Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)
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{"title"=>"Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)", "type"=>"journal", "authors"=>[{"first_name"=>"Fabian", "last_name"=>"Staubach", "scopus_author_id"=>"35087036400"}, {"first_name"=>"Anna", "last_name"=>"Lorenc", "scopus_author_id"=>"6603957640"}, {"first_name"=>"Philipp W.", "last_name"=>"Messer", "scopus_author_id"=>"34571138900"}, {"first_name"=>"Kun", "last_name"=>"Tang", "scopus_author_id"=>"35320361100"}, {"first_name"=>"Dmitri A.", "last_name"=>"Petrov", "scopus_author_id"=>"7103238750"}, {"first_name"=>"Diethard", "last_name"=>"Tautz", "scopus_author_id"=>"7005597480"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84866150090", "doi"=>"10.1371/journal.pgen.1002891", "pui"=>"365631165", "arxiv"=>"cs/9605103", "issn"=>"15537390", "pmid"=>"22956910", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)", "scopus"=>"2-s2.0-84866150090"}, "id"=>"247b5f88-0f50-3ccf-bf69-d8f75a232f28", "abstract"=>"General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin.", "link"=>"http://www.mendeley.com/research/genome-patterns-selection-introgression-haplotypes-natural-populations-house-mouse-mus-musculus", "reader_count"=>186, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>12, "Librarian"=>1, "Researcher"=>45, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>56, "Student > Postgraduate"=>11, "Student > Master"=>20, "Other"=>6, "Student > Bachelor"=>14, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>12, "Librarian"=>1, "Researcher"=>45, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>56, "Student > Postgraduate"=>11, "Student > Master"=>20, "Other"=>6, "Student > Bachelor"=>14, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>16, "Agricultural and Biological Sciences"=>153, "Medicine and Dentistry"=>1, "Chemical Engineering"=>1, "Physics and Astronomy"=>2, "Chemistry"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>153}, "Computer Science"=>{"Computer Science"=>4}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"United States"=>9, "United Kingdom"=>2, "Portugal"=>2, "Switzerland"=>1, "Greece"=>1, "Canada"=>1, "Austria"=>1, "Netherlands"=>1, "Norway"=>1, "Brazil"=>1, "France"=>1, "Australia"=>1, "Germany"=>4}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/584065"], "description"=>"1<p>Region in proximal half of chromosome 17 (t-region) omitted.</p>2<p>Corrected for omitted genome region.</p>", "links"=>[], "tags"=>["regions", "affected"], "article_id"=>254558, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.t003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_regions_affected_by_introgression_/254558", "title"=>"Genome regions affected by introgression.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-30 01:15:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/583704"], "description"=>"<p>Introgressed regions into <i>M. m. domesticus</i> in blue, into <i>M. m. musculus</i> in red. Elevated blocks indicate regions found in both populations of the respective subspecies. The figure was generated with the Genome Graphs utility of the UCSC Genome Browser <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Kent1\" target=\"_blank\">[59]</a>.</p>", "links"=>[], "tags"=>["introgressed", "regions"], "article_id"=>254195, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_introgressed_regions_across_the_chromosomes_/254195", "title"=>"Distribution of introgressed regions across the chromosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:09:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/583602"], "description"=>"<p>The figure was generated with the Genome Graphs utility of the UCSC Genome Browser <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Kent1\" target=\"_blank\">[59]</a> with custom supplied tracks that represent the XP-CLR values along the chromosomes for each population. Maximum peak sizes are up to 12, but only peaks above the simulation-derived significance cutoff at 3.5 are plotted.</p>", "links"=>[], "tags"=>["selective", "signatures", "xp-clr", "statistic", "comparisons"], "article_id"=>254092, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_selective_sweep_signatures_as_determined_by_the_XP_CLR_statistic_for_the_two_population_comparisons_across_all_autosomes_/254092", "title"=>"Distribution of selective sweep signatures as determined by the XP-CLR statistic for the two population comparisons across all autosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:08:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/584097"], "description"=>"1<p>Lists only genes in the region with functional information in the mouse.</p>2<p>Overlapping windows of different statistics combined.</p>3<p>Combines three neighboring XP-CLR positive regions.</p>", "links"=>[], "tags"=>["selective", "regions"], "article_id"=>254586, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_selective_sweep_regions_identified_by_multiple_statistics_/254586", "title"=>"Examples of selective sweep regions identified by multiple statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-30 01:16:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/583406"], "description"=>"<p>The scale bars refer to the number of substitutions per SNP genotyped. (A) For all autosomal SNPs in the study, grouped by sample and rooted by outgroup species. The shorter branch lengths for the <i>M. m. musculus</i> populations as well as the outgroups reflect the ascertainment bias for polymorphic SNPs in these subspecies and species. (B) For all haplotypes of a 6MB region on chromosome 6. Some haplotypes of Kaz group with <i>M. m. domesticus</i> due to introgression. The Cze population is partially introgressed by shorter fragments of <i>M. m. domesticus</i> haplotypes in this region (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891.s001\" target=\"_blank\">Figure S1</a> for depiction of haplotype tracks of this region), which results in some paraphyletic groupings for some haplotypes.</p>", "links"=>[], "tags"=>["joining", "trees", "manhattan"], "article_id"=>253892, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_trees_of_population_samples_based_on_Manhattan_distances_/253892", "title"=>"Neighbor joining trees of population samples, based on Manhattan distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:04:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/583787"], "description"=>"<p>Top: <i>M. m. domesticus</i> populations, bottom: <i>M. m. musculus</i> populations. Thick horizontal lines represent the median, boxes range from first to third quartile, whiskers extend to 1.5 times the interquartile range, data points outside that range are drawn as circles.