Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)
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{"title"=>"Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)", "type"=>"journal", "authors"=>[{"first_name"=>"Xin", "last_name"=>"Ma", "scopus_author_id"=>"57168947400"}, {"first_name"=>"Joanna L.", "last_name"=>"Kelley", "scopus_author_id"=>"8234514200"}, {"first_name"=>"Kirsten", "last_name"=>"Eilertson", "scopus_author_id"=>"36113468700"}, {"first_name"=>"Shaila", "last_name"=>"Musharoff", "scopus_author_id"=>"36131823300"}, {"first_name"=>"Jeremiah D.", "last_name"=>"Degenhardt", "scopus_author_id"=>"16238251700"}, {"first_name"=>"André L.", "last_name"=>"Martins", "scopus_author_id"=>"37361428100"}, {"first_name"=>"Tomas", "last_name"=>"Vinar", "scopus_author_id"=>"6507894445"}, {"first_name"=>"Carolin", "last_name"=>"Kosiol", "scopus_author_id"=>"16239349000"}, {"first_name"=>"Adam", "last_name"=>"Siepel", "scopus_author_id"=>"6701428520"}, {"first_name"=>"Ryan N.", "last_name"=>"Gutenkunst", "scopus_author_id"=>"15019501700"}, {"first_name"=>"Carlos D.", "last_name"=>"Bustamante", "scopus_author_id"=>"35228607000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"370091185", "sgr"=>"84886042608", "issn"=>"19326203", "pmid"=>"24194868", "scopus"=>"2-s2.0-84886042608", "doi"=>"10.1371/journal.pone.0077175", "isbn"=>"1932-6203"}, "id"=>"095cca4b-4e8a-37bf-8e66-3a57a7d6f92b", "abstract"=>"To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.", "link"=>"http://www.mendeley.com/research/population-genomic-analysis-reveals-rich-speciation-demographic-history-orangutans-pongo-pygmaeus-po", "reader_count"=>57, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>1, "Student > Doctoral Student"=>5, "Researcher"=>9, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>7, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>1, "Student > Doctoral Student"=>5, "Researcher"=>9, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>7, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>1, "Agricultural and Biological Sciences"=>45, "Physics and Astronomy"=>1, "Social Sciences"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Netherlands"=>1, "United States"=>2, "China"=>1, "United Kingdom"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1256463"], "description"=>"*<p>This is total aligned length.</p>", "links"=>[], "tags"=>["mcdonald-kreitman", "entries", "bornean", "sumatran"], "article_id"=>831296, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.t001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_McDonald_Kreitman_table_entries_for_Bornean_and_Sumatran_population_using_Human_hg19_as_outgroup_/831296", "title"=>"Summary statistics of McDonald-Kreitman table entries for Bornean and Sumatran population using Human (hg19) as outgroup.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256455"], "description"=>"<p>(<b>A</b>) The phylogenetic tree among human, chimpanzee, Bornean (red) and Sumatran (blue). The nodes shaded in cyan represent the grouping of the three Sumatran individuals that has the furthest distance to the rest clustering of the Sumatran group. The 10 re-sequenced individuals from our study are colored as red (Bornean) or blue (Sumatran). The corresponding geographic origins are shown on the right with the following annotation (SU: Sumatran; TU/SL: Tuanan or Sungai Lading; DV/K: Danum Valley or Kinabatangan; SA/GP: Sabangau or Gunung Palung; EK: East Kalimantan including Kutai national park or Sangatta; SAR/DS: Semongok Wildlife Rehabilitation Centre or Danau Sentarum). (<b>B</b>) The IBS allele sharing matrix among the 10 individuals from our study with the same group coloring scheme. The upper and lower triangular matrix represents the IBS sharing of all mtDNA variation loci (n = 1084) and autosomal variation loci (n = 11,866,619), respectively.</p>", "links"=>[], "tags"=>["mtdna", "hvri", "allele", "sharing", "matrix"], "article_id"=>831291, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.g001", "stats"=>{"downloads"=>0, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_mtDNA_HVRI_region_and_allele_sharing_matrix_of_mtDNA_and_autosomes_/831291", "title"=>"Phylogenetic tree of mtDNA HVRI region and allele sharing matrix of mtDNA and autosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256467"], "description"=>"<p>Percent of mutations within various selective classes for different models of the distribution of selection coefficients and different underlying demographic models.