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{"title"=>"Recurrent Evolution of Melanism in South American Felids", "type"=>"journal", "authors"=>[{"first_name"=>"Alexsandra", "last_name"=>"Schneider", "scopus_author_id"=>"55531159400"}, {"first_name"=>"Corneliu", "last_name"=>"Henegar", "scopus_author_id"=>"23012382400"}, {"first_name"=>"Kenneth", "last_name"=>"Day", "scopus_author_id"=>"55848565200"}, {"first_name"=>"Devin", "last_name"=>"Absher", "scopus_author_id"=>"57198406019"}, {"first_name"=>"Constanza", "last_name"=>"Napolitano", "scopus_author_id"=>"23397985400"}, {"first_name"=>"Leandro", "last_name"=>"Silveira", "scopus_author_id"=>"7004430232"}, {"first_name"=>"Victor A.", "last_name"=>"David", "scopus_author_id"=>"7102473618"}, {"first_name"=>"Stephen J.", "last_name"=>"O’Brien", "scopus_author_id"=>"57096319100"}, {"first_name"=>"Marilyn", "last_name"=>"Menotti-Raymond", "scopus_author_id"=>"6701581907"}, {"first_name"=>"Gregory S.", "last_name"=>"Barsh", "scopus_author_id"=>"35394756500"}, {"first_name"=>"Eduardo", "last_name"=>"Eizirik", "scopus_author_id"=>"6602181331"}], "year"=>2015, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84924355595", "sgr"=>"84924355595", "issn"=>"15537404", "doi"=>"10.1371/journal.pgen.1004892", "pmid"=>"25695801", "isbn"=>"10.1371/journal.pgen.1005126", "pui"=>"602901844"}, "id"=>"cc166c80-768d-348d-b425-2451f0d8036d", "abstract"=>"Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy's cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13-21 per species), achieving enrichment of ~500-2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy's cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations.", "link"=>"http://www.mendeley.com/research/recurrent-evolution-melanism-south-american-felids", "reader_count"=>69, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>13, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>9, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>13, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>9, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Nursing and Health Professions"=>1, "Materials Science"=>1, "Agricultural and Biological Sciences"=>51, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Environmental Science"=>{"Environmental Science"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>3, "United Kingdom"=>1, "Peru"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1912016"], "description"=>"<p>Contig lengths and spacing are drawn to scale (see Table S7 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.s001\" target=\"_blank\">S1 Data</a> for individual coordinates); sense or antisense transcription, relative to the chromosomal orientation, is indicated with (+)/(-).</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313248, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Positions_of_fosmids_and_neighboring_genes_at_melanism_loci_/1313248", "title"=>"Positions of fosmids and neighboring genes at melanism loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1912023"], "description"=>"<p>The left-hand side depicts relative EHH according to distance from the causative variant (vertical red line) plotted on the y-axis for ancestral (grey) vs. melanism-bearing (black) chromosomes, as a function of genomic location plotted on the x axis, indicated according to fosmid identity (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.g002\" target=\"_blank\">Fig. 2</a>). The right-hand side depicts haplotype bifurcation plots with origins at the causative variant: branches represent haplotype divergence, and the thickness of the lines is proportional to the number of chromosomes.</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313255, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g006", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Long_range_haplotype_analysis_for_pampas_cat_A_Geoffory_8217_s_cat_B_and_kodkod_C_respectively_/1313255", "title"=>"Long-range haplotype analysis for pampas cat (A), Geoffory’s cat (B) and kodkod (C) respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1912022"], "description"=>"<p>As described in the text, the latter approach allows comparison between loci within each species, illustrating, e.g. that patterns of nucleotide diversity are similar between melanistic individuals for the “control” locus (<i>ASIP</i> in the Geoffroy’s cat, <i>MC1R</i> in the pampas cat and kodkod). Error bars indicate standard error of the mean (SEM).</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313254, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g005", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_diversity_calculated_for_ancestral_yellow_vs_melanism_bearing_black_chromosomes_and_for_individuals_according_to_their_phenotype_melanistic_black_vs_non_melanistic_yellow_for_pampas_cat_A_D_Geoffory_8217_s_cat_B_E_and_kodkod_C_F_/1313254", "title"=>"Nucleotide diversity calculated for ancestral (yellow) vs. melanism-bearing (black) chromosomes, and for individuals according to their phenotype (melanistic, black vs. non-melanistic, yellow), for pampas cat (A, D), Geoffory’s cat (B, E) and kodkod (C, F).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1912018"], "description"=>"<p>Posterior probabilistic support for the main branches of the maximal clade credibility trees are: a – 0.987, b – 0.991, c – 0.988, d – 0.988, e – 0.999, f – 0.999, g – 0.995, h – 0.992. Colored squares on the right of each tree indicate whether each haplotype is linked to (<i>e.g.</i> contains) a melanism-associated mutation.</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313250, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_among_chromosomes_for_each_locus_inferred_with_BEAST2_34_/1313250", "title"=>"Phylogenetic relationships among chromosomes for each locus inferred with BEAST2 [34].