Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations
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{"title"=>"Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations", "type"=>"journal", "authors"=>[{"first_name"=>"Taras K.", "last_name"=>"Oleksyk", "scopus_author_id"=>"6507375375"}, {"first_name"=>"Kai", "last_name"=>"Zhao", "scopus_author_id"=>"36780671100"}, {"first_name"=>"Francisco M.", "last_name"=>"De La Vega", "scopus_author_id"=>"6701667422"}, {"first_name"=>"Dennis A.", "last_name"=>"Gilbert", "scopus_author_id"=>"7401956057"}, {"first_name"=>"Stephen J.", "last_name"=>"O'Brien", "scopus_author_id"=>"7402355306"}, {"first_name"=>"Michael W.", "last_name"=>"Smith", "scopus_author_id"=>"55698384100"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"45849145445", "scopus"=>"2-s2.0-45849145445", "doi"=>"10.1371/journal.pone.0001712", "isbn"=>"1932-6203", "pui"=>"351903001", "issn"=>"19326203", "pmid"=>"18320033"}, "id"=>"bec62823-146f-345b-9da9-7bba9fc10ed6", "abstract"=>"When a selective sweep occurs in the chromosomal region around a target gene in two populations that have recently separated, it produces three dramatic genomic consequences: 1) decreased multi-locus heterozygosity in the region; 2) elevated or diminished genetic divergence (FST) of multiple polymorphic variants adjacent to the selected locus between the divergent populations, due to the alternative fixation of alleles; and 3) a consequent regional increase in the variance of FST (S2FST) for the same clustered variants, due to the increased alternative fixation of alleles in the loci surrounding the selection target. In the first part of our study, to search for potential targets of directional selection, we developed and validated a resampling-based computational approach; we then scanned an array of 31 different-sized moving windows of SNP variants (5–65 SNPs) across the human genome in a set of European and African American population samples with 183,997 SNP loci after correcting for the recombination rate variation. The analysis revealed 180 regions of recent selection with very strong evidence in either population or both. In the second part of our study, we compared the newly discovered putative regions to those sites previously postulated in the literature, using methods based on inspecting patterns of linkage disequilibrium, population divergence and other methodologies. The newly found regions were cross-validated with those found in nine other studies that have searched for selection signals. Our study was replicated especially well in those regions confirmed by three or more studies. These validated regions were independently verified, using a combination of different methods and different databases in other studies, and should include fewer false positives. The main strength of our analysis method compared to others is that it does not require dense genotyping and therefore can be used with data from population-based genome SNP scans from smaller studies of humans or other species.", "link"=>"http://www.mendeley.com/research/identifying-selected-regions-heterozygosity-divergence-using-lightcoverage-genomic-dataset-two-human", "reader_count"=>70, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>10, "Researcher"=>23, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>10, "Researcher"=>23, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>2, "Student > Master"=>4, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>2, "Agricultural and Biological Sciences"=>57, "Medicine and Dentistry"=>1, "Sports and Recreations"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>57}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>4, "Finland"=>1, "Brazil"=>2, "Mexico"=>1, "France"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/936694"], "description"=>"†<p>Expectation for S<sup>2</sup>F<sub>ST</sub> from ancestral selection is dependent on its direction and magnitude, so this criterion was not evaluated in our analysis.</p><p>Ancestral selection is assumed to occur before the two populations separated, while recent selection is assumed in one or both isolated populations.</p>", "links"=>[], "tags"=>["types", "sweeps", "heterozygosity", "variance", "chromosome", "locus", "populations", "americans", "european"], "article_id"=>607130, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expected_effects_of_different_types_of_selection_sweeps_on_regional_levels_of_heterozygosity_H_and_F_ST_variance_S_2_F_ST_in_the_chromosome_neighborhood_of_a_selected_locus_in_two_populations_African_Americans_AA_and_European_Americans_EA_/607130", "title"=>"Expected effects of different types of selection sweeps on regional levels of heterozygosity (H`) and F<sub>ST</sub> variance (S<sup>2</sup>F<sub>ST</sub>) in the chromosome neighborhood of a selected locus in two populations (African Americans [AA] and European Americans [EA]).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-03-05 01:58:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/936415"], "description"=>"<p>Squares indicate the regions of the ancestral (old) selection, triangles indicate recent selection in Europeans, circles in Africans, and diamonds designate the new selection in both of these populations. A putative selected site is identified where two of the peaks overlap (as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g001\" target=\"_blank\">Figure 1A</a>). Both peaks are identified with a consecutive letter. Locations, genes, and evidence strength (λ) for the putative selection peaks are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s004\" target=\"_blank\">Table S3</a>. For clarity, the figure shows half of the genome: chromosomes 6, 10–14, 17–22 and chromosome X.