The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland
Publication Date
June 05, 2009
Journal
PLOS Genetics
Authors
Alkes L. Price, Agnar Helgason, Snaebjorn Palsson, Hreinn Stefansson, et al
Volume
5
Issue
6
Pages
e1000505
DOI
http://doi.org/10.1371/journal.pgen.1000505
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000505
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19503599
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684636
Europe PMC
http://europepmc.org/abstract/MED/19503599
Web of Science
000268444600038
Scopus
67651028392
Mendeley
http://www.mendeley.com/research/impact-divergence-time-nature-population-structure-example-iceland
Events
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Mendeley | Further Information

{"title"=>"The impact of divergence time on the nature of population structure: An example from Iceland", "type"=>"journal", "authors"=>[{"first_name"=>"Alkes L.", "last_name"=>"Price", "scopus_author_id"=>"57020794000"}, {"first_name"=>"Agnar", "last_name"=>"Helgason", "scopus_author_id"=>"7005948504"}, {"first_name"=>"Snaebjorn", "last_name"=>"Palsson", "scopus_author_id"=>"7004424940"}, {"first_name"=>"Hreinn", "last_name"=>"Stefansson", "scopus_author_id"=>"6604083232"}, {"first_name"=>"David", "last_name"=>"St. Clair", "scopus_author_id"=>"35354078200"}, {"first_name"=>"Ole A.", "last_name"=>"Andreassen", "scopus_author_id"=>"56600076200"}, {"first_name"=>"David", "last_name"=>"Reich", "scopus_author_id"=>"7102313000"}, {"first_name"=>"Augustine", "last_name"=>"Kong", "scopus_author_id"=>"34667880600"}, {"first_name"=>"Kari", "last_name"=>"Stefansson", "scopus_author_id"=>"7005997553"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "isbn"=>"1553-7404 (Electronic)", "doi"=>"10.1371/journal.pgen.1000505", "pui"=>"354995752", "sgr"=>"67651028392", "pmid"=>"19503599", "scopus"=>"2-s2.0-67651028392"}, "id"=>"de42f3f0-7c99-3a24-a0c7-11c0941e0fe5", "abstract"=>"The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.", "link"=>"http://www.mendeley.com/research/impact-divergence-time-nature-population-structure-example-iceland", "reader_count"=>153, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>13, "Researcher"=>45, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>9, "Other"=>13, "Student > Bachelor"=>8, "Lecturer"=>3, "Professor"=>11}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>13, "Researcher"=>45, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>9, "Other"=>13, "Student > Bachelor"=>8, "Lecturer"=>3, "Professor"=>11}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Agricultural and Biological Sciences"=>94, "Arts and Humanities"=>6, "Chemistry"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>6, "Engineering"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Mathematics"=>2, "Medicine and Dentistry"=>14, "Neuroscience"=>1, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>14}, "Social Sciences"=>{"Social Sciences"=>2}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>6}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>94}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"Uruguay"=>1, "United States"=>9, "United Kingdom"=>2, "Iceland"=>2, "Spain"=>1, "Canada"=>1, "Austria"=>1, "Netherlands"=>1, "Norway"=>1, "South Africa"=>2, "Mexico"=>2, "Italy"=>1, "Australia"=>1, "Germany"=>1}, "group_count"=>9}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/896030"], "description"=>"<p>PCA plot of samples from Norway and Scotland projected onto PCs computed using samples with most of their ancestry from 11 regions of Iceland.</p>", "links"=>[], "tags"=>["samples", "norway", "scotland", "projected", "pcs", "computed", "ancestry", "11", "regions"], "article_id"=>566477, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCA_plot_of_samples_from_Norway_and_Scotland_projected_onto_PCs_computed_using_samples_with_most_of_their_ancestry_from_11_regions_of_Iceland_/566477", "title"=>"PCA plot of samples from Norway and Scotland projected onto PCs computed using samples with most of their ancestry from 11 regions of Iceland.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:47:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/896314"], "description"=>"<p>Heterozygosity values are listed on the diagonal. Standard errors of <i>F</i><sub>ST</sub> estimates were equal to 0.0007 for all comparisons involving Region 1 and 0.0001 for all other comparisons.</p>", "links"=>[], "tags"=>["heterozygosity", "estimates", "11", "regions"], "article_id"=>566771, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_F_ST_and_heterozygosity_estimates_for_11_regions_of_Iceland_/566771", "title"=>"Pairwise <i>F</i><sub>ST</sub> and heterozygosity estimates for 11 regions of Iceland.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:52:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/896265"], "description"=>"<p>For each region, we list the total number of Icelandic samples with majority ancestry from that region, and the number of unrelated samples that were selected.