and its Supporting Information files.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article