</p>", "links"=>[], "tags"=>["putative", "regions", "autosomes"], "article_id"=>606855, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scans_for_putative_selection_regions_in_the_autosomes_and_X_chromosome_/606855", "title"=>"Scans for putative selection regions in the autosomes and X chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:54:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/936542"], "description"=>"<p>Solid figures indicate that selected regions detected in at least two of these studies are overlapping. Open symbols indicate that the peaks do not overlap. Locations of regions included in the regions cross-validated by more than one study are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s005\" target=\"_blank\">Table S4</a>. Sequential numbers and locations of all the regions in this comparison are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s006\" target=\"_blank\">Table S5</a>. For clarity, the figure shows half of the genome: chromosomes 1–11.</p>", "links"=>[], "tags"=>["regions", "implicated", "compared", "genome", "scans"], "article_id"=>606982, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g007", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Locations_of_regions_implicated_as_selected_by_our_study_compared_to_six_other_recent_genome_scans_for_selection_4_9_17_23_/606982", "title"=>"Locations of regions implicated as selected by our study compared to six other recent genome scans for selection [4], [9], [17]–[23].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:56:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/935866"], "description"=>"<p>(Bottom) Four kinds of putative selection sites where one of the two populations has either lower values of heterozygosity as well as a rise in S<sup>2</sup>F<sub>ST</sub> values at the same location, or a decreased local heterozygosity in both populations (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-t001\" target=\"_blank\">Table 1</a>). (B) Three examples of known selection regions. <i>CCR5</i> and <i>FOXP2</i> genes have low values of heterozygosity in both Europeans and Africans, implying putative selection in the ancestral population (“old”; see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g002\" target=\"_blank\">Figure 2A</a>, bottom). The region around <i>IL-4</i> (which includes the <i>IL-13</i> gene) shows a putative selection signature, as indicated by a decrease in H`<sub>EA</sub> and H`<sub>AA</sub> and increased S<sup>2</sup>F<sub>ST</sub>. Values of H<sub>EA</sub> (blue), H<sub>AA</sub> (green), and F<sub>ST </sub>(red) are plotted individually with most significant medians (H`<sub>EA </sub>and H`<sub>AA</sub>), and variance of F<sub>ST</sub> (S<sup>2</sup>F<sub>ST</sub>) across 31 sliding windows of size 5 to 65 loci. (Bottom) λ values derived from H`<sub>EA</sub>, H`<sub>AA</sub>, and S<sup>2</sup>F<sub>ST</sub> based on the 5 to 65 loci sliding windows around <i>CCR5</i>, <i>FOXP2</i> and <i>IL4</i>. (C) Similar plots of nine examples from 180 putative selection sites discovered in the current study (all plotted in Figure S3).</p>", "links"=>[], "tags"=>["types", "schematic", "lowest", "fractional", "distributions", "heterozygosity", "45", "european", "americans", "african", "variance", "divergence", "plotted"], "article_id"=>606292, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Evidence_and_types_of_selection_Top_Schematic_of_the_lowest_mean_value_fractional_rank_value_distributions_for_local_heterozygosity_in_a_sample_of_45_European_Americans_H_EA_45_African_Americans_955_H_AA_and_variance_of_population_divergence_955_S_2_F_/606292", "title"=>"(A) Evidence and types of selection: (Top) Schematic of the lowest mean value fractional rank value (λ) distributions for local heterozygosity in a sample of 45 European Americans λ(H`<sub>EA</sub>), 45 African Americans λ(H`<sub>AA</sub>), and variance of population divergence λ(S<sup>2</sup>F<sub>ST</sub>) plotted across a chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:44:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/936615"], "description"=>"<p>Solid figures indicate that selected regions detected in at least two of these studies are overlapping. Open symbols indicate that the peaks do not overlap. Locations of regions included in the regions cross-validated by more than one study are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s005\" target=\"_blank\">Table S4</a>. Sequential numbers and locations of all the regions in this comparison are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s006\" target=\"_blank\">Table S5</a>. For clarity, the figure shows half of the genome: chromosomes 12–23, and chromosome X.</p>", "links"=>[], "tags"=>["regions", "implicated", "compared", "genome", "scans"], "article_id"=>607056, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g008", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Locations_of_regions_implicated_as_selected_by_our_study_compared_to_six_other_recent_genome_scans_for_selection_4_9_17_23_/607056", "title"=>"Locations of regions implicated as selected by our study compared to six other recent genome scans for selection [4], [9], [17]–[23].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:57:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/936260"], "description"=>"<p>Squares indicate the regions of the ancestral (old) selection, triangles indicate recent selection in Europeans, circles in Africans, and diamonds designate the new selection in both of these populations. A putative selected site is identified where two of the peaks overlap (as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g001\" target=\"_blank\">Figure 1A</a>). Both peaks are identified with a consecutive letter. Locations, genes, and evidence strength (λ) for the putative selection peaks are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s004\" target=\"_blank\">Table S3</a>. For clarity, the figure shows half of the genome: chromosomes 1–5, 7–9, 15 and 16.