Extensive Copy-Number Variation of Young Genes across Stickleback Populations
Publication Date
December 04, 2014
Journal
PLOS Genetics
Authors
Frédéric J. J. Chain, Philine G. D. Feulner, Mahesh Panchal, Christophe Eizaguirre, et al
Volume
10
Issue
12
Pages
e1004830
DOI
https://dx.plos.org/10.1371/journal.pgen.1004830
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004830
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25474574
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256280
Europe PMC
http://europepmc.org/abstract/MED/25474574
Web of Science
000346649900035
Scopus
84919629938
Mendeley
http://www.mendeley.com/research/extensive-copynumber-variation-young-genes-across-stickleback-populations
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Mendeley | Further Information

{"title"=>"Extensive Copy-Number Variation of Young Genes across Stickleback Populations", "type"=>"journal", "authors"=>[{"first_name"=>"Frédéric J.J.", "last_name"=>"Chain", "scopus_author_id"=>"13407136300"}, {"first_name"=>"Philine G.D.", "last_name"=>"Feulner", "scopus_author_id"=>"8430413700"}, {"first_name"=>"Mahesh", "last_name"=>"Panchal", "scopus_author_id"=>"16417612700"}, {"first_name"=>"Christophe", "last_name"=>"Eizaguirre", "scopus_author_id"=>"23495784700"}, {"first_name"=>"Irene E.", "last_name"=>"Samonte", "scopus_author_id"=>"6508302013"}, {"first_name"=>"Martin", "last_name"=>"Kalbe", "scopus_author_id"=>"6601957030"}, {"first_name"=>"Tobias L.", "last_name"=>"Lenz", "scopus_author_id"=>"19640596400"}, {"first_name"=>"Monika", "last_name"=>"Stoll", "scopus_author_id"=>"7103215401"}, {"first_name"=>"Erich", "last_name"=>"Bornberg-Bauer", "scopus_author_id"=>"6603818279"}, {"first_name"=>"Manfred", "last_name"=>"Milinski", "scopus_author_id"=>"7003311659"}, {"first_name"=>"Thorsten B.H.", "last_name"=>"Reusch", "scopus_author_id"=>"7005058470"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84919629938", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "doi"=>"10.1371/journal.pgen.1004830", "pui"=>"601033497", "sgr"=>"84919629938", "issn"=>"15537404", "pmid"=>"25474574"}, "id"=>"972187ea-22ed-332b-8ece-2ee62c2bd708", "abstract"=>"Author Summary After a locus is duplicated in a genome, individuals from a population instantaneously differ in the number of copies of this locus producing a copy-number variation (CNV). Over time, the joint effects of selection and other evolutionary forces will act to either eliminate the extra genetic copy or retain it. Depending on this evolutionary interplay, young duplications, including newly duplicated genes, can persist for millions of years as CNVs. CNVs may especially be prevalent between populations that have colonized and adapted to disparate environments in which selective pressures differ. Using whole genome sequences from several populations of three-spined sticklebacks that inhabit different environments, we find that a third of young duplicated genes are CNVs. These young CNV genes are enriched with environmental response functions and evolving rapidly at the molecular level, making them promising candidates for a role in the rapid ecological adaptation to novel environments.", "link"=>"http://www.mendeley.com/research/extensive-copynumber-variation-young-genes-across-stickleback-populations", "reader_count"=>73, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>21, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>21, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>58, "Medicine and Dentistry"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>58}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Canada"=>2, "United States"=>1, "Japan"=>1, "United Kingdom"=>1, "Portugal"=>1, "Germany"=>6}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1821194"], "description"=>"<p><b>(A)</b> Allele frequency spectrum of bi-allelic CNVs across all 66 individuals, showing most deletions (white) and duplications (black) occurring at very low frequencies. See <b><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004830#pgen.1004830.s003\" target=\"_blank\">S3B Figure</a></b> for a comparison with intergenic SNPs. (<b>B</b>) Allele frequency spectrum of non-reference alleles from bi-allelic CNVs across 12 individuals from each population represented as boxplots. (<b>C</b>) The occurrence of CNVs across populations. (<b>D</b>) The proportion of CNVs shared across individuals within populations. (<b>E</b>) The proportion of CNVs specific (private) to groups of individuals depending on the scale of aggregation. Mutually exclusive groups for which CNVs are private include: those occurring across continents (Ancestral), those specific to a continent but shared across populations from different countries (Continent), those specific to a country but shared across populations within a country (Country), and those only found in one population (Population). (<b>F</b>) The average proportion of shared CNVs between individuals across mutually exclusive groups. The proportion of CNV sharing across individuals was calculated for four groups: “Between Continents” is sharing from different continents, “Between Countries” is sharing from different countries within the same continent, “Between Populations” is sharing from different populations from the same country, and “Within Populations” is sharing from the same population.