</p>", "links"=>[], "tags"=>["mutations", "selective", "classes", "coefficients"], "article_id"=>831299, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_of_mutations_within_various_selective_classes_for_different_models_of_the_distribution_of_selection_coefficients_and_different_underlying_demographic_models_/831299", "title"=>"Percent of mutations within various selective classes for different models of the distribution of selection coefficients and different underlying demographic models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256457"], "description"=>"<p>Error bars denote 95% confidence intervals on the proportion of SNPs in each category.</p>", "links"=>[], "tags"=>["snps", "polyphen", "categories", "polyphen-2"], "article_id"=>831293, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.g003", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_proportion_SNPs_within_each_of_the_PolyPhen_categories_based_on_PolyPhen_2_result_/831293", "title"=>"Distribution of the proportion SNPs within each of the PolyPhen categories based on PolyPhen-2 result.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256456"], "description"=>"<p>(<b>A</b>) SFS for all genomic SNPs (Genome), synonymous (S) or non-synonymous (NS) SNPs in Bornean (Red) and Sumatran (Blue) population. (<b>B</b>) Two-dimensional SFS (Bornean on Y axis and Sumatran on X axis). Top row: Spectra for different functional categories of SNPs. To make all the spectra directly comparable, the non-coding and synonymous spectra have been re-scaled to represent the same number of segregating SNPs as the non-synonymous spectrum. Bottom row: residuals between pairs of spectra. Bottom-left compares synonymous and non-coding spectra, and bottom-right compares non-synonymous and synonymous spectra. Red and blue entries indicate, respectively, that the first spectrum has greater or fewer SNPs in that entry than the second.</p>", "links"=>[], "tags"=>[], "article_id"=>831292, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SFS_analysis_/831292", "title"=>"SFS analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256469"], "description"=>"<div><p>To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (∼3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.</p></div>", "links"=>[], "tags"=>["genomic", "reveals", "speciation", "orang-utans"], "article_id"=>831300, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175", "stats"=>{"downloads"=>10, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Population_Genomic_Analysis_Reveals_a_Rich_Speciation_and_Demographic_History_of_Orang_utans_Pongo_pygmaeus_and_Pongo_abelii_/831300", "title"=>"Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (<i>Pongo pygmaeus</i> and <i>Pongo abelii</i>)", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256464"], "description"=>"*<p>and ** denote genes identified as putative positively selected on orang-utan and human lineage, respectively, in previous study <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077175#pone.0077175-Locke1\" target=\"_blank\">[22]</a>.</p>", "links"=>[], "tags"=>[], "article_id"=>831297, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_under_positive_selection_identified_by_SnIPRE_/831297", "title"=>"Genes under positive selection identified by SnIPRE.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:35:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1256462"], "description"=>"<p>Solid lines are for the full demographic model, dashed are for the model with no migration, and dotted are for the model with no growth. The break in the axes indicates that the scale is not continuous, because a logarithmic scale cannot span zero.</p>", "links"=>[], "tags"=>["cumulative"], "article_id"=>831295, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Xin Ma", "Joanna L. Kelley", "Kirsten Eilertson", "Shaila Musharoff", "Jeremiah D. Degenhardt", "André L. Martins", "Tomáš Vinař", "Carolin Kosiol", "Adam Siepel", "Ryan N. Gutenkunst", "Carlos D. Bustamante"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077175.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_cumulative_distribution_of_selection_coefficients_/831295", "title"=>"Inferred cumulative distribution of selection coefficients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:35:20"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[269, 448, 558, 658, 744, 830, 914, 995, 1068, 1139, 1214, 1284, 1349]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[284, 475, 603, 722, 826, 928, 1026, 1129, 1225, 1310, 1390, 1468, 1549]}, {"subject_area"=>"/Ecology and environmental sciences/Biogeography", "average_usage"=>[320, 517, 642, 738, 850, 955, 1039, 1136, 1226, 1315, 1406, 1495, 1565]}]}
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