A Spatial Framework for Understanding Population Structure and Admixture
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{"title"=>"A Spatial Framework for Understanding Population Structure and Admixture", "type"=>"journal", "authors"=>[{"first_name"=>"Gideon S.", "last_name"=>"Bradburd", "scopus_author_id"=>"48360914200"}, {"first_name"=>"Peter L.", "last_name"=>"Ralph", "scopus_author_id"=>"35424624800"}, {"first_name"=>"Graham M.", "last_name"=>"Coop", "scopus_author_id"=>"6507540172"}], "year"=>2016, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537404", "doi"=>"10.1371/journal.pgen.1005703", "sgr"=>"84958284610", "scopus"=>"2-s2.0-84958284610", "isbn"=>"1553-7390", "pmid"=>"26771578", "pui"=>"608034813"}, "id"=>"f2dbc859-bdc3-3c68-b50c-fd671591c41f", "abstract"=>"Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build \"geogenetic maps,\" which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.", "link"=>"http://www.mendeley.com/research/spatial-framework-understanding-population-structure-admixture", "reader_count"=>247, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>5, "Researcher"=>60, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>94, "Student > Postgraduate"=>7, "Student > Master"=>39, "Other"=>5, "Student > Bachelor"=>7, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>5, "Researcher"=>60, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>94, "Student > Postgraduate"=>7, "Student > Master"=>39, "Other"=>5, "Student > Bachelor"=>7, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>2, "Environmental Science"=>11, "Biochemistry, Genetics and Molecular Biology"=>32, "Mathematics"=>3, "Agricultural and Biological Sciences"=>180, "Medicine and Dentistry"=>4, "Arts and Humanities"=>3, "Social Sciences"=>2, "Computer Science"=>3, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>180}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>32}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>11}, "Arts and Humanities"=>{"Arts and Humanities"=>3}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>22, "United Kingdom"=>1, "Portugal"=>3, "Switzerland"=>1, "Spain"=>1, "Canada"=>2, "Austria"=>2, "Finland"=>1, "Brazil"=>3, "Australia"=>1, "France"=>1, "Germany"=>3}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4786549"], "description"=>"<p>Individual labels are colored by subspecies as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.g005\" target=\"_blank\">Fig 5a</a>. <b>a)</b> map inferred with admixture; <b>b)</b> close-up of all non-<i>nitidus</i> samples in the admixture map.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079840, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Inferred_maps_for_warbler_individuals_with_admixture_inference_/3079840", "title"=>"Inferred maps for warbler individuals with admixture inference.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786552"], "description"=>"<p><b>a)</b> complete map; <b>b)</b> close-up of Eurasian samples.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079843, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Geogenetic_map_of_human_samples_inferred_without_admixture_/3079843", "title"=>"Geogenetic map of human samples, inferred without admixture.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786555"], "description"=>"<p>Labels are colored as in as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.g005\" target=\"_blank\">Fig 5b</a>. Italicized labels denote locations of admixture sources, with opacity proportional to the amount of admixture drawn by the sample. <b>a)</b> complete map; <b>b)</b> close-up of Eurasian samples.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079846, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Geogenetic_map_of_human_samples_inferred_with_admixture_/3079846", "title"=>"Geogenetic map of human samples, inferred with admixture.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786558"], "description"=>"<p>Labels are colored as in as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.g005\" target=\"_blank\">Fig 5b</a>.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079849, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g010", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Admixture_proportions_95_CIs_for_each_human_population_sample_/3079849", "title"=>"Admixture proportions (95% CIs) for each human population sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786561"], "description"=>"<p>Lines show the covariances populations <i>A</i>, <i>C</i>, and <i>D</i> would have with population <i>B</i> as a function of <i>B</i>’s location with no admixture, under the parametric form of <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.e010\" target=\"_blank\">Eq (2)</a>. The colored dots above ‘<i>B</i>’ show the covariances observed with <i>B</i> at that location given that <i>B</i> has 40% admixture from <i>D</i>. There is no spatial configuration that induces unadmixed covariances remotely similar to those observed.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079852, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g011", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Illustrated_example_of_spatial_covariance_and_the_effects_of_admixture_/3079852", "title"=>"Illustrated example of spatial covariance and the effects of admixture.