Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure
Publication Date
December 09, 2005
Journal
PLOS Genetics
Authors
Noah A Rosenberg, Saurabh Mahajan, Sohini Ramachandran, Chengfeng Zhao, et al
Volume
1
Issue
6
Pages
e70
DOI
http://doi.org/10.1371/journal.pgen.0010070
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.0010070
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/16355252
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310579
Europe PMC
http://europepmc.org/abstract/MED/16355252
Web of Science
000234900800005
Scopus
33746410518
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/960995"], "description"=>"<p>Each point shows the mean clusteredness of 20 runs with the specified number of loci and allele frequency correlation model: two replicates for each of ten sets of loci (for 993 loci, it is the mean of two runs, as only one set of loci was used). From left to right, the three groups of points in each plot respectively represent sets of 100, 250, and 500 individuals.</p>", "links"=>[], "tags"=>["clusteredness", "geographic", "dispersion"], "article_id"=>630993, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_Clusteredness_versus_Geographic_Dispersion_as_Measured_by_A_n_/630993", "title"=>"Mean Clusteredness versus Geographic Dispersion as Measured by <i>A<sub>n</sub></i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:54:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/961080"], "description"=>"<p>The two sets of 100 individuals represent extremes of the distribution of <i>A<sub>n</sub>:</i> the plots on the left are based on a more geographically random sample, and those on the right are based on a less random sample. Each plot is based on the higher-likelihood run among the two runs performed with the given combination of loci and individuals. In all plots, individuals and populations are in the same order as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-g002\" target=\"_blank\">Figure 2</a>. Black vertical lines at the bottom of the figure separate populations from the different geographic regions described in [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-b003\" target=\"_blank\">3</a>], with the asterisk representing Oceania.</p>", "links"=>[], "tags"=>["sets", "100", "993", "markers", "correlated", "allele", "frequencies"], "article_id"=>631074, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_Population_Structure_Based_on_Two_Different_Sets_of_100_Individuals_Using_993_Markers_and_the_Correlated_Allele_Frequencies_Model_/631074", "title"=>"Inferred Population Structure Based on Two Different Sets of 100 Individuals, Using 993 Markers and the Correlated Allele Frequencies Model", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/960867"], "description"=>"<p>Each point shows the mean clusteredness of 2,000 runs with the specified sample size and allele frequency correlation model: two replicates for each of ten sets of loci for each of 100 sets of individuals (for 1,048 individuals, it is the mean of 20 runs, as only one set of individuals was used; for 1,048 individuals and 993 loci, it is the mean of two runs, as only one set of loci was used). Error bars denote standard deviations. The <i>x</i>-axis is plotted on a logarithmic scale.</p>", "links"=>[], "tags"=>["clusteredness"], "article_id"=>630868, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_Clusteredness_versus_Number_of_Loci_/630868", "title"=>"Mean Clusteredness versus Number of Loci", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:53:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/961156"], "description"=>"<p>Red circles indicate comparisons between pairs of populations with majority representation in the same cluster in the <i>K</i> = 5 plot of <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-g002\" target=\"_blank\">Figure 2</a>; blue triangles indicate pairs with one population from Eurasia and one from East Asia; brown squares indicate pairs with one population from Africa and the other from Eurasia; and green diamonds indicate pairs with one population from East Asia and the other from either Oceania or America. Comparisons involving one of Hazara, Kalash, and Uygur and other populations from Eurasia or East Asia are marked 1, 2, and 3, respectively. No comparisons are shown between any of these three groups and any African population.</p>", "links"=>[], "tags"=>["geographic", "pairs"], "article_id"=>631153, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g006", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_and_Geographic_Distance_for_Pairs_of_Populations_/631153", "title"=>"Genetic and Geographic Distance for Pairs of Populations", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:55:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/960784"], "description"=>"<p>Each individual is represented by a thin line partitioned into <i>K</i> colored segments that represent the individual's estimated membership fractions in <i>K</i> clusters. Each plot, produced with DISTRUCT [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-b023\" target=\"_blank\">23</a>], is based on the highest-likelihood run of ten runs: the two runs that were used in further analysis, and the eight runs described under “Cluster Analysis using STRUCTURE.” As in [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-b003\" target=\"_blank\">3</a>], four of ten runs with <i>K</i> = 3 separated a cluster corresponding to East Asia instead of one corresponding to Europe, the Middle East, and Central/South Asia. Two of ten runs with <i>K</i> = 5 separated Surui instead of Oceania. The highest-likelihood run of the ten runs with <i>K</i> = 6, shown in the figure, had a different pattern from the other nine runs (not shown). These other runs, instead of subdividing native Americans into two clusters, subdivided a cluster roughly similar to the Kalash cluster seen in [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070#pgen-0010070-b003\" target=\"_blank\">3</a>], except with a less pronounced separation of the Kalash population. The clusteredness scores for the plots shown with <i>K</i> = 2, 3, 4, 5, and 6 are 0.50, 0.76, 0.84, 0.86, and 0.87, respectively.</p>", "links"=>[], "tags"=>["individuals", "993", "assuming", "correlations", "allele", "frequencies"], "article_id"=>630778, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_Population_Structure_Based_on_1_048_Individuals_and_993_Markers_Assuming_Correlations_among_Allele_Frequencies_across_Clusters_/630778", "title"=>"Inferred Population Structure Based on 1,048 Individuals and 993 Markers, Assuming Correlations among Allele Frequencies across Clusters", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:52:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/960661"], "description"=>"<p>Each distribution is obtained by binning the values of <i>A<sub>n</sub></i> for 100,000 sets of points.</p>", "links"=>[], "tags"=>["geographic", "dispersion", "statistic", "sets", "100", "points", "randomly", "sampled", "plotted", "locations", "individuals"], "article_id"=>630653, "categories"=>["Biological Sciences", "Mathematics", "Genetics", "Evolutionary Biology"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Sohini Ramachandran", "Chengfeng Zhao", "Jonathan K Pritchard", "Marcus W Feldman"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0010070.g001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_Geographic_Dispersion_Statistic_A_n_for_Sets_of_100_Points_Randomly_Sampled_from_a_Sphere_Randomly_Sampled_from_the_Land_Area_of_the_Earth_from_among_the_Points_Plotted_in_Figure_5_of_11_and_Randomly_Sampled_from_the_Reported_Location/630653", "title"=>"Distribution of the Geographic Dispersion Statistic <i>(A<sub>n</sub>)</i> for Sets of 100 Points Randomly Sampled from a Sphere, Randomly Sampled from the Land Area of the Earth (from among the Points Plotted in Figure 5 of [11]), and Randomly Sampled from the Reported Locations of Individuals in the Dataset", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:51:41"}

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  • {"unique-ip"=>"24", "full-text"=>"27", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"50", "full-text"=>"58", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"0", "cited-by"=>"5", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"43", "full-text"=>"45", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"32", "full-text"=>"34", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"30", "full-text"=>"33", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"23", "full-text"=>"26", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}

Relative Metric

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