</p>", "links"=>[], "tags"=>["putative", "regions", "autosomes"], "article_id"=>606702, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g005", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scans_for_putative_selection_regions_in_the_autosomes_and_X_chromosome_/606702", "title"=>"Scans for putative selection regions in the autosomes and X chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/461124", "https://ndownloader.figshare.com/files/461131", "https://ndownloader.figshare.com/files/461137", "https://ndownloader.figshare.com/files/461143", "https://ndownloader.figshare.com/files/461159", "https://ndownloader.figshare.com/files/461170", "https://ndownloader.figshare.com/files/461186", "https://ndownloader.figshare.com/files/461194", "https://ndownloader.figshare.com/files/461202"], "description"=>"<div><p>When a selective sweep occurs in the chromosomal region around a target gene in two populations that have recently separated, it produces three dramatic genomic consequences: 1) decreased multi-locus heterozygosity in the region; 2) elevated or diminished genetic divergence (F<sub>ST</sub>) of multiple polymorphic variants adjacent to the selected locus between the divergent populations, due to the alternative fixation of alleles; and 3) a consequent regional increase in the variance of F<sub>ST</sub> (S<sup>2</sup>F<sub>ST</sub>) for the same clustered variants, due to the increased alternative fixation of alleles in the loci surrounding the selection target. In the first part of our study, to search for potential targets of directional selection, we developed and validated a resampling-based computational approach; we then scanned an array of 31 different-sized moving windows of SNP variants (5–65 SNPs) across the human genome in a set of European and African American population samples with 183,997 SNP loci after correcting for the recombination rate variation. The analysis revealed 180 regions of recent selection with very strong evidence in either population or both. In the second part of our study, we compared the newly discovered putative regions to those sites previously postulated in the literature, using methods based on inspecting patterns of linkage disequilibrium, population divergence and other methodologies. The newly found regions were cross-validated with those found in nine other studies that have searched for selection signals. Our study was replicated especially well in those regions confirmed by three or more studies. These validated regions were independently verified, using a combination of different methods and different databases in other studies, and should include fewer false positives. The main strength of our analysis method compared to others is that it does not require dense genotyping and therefore can be used with data from population-based genome SNP scans from smaller studies of humans or other species.</p></div>", "links"=>[], "tags"=>["identifying", "regions", "heterozygosity", "divergence", "light-coverage", "genomic", "dataset", "populations"], "article_id"=>150873, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001712.s001", "https://dx.doi.org/10.1371/journal.pone.0001712.s002", "https://dx.doi.org/10.1371/journal.pone.0001712.s003", "https://dx.doi.org/10.1371/journal.pone.0001712.s004", "https://dx.doi.org/10.1371/journal.pone.0001712.s005", "https://dx.doi.org/10.1371/journal.pone.0001712.s006", "https://dx.doi.org/10.1371/journal.pone.0001712.s007", "https://dx.doi.org/10.1371/journal.pone.0001712.s008", "https://dx.doi.org/10.1371/journal.pone.0001712.s009"], "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identifying_Selected_Regions_from_Heterozygosity_and_Divergence_Using_a_Light_Coverage_Genomic_Dataset_from_Two_Human_Populations/150873", "title"=>"Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-03-05 00:14:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/936096"], "description"=>"<p>(A) Our scan for putative selection regions. A putative selected site is identified as the locus of a peak in two of three tests (λ(H`<sub>EA</sub>), λ(H`<sub>AA</sub>), or λ(S<sup>2</sup>F<sub>ST</sub>)) overlapped (as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g002\" target=\"_blank\">Figure 2A</a>) with ancestral selection (H`<sub>EA</sub> and H`<sub>AA</sub>, squares), along with recent selection in Europeans (H`<sub>EA</sub> and S<sup>2</sup>F<sub>ST</sub>, triangles) and Africans (H`<sub>AA</sub> and S<sup>2</sup>F<sub>ST</sub>, circles; see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g005\" target=\"_blank\">Figures 5</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g006\" target=\"_blank\">6</a> for a full genome scan). Locations, genes, and evidence strength (λ) for the putative selection peaks are in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s004\" target=\"_blank\">Table S3</a>. (B) Locations of regions implicated as selected by our study compared to nine other recent genome scans for selection <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Akey1\" target=\"_blank\">[4]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Huttley1\" target=\"_blank\">[9]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Frazer1\" target=\"_blank\">[17]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Altshuler1\" target=\"_blank\">[18]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Wang1\" target=\"_blank\">[20]</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Nielsen1\" target=\"_blank\">[23]</a>. Solid