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259944, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g002", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_and_occurrence_of_CNVs_across_individuals_and_populations_/1259944", "title"=>"Frequency and occurrence of CNVs across individuals and populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821271"], "description"=>"<p>Genes with the most extreme V<sub>ST</sub> values between paraptric populations, where positive values represent higher copy-numbers in rivers and negative values represent higher copy-numbers in lakes.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259980, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.t003", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_with_the_most_extreme_V_ST_values_between_paraptric_populations_where_positive_values_represent_higher_copy_numbers_in_rivers_and_negative_values_represent_higher_copy_numbers_in_lakes_/1259980", "title"=>"Genes with the most extreme V<sub>ST</sub> values between paraptric populations, where positive values represent higher copy-numbers in rivers and negative values represent higher copy-numbers in lakes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821230"], "description"=>"<p>(<b>A</b>) Five mutually-exclusive gene categories based on orthology and paralogy: Non LSGs (Non-Lineage Specific Gene singletons), Non-LSG paralogs (Non-Lineage Specific Gene paralogs), Non-LSG LSD (Non-Lineage Specific Genes that are Lineage-Specific Duplicates), LSG LSD (Lineage-Specific Genes that are Lineage-Specific Duplicates) and LSG singletons (Lineage-Specific Gene singletons). Young genes are determined from broader overlapping categories, inferred as having no detectable orthologs (LSGs: lineage-specific genes) or recent paralogs (LSDs: lineage-specific duplications). LSGs are normally singletons but can also be duplicated, in which case they are both LSGs and LSDs (LSG LSD). LSGs and LSDs were found to have characteristic properties of young genes such as short gene lengths, narrow gene expression and rapid molecular evolution (<b><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004830#pgen.1004830.s038\" target=\"_blank\">S1 Text</a></b>). The relationship of corresponding genes across and within species (orthologs and paralogs) is represented for each category, wherein “>1” represents paralogs and “0” represents no detectable ortholog. For example, non-LSG singletons have a one-to-one relationship between sticklebacks and at least one other species, non-LSG paralogs have a many-to-many relationship due to an old duplication event (black dot in tree), and non-LSG LSD have a one-to-many relationship due to a recent duplication event along the stickleback lineage (purple dot in tree). The number of autosomal protein-coding genes belonging to each category is reported below each category name. (<b>B</b>) Proportion of genes (both protein-coding and RNA) completely encompassed within CNV regions (deletions in white, duplications in black, both deletion and duplication in stripes). (<b>C</b>) Overlap between protein-coding genes in segmental duplication (SD genes), CNV genes, and LSGs and LSDs. The majority of SD genes are LSGs and LSDs, many of which are also CNV genes.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259962, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_young_genes_and_CNVs_/1259962", "title"=>"Relationship between young genes and CNVs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821254"], "description"=>"<p>Summary of sequencing and variation statistics across sampled populations.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259976, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_sequencing_and_variation_statistics_across_sampled_populations_/1259976", "title"=>"Summary of sequencing and variation statistics across sampled populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821252"], "description"=>"<p>(<b>A</b>) Population differentiation of genes along linkage group II, measured by the V<sub>ST</sub> statistic between a German lake-river pair (G1_R vs G1_L). Color shades of dots (that are jittered for ease of visualization) refer to higher average copy-number in river (light) or in lake (dark). The dashed line is drawn at V<sub>ST</sub> of 0.89. (<b>B</b>) The gene with the highest V<sub>ST</sub> is a lysosome protective protein (<i>CTSA</i>) paralog, which has higher copy-numbers in both German river populations compared to their German lake counterparts. Normalized read depth approximating copy-number is plotted across 66 individuals grouped and colored by population, with an expected copy-number of two for a diploid locus. V<sub>ST</sub> values are reported beside the population pairs.