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786531"], "description"=>"<p>The smaller circles in the simulation scenarios represent unsampled populations. <b>a)</b> the configuration of simulated populations on a simple lattice with spatially homogeneous migration rates (a plot showing the first two Principal Component axes for this simulation is given in a); <b>b)</b> a lattice with a barrier along the center line of longitude, across which migration rates are reduced by a factor of 5; <b>c)</b> a lattice with recent expansion on the eastern margin; <b>d)</b> the maximum <i>a posteriori</i> (MAP) estimate from the posterior distribution of population locations under the scenario in 1a; <b>e)</b> MAP estimate of population locations under the scenario in 1b; <b>f)</b> MAP estimate of population locations under the scenario in 1c.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079822, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Simulation_scenarios_and_their_corresponding_geogenetic_maps_estimated_with_SpaceMix_/3079822", "title"=>"Simulation scenarios and their corresponding geogenetic maps estimated with SpaceMix.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786564"], "description"=>"<p>List of models that may be specified using SpaceMix, along with the number and identity of free parameters in each.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079855, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/List_of_models_that_may_be_specified_using_SpaceMix_along_with_the_number_and_identity_of_free_parameters_in_each_/3079855", "title"=>"List of models that may be specified using SpaceMix, along with the number and identity of free parameters in each.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786534"], "description"=>"<p><b>a)</b> a lattice with a recent admixture event between population 1 in the southwest corner and population 30 in the northeast corner, so that population 30 is drawing half of its ancestry from population 1 (a plot showing the first two Principal Component axes for this simulation is given in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.s002\" target=\"_blank\">S2 Fig</a> panel b); <b>b)</b> the estimate of population locations under this scenario; <b>c)</b> the estimate of population locations and their sources of admixture under this scenario. The 95% credible interval on <i>w</i><sub>30</sub> is 0.36–0.40. In panel (c), the width and opacity of the admixture arrows are drawn proportional the admixture proportions.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079825, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Simulation_scenarios_and_SpaceMix_inference_/3079825", "title"=>"Simulation scenarios and SpaceMix inference.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786567"], "description"=>"<p> is the mean of the pairwise distances between observed locations <i>G</i><sup>(<i>obs</i>)</sup>.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079858, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/List_of_parameters_used_in_the_SpaceMix_models_along_with_their_descriptions_and_priors_/3079858", "title"=>"List of parameters used in the SpaceMix models, along with their descriptions and priors.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786537"], "description"=>"<p>Following <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.e025\" target=\"_blank\">Eq (6)</a>, populations <i>i</i> and <i>j</i> are drawing admixture in proportions <i>w</i><sub><i>i</i></sub> and <i>w</i><sub><i>j</i></sub> from their respective sources of admixture, <i>i</i>* and <i>j</i>*, and all pairwise spatial covariances (the <i>F</i>’s) are shown. In this cartoon example, population <i>j</i> is drawing more admixture from its source <i>j</i>* than <i>i</i> is from its source <i>i</i>* (i.e., <i>w</i><sub><i>j</i></sub> > <i>w</i><sub><i>i</i></sub>).</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079828, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_illustration_of_the_form_of_the_admixed_covariance_/3079828", "title"=>"An illustration of the form of the admixed covariance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786540"], "description"=>"<p>Green arrows denote admixture from a source to a target population in the simulation. <b>a)</b> lattice with a barrier and an admixture event (10%) across the barrier to an ‘inland’ population; <b>b)</b> the inferred population map for the scenario in (a), where the admixed population 23 is the only population drawing non-negligible admixture (95% CI: 0.02-0.08); <b>c)</b> lattice with a barrier and an admixture event (40%) across the barrier to a ‘neighbor’ population on the border of the barrier; <b>(d)</b> the inferred population map for the scenario in (c), where the admixed population 18 is the only population drawing non-negligible admixture (95% CI: 0.04–0.14).</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079831, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Simulation_scenarios_and_inferred_population_maps_for_two_different_admixture_scenarios_/3079831", "title"=>"Simulation scenarios and inferred population maps for two different admixture scenarios.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4749214", "https://ndownloader.figshare.com/files/4749274", "https://ndownloader.figshare.com/files/4749277", "https://ndownloader.figshare.com/files/4749280", "https://ndownloader.figshare.com/files/4749283", "https://ndownloader.figshare.com/files/4749286", "https://ndownloader.figshare.com/files/4749289", "https://ndownloader.figshare.com/files/4749292", "https://ndownloader.figshare.com/files/4749295", "https://ndownloader.figshare.com/files/4749298", "https://ndownloader.figshare.com/files/4749301", "https://ndownloader.figshare.com/files/4749304", "https://ndownloader.figshare.com/files/4749307", "https://ndownloader.figshare.com/files/4786513", "https://ndownloader.figshare.com/files/4786516", "https://ndownloader.figshare.com/files/4786519", "https://ndownloader.figshare.com/files/4786522", "https://