figures indicate that selected regions detected in at least two of these studies are overlapping (cross-validated). Open symbols indicate that the peaks do not overlap. Our full genome scan (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g005\" target=\"_blank\">Figures 5</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g006\" target=\"_blank\">6</a>) cross-validated 356 regions whose locations are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712.s005\" target=\"_blank\">Table S4</a>. Dotted lines indicate cross-verified for which evidence of a signal is apparent in regions from other studies, but did not pass our criteria for inclusion (See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#s3\" target=\"_blank\">Materials and Methods</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g007\" target=\"_blank\">Figures 7</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone-0001712-g008\" target=\"_blank\">8</a>).</p>", "links"=>[], "tags"=>["regions", "chromosome"], "article_id"=>606538, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scans_for_selected_regions_on_chromosome_2_from_this_work_and_others_4_9_18_20_22_23_/606538", "title"=>"Scans for selected regions on chromosome 2 from this work and others [4], [9], [18], [20], [22], [23].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:48:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/935759"], "description"=>"<p>(A) Sampling and resampling process: (Top) We selected five adjacent SNPs at the beginning of a single chromosome and computed H`<sub>EA</sub>, H`<sub>AA</sub> and S<sup>2</sup>F<sub>ST </sub>for the group, then moved the window sequentially to the right, one SNP at a time (observed values). (Bottom) To establish the baseline, we randomly resampled 10 million groups of five random SNPs on the same chromosome with replacements and computed H`<sub>EA</sub>, H`<sub>AA</sub> and S<sup>2</sup>F<sub>ST </sub>(random values). (B) Determining observed and random distributions of H`<sub>EA,</sub> H`<sub>AA</sub> and S<sup>2</sup>F<sub>ST</sub>: (Top) We built a frequency distribution for each chromosome using observed values; (Bottom) we built a frequency distribution and assigned fractional rank values to the distribution of random values. (C) Superimposing the distributions to derive fractional rank values: the two distributions were combined and each observed value assigned a fractional rank from the closest larger random value. The same computation was done for all 31 SNP window group sizes (N = 5, 7, 9 … 65) 100 times, and mean values were calculated. For each SNP, the lowest mean value (λ) for H`<sub>EA</sub> was chosen from the 31 windows of size 5 to 65, and plotted across the length of each chromosome in cM. Likewise, the same derivation was applied to H`<sub>AA</sub> and S<sup>2</sup>F<sub>ST</sub>.</p>", "links"=>[], "tags"=>["analyzing", "regions", "heterozygosity", "african", "americans", "european", "variance", "lowest", "fractional"], "article_id"=>606198, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_flow_chart_for_analyzing_regions_for_local_heterozygosity_in_African_Americans_H_AA_and_European_Americans_H_EA_along_with_the_variance_of_F_ST_S_2_F_ST_to_derive_the_lowest_mean_value_fractional_rank_955_for_each_SNP_/606198", "title"=>"A flow chart for analyzing regions for local heterozygosity in African Americans (H`<sub>AA</sub>) and European Americans (H`<sub>EA</sub>), along with the variance of F<sub>ST</sub> (S<sup>2</sup>F<sub>ST</sub>) to derive the lowest mean value fractional rank (λ) for each SNP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:43:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/936022"], "description"=>"<p>These simulations were performed using SelSim <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#pone.0001712-Spencer1\" target=\"_blank\">[24]</a>, assuming equal sampling (48 chromosomes) and a complete separation between the two populations. Selection parameter (s) ranged from neutral to 0.3% to 3% (left to right) and recombination intensity per site (r) from 0.3 to 0.6 (from the top down), assuming 10,000 effective population size in each of the two simulated populations (See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001712#s3\" target=\"_blank\">Materials and Methods</a>).</p>", "links"=>[], "tags"=>["simulation", "summarizing", "estimates", "100", "replicate", "mb", "simulated", "chromosomes", "parameter", "varying", "coefficient", "recombination"], "article_id"=>606450, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Taras K. Oleksyk", "Kai Zhao", "Francisco M. De La Vega", "Dennis A. Gilbert", "Stephen J. O'Brien", "Michael W. Smith"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001712.g003", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SelSim_simulation_results_summarizing_the_effect_of_selection_on_the_estimates_of_A_H_D_and_B_955_S_2_F_ST_among_100_replicate_of_2_61_Mb_simulated_chromosomes_of_chromosomes_for_each_of_the_four_parameter_combination_with_varying_selection_coefficient_a/606450", "title"=>"SelSim simulation results summarizing the effect of selection on the estimates of (A) λ(H`<sub>D</sub>) and (B) λ(S<sup>2</sup>F<sub>ST</sub>) among 100 replicate of 2.61 Mb simulated chromosomes of chromosomes for each of the four parameter combination with varying selection coefficient and recombination rate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-03-05 01:47:30"}

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Relative Metric

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