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259974, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g006", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_differentiation_in_gene_copy_number_/1259974", "title"=>"Population differentiation in gene copy-number.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821224"], "description"=>"<p>(<b>A</b>) Proportion of deletions (white) and duplications (black) overlapping four mutually exclusive genomic categories; entirely within intergenic regions, entirely within intronic regions, partially overlapping a gene including an exonic region, or completely overlapping at least one gene. (<b>B</b>) Read depth coverage (grey histograms) along a gene (blocks are exons) for one representative individual from each population, showing CNV deletions. Examples include an intronic loss from a small G protein signaling modulator 3 gene (<i>SGSM3</i>) in Atlantic individuals, an exonic partial gene loss of a carbonic anhydrase gene (<i>CA4</i>) in Norwegian individuals, and the complete gene loss of a pogo transposable element with <i>KRAB</i> domain gene (<i>POGK</i>) in Atlantic individuals.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259956, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g003", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CNV_proportions_across_genomic_regions_and_homozygous_deletions_/1259956", "title"=>"CNV proportions across genomic regions and homozygous deletions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821183"], "description"=>"<p>(<b>A</b>) Phylogenomic network of the 66 genomes was constructed using the Neighbor-net method based on 50,000 randomly selected high-quality SNPs. Parapatric population pairs were sampled from the United States (Us), Canada (Ca), Norway (No), and two sites in Germany (G1 and G2), and a marine population from Denmark (Dk). Ecotypes include rivers (_R), lakes (_L) and marine (_M) samples. (<b>B–C</b>) Principal components analysis plots of CNV deletions and duplications. Clustering of individuals is based on shared CNVs, which follow patterns of geographic distributions (highlighted with ellipses).</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259933, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g001", "stats"=>{"downloads"=>2, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenomic_relationships_among_samples_/1259933", "title"=>"Phylogenomic relationships among samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821262"], "description"=>"<p>Genes under positive selection in the stickleback lineage from the Selectome database, indicating whether they are deletions, duplications, or both.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259979, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.t002", "stats"=>{"downloads"=>5, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_under_positive_selection_in_the_stickleback_lineage_from_the_Selectome_database_indicating_whether_they_are_deletions_duplications_or_both_/1259979", "title"=>"Genes under positive selection in the stickleback lineage from the Selectome database, indicating whether they are deletions, duplications, or both.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 02:59:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/1823704", "https://ndownloader.figshare.com/files/1823705", "https://ndownloader.figshare.com/files/1823706", "https://ndownloader.figshare.com/files/1823707", "https://ndownloader.figshare.com/files/1823708", "https://ndownloader.figshare.com/files/1823709", "https://ndownloader.figshare.com/files/1823710", "https://ndownloader.figshare.com/files/1823711", "https://ndownloader.figshare.com/files/1823712", "https://ndownloader.figshare.com/files/1823713", "https://ndownloader.figshare.com/files/1823714", "https://ndownloader.figshare.com/files/1823715", "https://ndownloader.figshare.com/files/1823716", "https://ndownloader.figshare.com/files/1823717", "https://ndownloader.figshare.com/files/1823718", "https://ndownloader.figshare.com/files/1823719", "https://ndownloader.figshare.com/files/1823720", "https://ndownloader.figshare.com/files/1823721", "https://ndownloader.figshare.com/files/1823722", "https://ndownloader.figshare.com/files/1823723", "https://ndownloader.figshare.com/files/1823724", "https://ndownloader.figshare.com/files/1823725", "https://ndownloader.figshare.com/files/1823726", "https://ndownloader.figshare.com/files/1823727", "https://ndownloader.figshare.com/files/1823728", "https://ndownloader.figshare.com/files/1823729", "https://ndownloader.figshare.com/files/1823730", "https://ndownloader.figshare.com/files/1823731", "https://ndownloader.figshare.com/files/1823732", "https://ndownloader.figshare.com/files/1823733", "https://ndownloader.figshare.com/files/1823734", "https://ndownloader.figshare.com/files/1823735", "https://ndownloader.figshare.com/files/1823736", "https://ndownloader.figshare.com/files/1823737", "https://ndownloader.figshare.com/files/1823738", "https://ndownloader.figshare.com/files/1823739", "https://ndownloader.figshare.com/files/1823740", "https://ndownloader.figshare.com/files/1823741"], "description"=>"<div><p>Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.