ndownloader.figshare.com/files/4786525", "https://ndownloader.figshare.com/files/4749271", "https://ndownloader.figshare.com/files/4749268", "https://ndownloader.figshare.com/files/4749217", "https://ndownloader.figshare.com/files/4749220", "https://ndownloader.figshare.com/files/4749223", "https://ndownloader.figshare.com/files/4749226", "https://ndownloader.figshare.com/files/4749229", "https://ndownloader.figshare.com/files/4749232", "https://ndownloader.figshare.com/files/4749235", "https://ndownloader.figshare.com/files/4749238", "https://ndownloader.figshare.com/files/4749241", "https://ndownloader.figshare.com/files/4749244", "https://ndownloader.figshare.com/files/4749247", "https://ndownloader.figshare.com/files/4749250", "https://ndownloader.figshare.com/files/4749253", "https://ndownloader.figshare.com/files/4749256", "https://ndownloader.figshare.com/files/4749259", "https://ndownloader.figshare.com/files/4749262", "https://ndownloader.figshare.com/files/4749265", "https://ndownloader.figshare.com/files/4786528"], "description"=>"<div><p>Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (<i>Phylloscopus trochiloides</i>), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.</p></div>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3044185, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1005703.s001", "https://dx.doi.org/10.1371/journal.pgen.1005703.s021", "https://dx.doi.org/10.1371/journal.pgen.1005703.s022", "https://dx.doi.org/10.1371/journal.pgen.1005703.s023", "https://dx.doi.org/10.1371/journal.pgen.1005703.s024", "https://dx.doi.org/10.1371/journal.pgen.1005703.s025", "https://dx.doi.org/10.1371/journal.pgen.1005703.s026", "https://dx.doi.org/10.1371/journal.pgen.1005703.s027", "https://dx.doi.org/10.1371/journal.pgen.1005703.s028", "https://dx.doi.org/10.1371/journal.pgen.1005703.s029", "https://dx.doi.org/10.1371/journal.pgen.1005703.s030", "https://dx.doi.org/10.1371/journal.pgen.1005703.s031", "https://dx.doi.org/10.1371/journal.pgen.1005703.s032", "https://dx.doi.org/10.1371/journal.pgen.1005703.s033", "https://dx.doi.org/10.1371/journal.pgen.1005703.s034", "https://dx.doi.org/10.1371/journal.pgen.1005703.s035", "https://dx.doi.org/10.1371/journal.pgen.1005703.s036", "https://dx.doi.org/10.1371/journal.pgen.1005703.s037", "https://dx.doi.org/10.1371/journal.pgen.1005703.s020", "https://dx.doi.org/10.1371/journal.pgen.1005703.s019", "https://dx.doi.org/10.1371/journal.pgen.1005703.s002", "https://dx.doi.org/10.1371/journal.pgen.1005703.s003", "https://dx.doi.org/10.1371/journal.pgen.1005703.s004", "https://dx.doi.org/10.1371/journal.pgen.1005703.s005", "https://dx.doi.org/10.1371/journal.pgen.1005703.s006", "https://dx.doi.org/10.1371/journal.pgen.1005703.s007", "https://dx.doi.org/10.1371/journal.pgen.1005703.s008", "https://dx.doi.org/10.1371/journal.pgen.1005703.s009", "https://dx.doi.org/10.1371/journal.pgen.1005703.s010", "https://dx.doi.org/10.1371/journal.pgen.1005703.s011", "https://dx.doi.org/10.1371/journal.pgen.1005703.s012", "https://dx.doi.org/10.1371/journal.pgen.1005703.s013", "https://dx.doi.org/10.1371/journal.pgen.1005703.s014", "https://dx.doi.org/10.1371/journal.pgen.1005703.s015", "https://dx.doi.org/10.1371/journal.pgen.1005703.s016", "https://dx.doi.org/10.1371/journal.pgen.1005703.s017", "https://dx.doi.org/10.1371/journal.pgen.1005703.s018", "https://dx.doi.org/10.1371/journal.pgen.1005703.s038"], "stats"=>{"downloads"=>4, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Spatial_Framework_for_Understanding_Population_Structure_and_Admixture/3044185", "title"=>"A Spatial Framework for Understanding Population Structure and Admixture", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786543"], "description"=>"<p><b>(a)</b> greenish warbler subspecies distributions of all 22 sampled populations (breeding grounds), consisting of 95 individuals and colored by subspecies [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.ref046\" target=\"_blank\">46</a>]; <b>(b)</b> sampling map for human dataset, consisting of 1,490 individuals from 95 population samples [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.ref050\" target=\"_blank\">50</a>].</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079834, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sampling_maps_of_both_empirical_systems_analyzed_/3079834", "title"=>"Sampling maps of both empirical systems analyzed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786546"], "description"=>"<p>Population labels are colored as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005703#pgen.1005703.g005\" target=\"_blank\">Fig 5a</a>. <b>a)</b> the map inferred with no admixture inference; <b>b)</b> the map inferred with admixture inference.</p>", "links"=>[], "tags"=>["nonlocal gene flow", "gene flow", "sample", "geogenetic", "sampling", "admixture", "allele frequency covariance", "Admixture Geographic patterns"], "article_id"=>3079837, "categories"=>["Genetics", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified"], "users"=>["Gideon S. Bradburd", "Peter L. Ralph", "Graham M. Coop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1005703.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Inferred_maps_for_warbler_populations_/3079837", "title"=>"Inferred maps for warbler populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-15 08:27:06"}

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  • {"unique-ip"=>"16", "full-text"=>"13", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"14", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"12", "full-text"=>"13", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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