</p>", "links"=>[], "tags"=>["introgression", "parameters", "models", "numbers", "x-axis", "rates"], "article_id"=>254275, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_introgression_parameters_colored_bars_with_neutral_models_for_introgression_white_bars_numbers_on_the_x_axis_refer_to_migration_rates_in_4Nm_/254275", "title"=>"Comparison of introgression parameters (colored bars) with neutral models for introgression (white bars, numbers on the x-axis refer to migration rates in 4Nm).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:11:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/584031"], "description"=>"1<p>Cross-population composite likelihood ratio test <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Chen1\" target=\"_blank\">[5]</a>.</p>2<p>Difference in derived allele frequency <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Grossman1\" target=\"_blank\">[6]</a>.</p>3<p>Ratio of integrated extended haplotypes between populations <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Tang1\" target=\"_blank\">[4]</a>.</p>4<p>Fixation index in 100 kb windows.</p><p>N = number of significant regions detected for the respective statistics.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>254525, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.t001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_for_sweep_statistics_/254525", "title"=>"Summary for sweep statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-30 01:15:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/583330"], "description"=>"<p><i>M. m. domesticus</i> occurs in Western Europe, <i>M. m. musculus</i> in Eastern Europe and Asia. The dashed red line marks the contact region where a classical hybrid zone has formed. Samples come from France (Fra – region Massif Central), Germany (Ger – region Cologne/Bonn), Czech Republic (Cze – region Studenec) and Kazhakstan (Kaz – region Almaty, note that this is not on the map anymore, as indicated by the arrow). The inset depicts the phylogenetic relationship between the populations, as well as an indication of the parameters used for population modeling. Map picture based on a map from <a href=\"http://d-maps.com\" target=\"_blank\">http://d-maps.com</a>.</p>", "links"=>[], "tags"=>["populations", "subspecies"], "article_id"=>253816, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g001", "stats"=>{"downloads"=>0, "page_views"=>65, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_populations_and_subspecies_sampled_/253816", "title"=>"Distribution of populations and subspecies sampled.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:03:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/583931"], "description"=>"<p>Lines represent two reconstructed haplotypes for each individual. The data are displayed as custom tracks in the UCSC browser <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Kent1\" target=\"_blank\">[59]</a>. SNP positions are depicted as vertical bars, SNP variants that are more frequent in <i>M. m. domesticus</i> are in red, <i>M. m. musculus</i> in blue. Spaces between the SNP positions are filled with the color corresponding to the flanking SNPs. If these are of different color, the space is broken up in the middle. Known genes in the regions are depicted below (taken from the UCSC Genome Browser database - <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891-Salazar1\" target=\"_blank\">[14]</a>). Sweep regions and corresponding genes are highlighted as yellow boxes, introgressed haplotypes are indicated by yellow arrows that point to the respective haplotype tracks that include them. (A) Genome region around the Huntingtin (Htt) locus on chromosome 5, showing a sweep in the Fra population and introgression into the Kaz population. (B) Genome region around the alpha-amylase gene cluster (Amy) on chromosome 3, with mutual sweeps in the Ger and Fra population and introgression in the Kaz and Fra population. Note that the introgressed haplotype in Kaz extends further than depicted here (covering approx. 33 Mb in several pieces).</p>", "links"=>[], "tags"=>["tracks", "sweeps", "introgression"], "article_id"=>254422, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g007", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_tracks_showing_sweeps_and_introgression_regions_/254422", "title"=>"Haplotype tracks showing sweeps and introgression regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:13:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/308232", "https://ndownloader.figshare.com/files/308441", "https://ndownloader.figshare.com/files/308576", "https://ndownloader.figshare.com/files/308707", "https://ndownloader.figshare.com/files/308741"], "description"=>"<div><p>General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (<em>Mus musculus</em>) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies <em>M. m. domesticus</em> and <em>M. m. musculus</em>. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin.</p> </div>", "links"=>[], "tags"=>["genome", "patterns", "introgression", "haplotypes", "populations"], "article_id"=>120819, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002891.s001", "https://dx.doi.org/10.1371/journal.pgen.1002891.s002", "https://dx.doi.org/10.1371/journal.pgen.1002891.s003", "https://dx.doi.org/10.1371/journal.pgen.1002891.s004", "https://dx.doi.org/10.1371/journal.pgen.1002891.s005"], "stats"=>{"downloads"=>13, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Patterns_of_Selection_and_Introgression_of_Haplotypes_in_Natural_Populations_of_the_House_Mouse_Mus_musculus_/120819", "title"=>"Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (<em>Mus musculus</em>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-30 00:13:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/583499"], "description"=>"<p>(A) full dataset, (B) all regions of introgression removed.</p>", "links"=>[], "tags"=>["ld", "markers", "populations"], "article_id"=>253988, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Fabian Staubach", "Anna Lorenc", "Philipp W. Messer", "Kun Tang", "Dmitri A. Petrov", "Diethard Tautz"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002891.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_LD_r_2_between_markers_over_distance_for_each_of_the_populations_in_the_study_/253988", "title"=>"Pairwise LD (r<sup>2</sup>) between markers over distance for each of the populations in the study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-30 01:06:28"}

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Relative Metric

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