</p></div>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1261343, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004830.s001", "https://dx.doi.org/10.1371/journal.pgen.1004830.s002", "https://dx.doi.org/10.1371/journal.pgen.1004830.s003", "https://dx.doi.org/10.1371/journal.pgen.1004830.s004", "https://dx.doi.org/10.1371/journal.pgen.1004830.s005", "https://dx.doi.org/10.1371/journal.pgen.1004830.s006", "https://dx.doi.org/10.1371/journal.pgen.1004830.s007", "https://dx.doi.org/10.1371/journal.pgen.1004830.s008", "https://dx.doi.org/10.1371/journal.pgen.1004830.s009", "https://dx.doi.org/10.1371/journal.pgen.1004830.s010", "https://dx.doi.org/10.1371/journal.pgen.1004830.s011", "https://dx.doi.org/10.1371/journal.pgen.1004830.s012", "https://dx.doi.org/10.1371/journal.pgen.1004830.s013", "https://dx.doi.org/10.1371/journal.pgen.1004830.s014", "https://dx.doi.org/10.1371/journal.pgen.1004830.s015", "https://dx.doi.org/10.1371/journal.pgen.1004830.s016", "https://dx.doi.org/10.1371/journal.pgen.1004830.s017", "https://dx.doi.org/10.1371/journal.pgen.1004830.s018", "https://dx.doi.org/10.1371/journal.pgen.1004830.s019", "https://dx.doi.org/10.1371/journal.pgen.1004830.s020", "https://dx.doi.org/10.1371/journal.pgen.1004830.s021", "https://dx.doi.org/10.1371/journal.pgen.1004830.s022", "https://dx.doi.org/10.1371/journal.pgen.1004830.s023", "https://dx.doi.org/10.1371/journal.pgen.1004830.s024", "https://dx.doi.org/10.1371/journal.pgen.1004830.s025", "https://dx.doi.org/10.1371/journal.pgen.1004830.s026", "https://dx.doi.org/10.1371/journal.pgen.1004830.s027", "https://dx.doi.org/10.1371/journal.pgen.1004830.s028", "https://dx.doi.org/10.1371/journal.pgen.1004830.s029", "https://dx.doi.org/10.1371/journal.pgen.1004830.s030", "https://dx.doi.org/10.1371/journal.pgen.1004830.s031", "https://dx.doi.org/10.1371/journal.pgen.1004830.s032", "https://dx.doi.org/10.1371/journal.pgen.1004830.s033", "https://dx.doi.org/10.1371/journal.pgen.1004830.s034", "https://dx.doi.org/10.1371/journal.pgen.1004830.s035", "https://dx.doi.org/10.1371/journal.pgen.1004830.s036", "https://dx.doi.org/10.1371/journal.pgen.1004830.s037", "https://dx.doi.org/10.1371/journal.pgen.1004830.s038"], "stats"=>{"downloads"=>104, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extensive_Copy_Number_Variation_of_Young_Genes_across_Stickleback_Populations_/1261343", "title"=>"Extensive Copy-Number Variation of Young Genes across Stickleback Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-04 09:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821236"], "description"=>"<p>(<b>A</b>) Association between dS of LSD pairs and CNV regions, where dS is a proxy for age since duplication. Boxplots representing the distributions of pairwise dS (synonymous rates of substitution) between LSD pairs where neither (0, n = 129), one (1, n = 59) or both (2, n = 39) genes overlap CNVs. The whiskers represent values beyond the interquartile range (IQR) reaching the highest/lowest value within 1.5 * IQR as implemented in R (ggplot2). (<b>B</b>) Gene families and CNVs. Proportion of protein-coding CNV gene members (genes entirely overlapping CNV regions) by gene family size (mean with standard error, plotted with jittering). In red is the mean proportion of LSG singletons (single-gene families – no paralogs), in purple are LSD members and black are non-LSD members. Linear regressions are drawn with the 95% confidence intervals shaded grey.</p>", "links"=>[], "tags"=>["adaptive benefits", "Stickleback Populations Duplicate genes", "gene content differences", "population differentiation", "population level", "teleost genomes", "population genomics analyses", "CNV genes", "Young Genes", "11 populations", "genome sequences", "66 individuals"], "article_id"=>1259967, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frédéric J. J. Chain", "Philine G. D. Feulner", "Mahesh Panchal", "Christophe Eizaguirre", "Irene E. Samonte", "Martin Kalbe", "Tobias L. Lenz", "Monika Stoll", "Erich Bornberg-Bauer", "Manfred Milinski", "Thorsten B. H. Reusch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004830.g005", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_gene_duplications_and_CNVs_/1259967", "title"=>"Relationship between gene duplications and CNVs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 02:59:09"}

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