Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure
Publication Date
November 04, 2013
Journal
PLOS ONE
Authors
Pongsakorn Wangkumhang, Philip James Shaw, Kridsadakorn Chaichoompu, Chumpol Ngamphiw, et al
Volume
8
Issue
11
Pages
e79522
DOI
https://dx.plos.org/10.1371/journal.pone.0079522
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0079522
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24223962
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817124
Europe PMC
http://europepmc.org/abstract/MED/24223962
Web of Science
000326503400122
Scopus
84891952928
Mendeley
http://www.mendeley.com/research/insight-peopling-mainland-southeast-asia-thai-population-genetic-structure
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1266560", "https://ndownloader.figshare.com/files/1266561", "https://ndownloader.figshare.com/files/1266562", "https://ndownloader.figshare.com/files/1266563", "https://ndownloader.figshare.com/files/1266564", "https://ndownloader.figshare.com/files/1266565", "https://ndownloader.figshare.com/files/1266566", "https://ndownloader.figshare.com/files/1266567"], "description"=>"<div><p>There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects. </p> </div>", "links"=>[], "tags"=>["peopling", "mainland", "asia", "thai"], "article_id"=>840711, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079522.s001", "https://dx.doi.org/10.1371/journal.pone.0079522.s002", "https://dx.doi.org/10.1371/journal.pone.0079522.s003", "https://dx.doi.org/10.1371/journal.pone.0079522.s004", "https://dx.doi.org/10.1371/journal.pone.0079522.s005", "https://dx.doi.org/10.1371/journal.pone.0079522.s006", "https://dx.doi.org/10.1371/journal.pone.0079522.s007", "https://dx.doi.org/10.1371/journal.pone.0079522.s008"], "stats"=>{"downloads"=>27, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Insight_into_the_Peopling_of_Mainland_Southeast_Asia_from_Thai_Population_Genetic_Structure_/840711", "title"=>"Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-04 02:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1266555"], "description"=>"<p>992 Thai individuals from datasets no. 2 and 3 were combined and analyzed by ipPCA utilizing 438,503 SNP markers. Four subpopulations (SPA, B, C and D) were resolved by ipPCA, whereas 20 individuals could not be assigned to a subpopulation and are separated as “Outliers”. The proportions of individuals assigned to each subpopulation are shown for each geographical region based on the available information of self-reported origin (North, Northeast, Central, and South). </p>", "links"=>[], "tags"=>["ippca", "992", "thai"], "article_id"=>840706, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079522.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_resolution_ipPCA_assignment_of_992_Thai_individuals_/840706", "title"=>"High-resolution ipPCA assignment of 992 Thai individuals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-04 02:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1266550"], "description"=>"<p>An amalgamated worldwide dataset of 1842 individuals genotyped for 41,569 SNPs was analyzed by PHYLIP. The minor allele frequencies for each population were calculated and used as input to produce the dissimilarity matrix using Nei’s approach for unrooted NJ tree. The data were comprised of 850 individuals from 40 populations (dataset no.1; [29]), 618 Thai individuals (dataset no. 2; [30]) and 374 Thai individuals (dataset no. 3; this study). The Thai individuals from datasets no. 2 and 3 were assumed to belong to the same population and then separated into regional subpopulations based on self-reported origins: Thai (C), Thai (NE), Thai (N) and Thai (S). The other population labels are the same as those reported previously in [29], except “Thai” which has been re-labeled as “Thai-Moken”. The consensus tree from 100 bootstrap replicates is shown, and the bootstrap values are indicated on each node of the tree. Southeast and East Asian populations are ringed and the clades separating Thai subpopulations are in red.</p>", "links"=>[], "tags"=>["neighbor-joining", "unrooted"], "article_id"=>840701, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079522.g001", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Consensus_population_Neighbor_Joining_unrooted_Tree_/840701", "title"=>"Consensus population Neighbor-Joining unrooted Tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-04 02:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1266557"], "description"=>"<div><p>A)\t972 individuals from datasets no. 2 and 3 (ipPCA Outliers removed) were combined and analyzed by ADMIXTURE utilizing 438,503 SNP markers. The individuals were grouped according to the subpopulation assignments made by ipPCA shown in Figure 4. </p>\n\t\t\t\t\t<p>B)\tBox and whiskers plots for K=3 ADMIXTURE-inferred ancestral components (blue, yellow and red) of ipPCA-assigned subpopulations SPA, B, C and D.</p></div>", "links"=>[], "tags"=>["ancestry", "972"], "article_id"=>840708, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079522.g005", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_resolution_ancestry_analysis_of_972_Thais_/840708", "title"=>"High-resolution ancestry analysis of 972 Thais.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-04 02:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1266554"], "description"=>"<p>The amalgamated worldwide dataset of 1842 individuals was analyzed by the ADMIXTURE program. The number of K ancestral clusters was varied from 2 to 10. Individuals were grouped according to the subpopulation assignments made by ipPCA (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079522#pone-0079522-g002\" target=\"_blank\">Figure 2</a>). The ordering of individuals within each subpopulation group is arbitrary.</p>", "links"=>[], "tags"=>[], "article_id"=>840705, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079522.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ancestry_analysis_by_ADMIXTURE_/840705", "title"=>"Ancestry analysis by ADMIXTURE.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-04 02:50:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1266552"], "description"=>"<p>The amalgamated worldwide dataset of 1842 individuals was analyzed by ipPCA. The Thai ethno/geographical labels pertaining to datasets 2 and 3 are italicized; all other labels are the same as those shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079522#pone-0079522-g001\" target=\"_blank\">Figure 1</a>. Individuals were assigned into 24 genetically distinct subpopulations (SP1 to 24) by ipPCA. 20 Thai individuals that could not be assigned to subpopulations are not shown. The height of each subpopulation bar is proportional to the number of assigned individuals. </p>", "links"=>[], "tags"=>["subpopulation"], "article_id"=>840703, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Pongsakorn Wangkumhang", "Philip James Shaw", "Kridsadakorn Chaichoompu", "Chumpol Ngamphiw", "Anunchai Assawamakin", "Manit Nuinoon", "Orapan Sripichai", "Saovaros Svasti", "Suthat Fucharoen", "Verayuth Praphanphoj", "Sissades Tongsima"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079522.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ipPCA_subpopulation_assignment_/840703", "title"=>"ipPCA subpopulation assignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-04 02:50:00"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"21", "full-text"=>"25", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"17", "full-text"=>"16", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"23", "full-text"=>"24", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"21", "full-text"=>"21", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[269, 448, 558, 658, 744, 830, 914, 995, 1068, 1139, 1214, 1284, 1349]}, {"subject_area"=>"/People and places", "average_usage"=>[270, 456, 573, 676, 773, 867, 955, 1037, 1120, 1205, 1286, 1363, 1436]}, {"subject_area"=>"/People and places/Geographical locations", "average_usage"=>[263, 456, 571, 673, 776, 866, 955, 1040, 1132, 1217, 1310, 1391, 1454]}, {"subject_area"=>"/People and places/Population groupings", "average_usage"=>[265, 456, 578, 682, 782, 881, 965, 1053, 1133, 1223, 1310, 1391, 1457]}]}
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