ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles
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{"title"=>"ObStruct: A method to objectively analyse factors driving population structure using Bayesian ancestry profiles", "type"=>"journal", "authors"=>[{"first_name"=>"Velimir", "last_name"=>"Gayevskiy", "scopus_author_id"=>"57199511807"}, {"first_name"=>"Steffen", "last_name"=>"Klaere", "scopus_author_id"=>"23497541200"}, {"first_name"=>"Sarah", "last_name"=>"Knight", "scopus_author_id"=>"7202604020"}, {"first_name"=>"Matthew R.", "last_name"=>"Goddard", "scopus_author_id"=>"7103363983"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24416362", "doi"=>"10.1371/journal.pone.0085196", "sgr"=>"84897464804", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84897464804", "issn"=>"19326203", "pui"=>"372730859"}, "id"=>"3fd7c304-5f78-3c39-843a-f54421e2d2fd", "abstract"=>"Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin) correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.", "link"=>"http://www.mendeley.com/research/obstruct-method-objectively-analyse-factors-driving-population-structure-using-bayesian-ancestry-pro", "reader_count"=>58, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>47, "Physics and Astronomy"=>2, "Chemical Engineering"=>1, "Psychology"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1, "South Africa"=>1, "United Kingdom"=>1, "France"=>1, "Germany"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1343492"], "description"=>"<p>Error bars denote the standard error of three separate simulations for each sampling time point.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "generations", "simulated", "divergence", "inferred"], "article_id"=>898112, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Change_in_population_structure_over_1_000_generations_of_simulated_population_divergence_as_inferred_by_a_Structure_and_b_InStruct_/898112", "title"=>"Change in population structure over 1,000 generations of simulated population divergence as inferred by (a) Structure and (b) InStruct.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343498", "https://ndownloader.figshare.com/files/1343499"], "description"=>"<div><p>Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin) correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 <i>Saccharomyces cerevisiae</i> from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.</p></div>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "objectively", "analyse", "bayesian", "ancestry"], "article_id"=>898118, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>[nil, nil], "stats"=>{"downloads"=>7, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/ObStruct_A_Method_to_Objectively_Analyse_Factors_Driving_Population_Structure_Using_Bayesian_Ancestry_Profiles/898118", "title"=>"ObStruct: A Method to Objectively Analyse Factors Driving Population Structure Using Bayesian Ancestry Profiles", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343495"], "description"=>"<p>(a) Mapping the individual data according to the CDA variables. The inner ellipsoid contains 50% of all individuals, the outer ellipsoid contains 95% of all individuals. Individuals are colour- and shape-coded according to their respective sampled region. (b) The HE plot shows the relation of variation in the group means on two variables relative to the error variance. The coloured arrows indicate the position of the inferred populations relative to the axes obtained by the canonical discriminant analysis. The black points indicate predefined populations (WA  =  West Auckland; WI  =  Waiheke Island; HB  =  Hawke's Bay) while numbers at the arrows indicate inferred populations.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "discriminant"], "article_id"=>898115, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Canonical_discriminant_analysis_on_the_i_Saccharomyces_cerevisiae_i_dataset_/898115", "title"=>"Canonical discriminant analysis on the <i>Saccharomyces cerevisiae</i> dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343494"], "description"=>"<p>Ancestry profiles were generated using InStruct with .</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "zealand", "ancestry", "profiles", "179", "sampled", "regions"], "article_id"=>898114, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/of_New_Zealand_showing_distruct_plots_of_ancestry_profiles_for_179_i_S_cerevisiae_i_sampled_from_three_regions_from_19_/898114", "title"=>"of New Zealand showing distruct plots of ancestry profiles for 179 <i>S. cerevisiae</i> sampled from three regions from [19].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343497"], "description"=>"<p>The colours for inferred populations correspond to those seen in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085196#pone-0085196-g002\" target=\"_blank\">Figure 2</a>. The error reported for the continents is the standard error of calculated for three separate chains of each dataset. No such error is reported for inferred populations because the designations for inferred populations differ between chains.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "observed", "inferred", "removed"], "article_id"=>898117, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.t002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Changes_from_the_observed_value_when_each_continent_and_inferred_population_is_removed_in_turn_for_the_human_dataset_/898117", "title"=>"Changes from the observed value when each continent and inferred population is removed in turn for the human dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343496"], "description"=>"<p>The error reported is the standard error of calculating for three separate chains of each dataset.</p><p>Denotes ().</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "calculated", "datasets", "microsatellite"], "article_id"=>898116, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/values_calculated_for_two_experimental_datasets_of_human_and_i_S_cerevisiae_i_microsatellite_profiles_/898116", "title"=>"values calculated for two experimental datasets of human and <i>S. cerevisiae</i> microsatellite profiles.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 02:56:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343493"], "description"=>"<p>Ancestry profiles were generated using structure with .</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Population ecology", "Evolutionary biology", "population genetics", "genetics", "Population biology", "algorithms", "Applied mathematics", "statistics", "Biostatistics", "ancestry", "profiles", "humans", "sampled", "continents"], "article_id"=>898113, "categories"=>["Mathematics", "Biological Sciences", "Information And Computing Sciences"], "users"=>["Velimir Gayevskiy", "Steffen Klaere", "Sarah Knight", "Matthew R. Goddard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085196.g002", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/map_showing_distruct_plots_of_ancestry_profiles_for_humans_sampled_from_seven_continents_from_18_/898113", "title"=>"map showing distruct plots of ancestry profiles for humans sampled from seven continents from [18].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 02:56:46"}

PMC Usage Stats | Further Information

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Relative Metric

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