</p>", "links"=>[], "tags"=>["icelandic", "samples", "ancestry", "11"], "article_id"=>566714, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_for_Icelandic_samples_with_majority_ancestry_from_each_of_the_11_regions_/566714", "title"=>"Data for Icelandic samples with majority ancestry from each of the 11 regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:51:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/896290"], "description"=>"<p>A total of 12 markers in the <i>TLR</i> region and 5 markers in the <i>NADSYN1</i> region achieved a nominal P-value of 0.0001 or lower (data not shown). We list with an asterisk one additional marker whose differentiation is highly suggestive (see text). Gene names are listed for markers located between the transcription start and end sites of a gene.</p>", "links"=>[], "tags"=>["markers", "differentiation", "iceland", "scotland"], "article_id"=>566741, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_markers_whose_unusual_differentiation_between_Iceland_and_Scotland_is_genomewide_significant_/566741", "title"=>"List of markers whose unusual differentiation between Iceland and Scotland is genomewide-significant.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:52:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/896114"], "description"=>"<p>P-P plots of allele frequency differentiation between region <i>r</i> and the union of all other regions, for each value of <i>r</i> ().</p>", "links"=>[], "tags"=>["plots", "allele", "differentiation"], "article_id"=>566566, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_P_plots_of_allele_frequency_differentiation_between_region_r_and_the_union_of_all_other_regions_for_each_value_of_r_/566566", "title"=>"P-P plots of allele frequency differentiation between region <i>r</i> and the union of all other regions, for each value of <i>r</i> ().", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:49:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/443904", "https://ndownloader.figshare.com/files/443934", "https://ndownloader.figshare.com/files/443964", "https://ndownloader.figshare.com/files/444010"], "description"=>"<div><p>The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.</p></div>", "links"=>[], "tags"=>["divergence", "iceland"], "article_id"=>147508, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000505.s001", "https://dx.doi.org/10.1371/journal.pgen.1000505.s002", "https://dx.doi.org/10.1371/journal.pgen.1000505.s003", "https://dx.doi.org/10.1371/journal.pgen.1000505.s004"], "stats"=>{"downloads"=>23, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Impact_of_Divergence_Time_on_the_Nature_of_Population_Structure_An_Example_from_Iceland/147508", "title"=>"The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-06-05 02:05:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/896203"], "description"=>"<p>The nine SNPs from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000505#pgen-1000505-t003\" target=\"_blank\">Table 3</a> are displayed as squares.</p>", "links"=>[], "tags"=>["allele", "differentiation", "norway"], "article_id"=>566653, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_P_plot_of_allele_frequency_differentiation_between_Norway_and_Scotland_/566653", "title"=>"P-P plot of allele frequency differentiation between Norway and Scotland.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:50:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/895810"], "description"=>"<p>The interior region is not numbered, as it is uninhabited. Sample sizes for each region are listed in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000505#pgen-1000505-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["11", "regions", "color-coded"], "article_id"=>566259, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_11_regions_of_Iceland_color_coded_to_match_Figures_2_and_3_/566259", "title"=>"Map of 11 regions of Iceland, color-coded to match Figures 2 and 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:44:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/895921"], "description"=>"<p>PCA plots of (A) samples with most of their ancestry from 11 regions of Iceland and (B) samples with most of their ancestry from 11 regions of Iceland, together with a set of 250 randomly selected Icelandic samples.</p>", "links"=>[], "tags"=>["plots", "samples", "ancestry", "11", "regions", "iceland", "250", "randomly", "icelandic"], "article_id"=>566369, "categories"=>["Genetics"], "users"=>["Alkes L. Price", "Agnar Helgason", "Snaebjorn Palsson", "Hreinn Stefansson", "David St. Clair", "Ole A. Andreassen", "David Reich", "Augustine Kong", "Kari Stefansson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000505.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCA_plots_of_A_samples_with_most_of_their_ancestry_from_11_regions_of_Iceland_and_B_samples_with_most_of_their_ancestry_from_11_regions_of_Iceland_together_with_a_set_of_250_randomly_selected_Icelandic_samples_/566369", "title"=>"PCA plots of (A) samples with most of their ancestry from 11 regions of Iceland and (B) samples with most of their ancestry from 11 regions of Iceland, together with a set of 250 randomly selected Icelandic samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:46:09"}

PMC Usage Stats | Further Information

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