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1930375"], "description"=>"<p><sup>a</sup> Datasets include 150 bp PE and 100 bp PE Illumina reads; theoretical coverage per sample was calculated assuming an average of 75 bp aligned sequence per end, e.g. (699,823,384 x 150)/(54 x 2.43 x 10<sup>9</sup>). The number of aligned reads shown here represents the results from all 54 <i>Leopardus</i> spp. libraries; results for each species are given in Table S9 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.s001\" target=\"_blank\">S1 Data</a>.</p><p><sup>b</sup> Target sizes represent the sum of the 13 fosmid sizes before and after use of RepeatMasker with default parameters (Table S8 in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.s001\" target=\"_blank\">S1 Data</a>).</p><p>Alignment coverage summary for CATCH-Seq libraries.</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1322447, "categories"=>["Biological Sciences"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.t002", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_coverage_summary_for_CATCH_Seq_libraries_/1322447", "title"=>"Alignment coverage summary for CATCH-Seq libraries.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-02-19 17:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1930376"], "description"=>"<div><p>Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of <i>Agouti signaling protein (ASIP)</i> or the <i>Melanocortin 1 receptor (MC1R)</i> as independent causes of melanism in three closely related South American species: the pampas cat (<i>Leopardus colocolo</i>), the kodkod (<i>Leopardus guigna</i>), and Geoffroy’s cat (<i>Leopardus geoffroyi</i>). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain <i>ASIP</i> and <i>MC1R</i>, respectively, from 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations.</p></div>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1322448, "categories"=>["Biological Sciences"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recurrent_Evolution_of_Melanism_in_South_American_Felids_/1322448", "title"=>"Recurrent Evolution of Melanism in South American Felids", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-02-19 17:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1912021"], "description"=>"<p>Major and minor alleles are depicted in blue and red respectively, and genomic coordinates are represented in kb upstream or downstream from the causative position. Letters indicating the fosmids that correspond to each targeted segments are shown at the bottom of each plot.</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313253, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g004", "stats"=>{"downloads"=>2, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_structures_for_melanism_loci_for_pampas_cat_A_Geoffroy_8217_s_cat_B_and_kodkod_C_arranged_according_to_whether_they_carry_an_ancestral_yellow_or_derivative_black_allele_at_the_causative_position_and_whether_they_were_observed_in_a_non_melanisti/1313253", "title"=>"Haplotype structures for melanism loci for pampas cat (A), Geoffroy’s cat (B), and kodkod (C), arranged according to whether they carry an ancestral (yellow) or derivative (black) allele at the causative position, and whether they were observed in a non-melanistic (+/+, +/m) or melanistic (m/m, +/M) individual.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1912015"], "description"=>"<p>(A) Color phenotypes of the pampas cat (<i>L. colocolo</i>), Geoffroy’s cat (<i>L. geoffroyi</i>), and kodkod (<i>L. guigna</i>). Tabby markings in the non-melanistic (NM) forms shown here are obscured in the melanistic (M) forms. (B) Geographic distribution (modified from [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.ref007\" target=\"_blank\">7</a>]); red circles represent the approximate origin of samples as described in the text. Right upper panel indicates phylogenetic relationships and estimated divergence times based on [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.ref004\" target=\"_blank\">4</a>] (C, D) Location of missense variants in <i>ASIP</i> (kodkod, pampas cat) and <i>MC1R</i> (Geoffroy’s cat). (C) The kodkod and pampas cat variants are predicted to disrupt the three dimensional structure of a disulfide-stabilized loop in ASIP that is critical for MC1R binding [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004892#pgen.1004892.ref030\" target=\"_blank\">30</a>]. (D) The Geoffroy’s cat melanism allele carries three missense variants in MC1R; C125R is likely to be causative as described in the text.</p>", "links"=>[], "tags"=>["251 kb segments", "Many felid species exhibit polymorphism", "genomic test bed", "mutation", "Leopardu", "Melanocortin 1 receptor", "melanism", "pampas cat", "Geoffroy", "population level variation", "kodkod", "South American Felids Morphological variation", "South American species", "MC 1R", "role", "asip"], "article_id"=>1313247, "categories"=>["Uncategorised"], "users"=>["Alexsandra Schneider", "Corneliu Henegar", "Kenneth Day", "Devin Absher", "Constanza Napolitano", "Leandro Silveira", "Victor A. David", "Stephen J. O’Brien", "Marilyn Menotti-Raymond", "Gregory S. Barsh", "Eduardo Eizirik"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004892.g001", "stats"=>{"downloads"=>3, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Melanism_mutations_and_phenotypes_in_three_Leopardus_species_/1313247", "title"=>"Melanism mutations and phenotypes in three <i>Leopardus</i> species", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-19 03:06:07"}

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  • {"unique-ip"=>"21", "full-text"=>"23", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"26", "full-text"=>"15", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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