Genome Sequencing Highlights the Dynamic Early History of Dogs
Publication Date
January 16, 2014
Journal
PLOS Genetics
Authors
Adam H. Freedman, Ilan Gronau, Rena M. Schweizer, Diego Ortega Del Vecchyo, et al
Volume
10
Issue
1
Pages
e1004016
DOI
http://doi.org/10.1371/journal.pgen.1004016
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004016
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24453982
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894170
Europe PMC
http://europepmc.org/abstract/MED/24453982
Web of Science
000336525000012
Scopus
84893803193
Mendeley
http://www.mendeley.com/research/genome-sequencing-highlights-dynamic-early-history-dogs
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  • {"files"=>["https://ndownloader.figshare.com/files/1349671"], "description"=>"<p>Divergence times, effective population sizes (<i>N<sub>e</sub></i>), and post-divergence gene flow inferred by <i>G-PhoCS</i> in joint analysis of the Boxer reference genome, and the sequenced genomes of two basal dog breeds, three wolves, and a golden jackal. The width of each population branch is proportional to inferred population size, and stated ranges of parameter estimates indicate 95% Bayesian credible intervals. Horizontal gray dashed lines indicate timing of lineage divergences, with associated means in bold, and 95% credible intervals in parentheses. Migration bands are shown in green with associated values indicating estimates of total migration rates, which equal the probability that a lineage will migrate through the band during the time period when the two populations co-occur. Panels show parameter estimates for (A) the population tree best supported by genome-wide sequence divergence (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen-1004016-g004\" target=\"_blank\">Fig. 4A</a>) (B) a regional domestication model, and (C) a single wolf lineage origin model in which dogs diverged most recently from the Israeli wolf lineage (similar star-like divergences are found assuming alternative choices for the single wolf ancestor. Estimated divergence times and effective population sizes are calibrated assuming an average mutation rate of 1×10<sup>−8</sup> substitutions per generation and an average generation time of three years. See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s028\" target=\"_blank\">Text S9</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s018\" target=\"_blank\">Table S12</a> for details.</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing"], "article_id"=>902782, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g005", "stats"=>{"downloads"=>5, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_model_of_domestication_/902782", "title"=>"Demographic model of domestication.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349668"], "description"=>"<p>PCA plot of next-generation sequencing (NGS) samples generated in this study (open circles) along with corresponding samples genotyped on the Affymetrix canid array <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016-vonHoldt1\" target=\"_blank\">[10]</a> (colors and two letter codes: red M = Mid-East Wolf, green E = European Wolf, black Ch = Chinese Wolf, purple Ba = Basenji, brown Bo = Boxer, orange D = Dingo, cyan J = Golden Jackal).</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing", "sequencing", "typed"], "article_id"=>902779, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g002", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_next_generation_sequencing_with_array_typed_samples_and_historical_changes_in_effective_population_size_/902779", "title"=>"Comparison of next generation sequencing with array typed samples, and historical changes in effective population size.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349667"], "description"=>"<p>Geographic distribution of sampled lineages.</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing", "sampled"], "article_id"=>902778, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g001", "stats"=>{"downloads"=>6, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_distribution_of_sampled_lineages_/902778", "title"=>"Geographic distribution of sampled lineages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349670"], "description"=>"<p>(A) NJ tree constructed from genome-wide pairwise divergence, calculated using equation E8.1 in . All nodes have 100% bootstrap support. Dashed lines indicate admixture edges that were statistically significant in ABBA/BABA tests. (B) ABBA/BABA tests with significant Z-scores (values ≥3 are significant). All comparisons made are shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s017\" target=\"_blank\">Table S11</a>. For each row, boldfaced labels indicate admixing lineages.</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing", "admixture", "signatures"], "article_id"=>902781, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g004", "stats"=>{"downloads"=>7, "page_views"=>185, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neighbor_joining_tree_and_admixture_signatures_from_ABBA_BABA_tests_/902781", "title"=>"Neighbor-joining tree and admixture signatures from ABBA/BABA tests.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349669"], "description"=>"<p>(A) Box plots of heterozygosity measured in 5000 100 kb windows for each sample. (B) Reconstruction of historical patterns of effective population size (N<sub>e</sub>) for individual genome sequences. Based upon the genomic distribution of heterozygous sites using the pairwise sequential Markovian coalescent (PSMC) method of Li and Durbin 2011 <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016-Li2\" target=\"_blank\">[20]</a>. Time scale on the x-axis is calculated assuming a mutation rate of 1×10<sup>−8</sup> per generation (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s027\" target=\"_blank\">Text S8</a>); estimates from the full data and 50 bootstraps are depicted by darker and lighter lines, respectively.</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing"], "article_id"=>902780, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g003", "stats"=>{"downloads"=>2, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heterozygosity_and_historical_changes_in_effective_population_size_/902780", "title"=>"Heterozygosity and historical changes in effective population size.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349672"], "description"=>"<p>(A) Copy number variation (CNV) at <i>AMY2B</i> estimated from whole genome sequence data, showing presence of elevated copy number in Basenji but not in other lineages. Results are based on SOLiD data, except for the Chinese wolf (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s025\" target=\"_blank\">Text S6</a> for supporting results and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004016#pgen.1004016.s029\" target=\"_blank\">Text S10</a> for CNV analyses in an additional 12 dog breeds). (B) qPCR results on CNV state in an expanded set of wolf and dog lineages. Abbreviations for lineages are: AFG, Afgan Hound; AFR, Africanis; AKI, Akita; BSJ, Basenji; BE, Beagle; BU, Bulldog, CAN, Canaan Dog; CU, Chihuahua; CC, Chinese Crested; FC, Flat-coated Retriever; GD, Great Dane; IH, Ibizan Hound; KUV, Kuvasz; MAS, Mastiff; NGS, New Guinea Singing Dog; PEK, Pekinese; PHU, Phu Quoc; SAL, Saluki; SAM, Samoyed; SCT, Scottish Terrier; SHA, Shar Pei; SIH, Siberian Husky; THD, Thai Dog; TOP, Toy Poodle; DNG, Dingo; CHW, Chinese wolf; INW, Indian wolf; ISW, Israeli wolf; ITW, Italian wolf; RUW, Russian wolf; SPW, Spanish wolf; YSW, Yellowstone wolf; GLW, Great Lakes wolf.</p>", "links"=>[], "tags"=>["genetics", "population genetics", "genomics", "Comparative genomics", "Genome sequencing", "amylase"], "article_id"=>902783, "categories"=>["Biological Sciences"], "users"=>["Adam H. Freedman", "Ilan Gronau", "Rena M. Schweizer", "Diego Ortega-Del Vecchyo", "Eunjung Han", "Pedro M. Silva", "Marco Galaverni", "Zhenxin Fan", "Peter Marx", "Belén Lorente-Galdos", "Holly Beale", "Oscar Ramírez", "Farhad Hormozdiari", "Can Alkan", "Carles Vilà", "Kevin Squire", "Eli Geffen", "Josip Kusak", "Adam R. Boyko", "Heidi G. Parker", "Clarence Lee", "Vasisht Tadigotla", "Adam Siepel", "Carlos D. Bustamante", "Timothy T. Harkins", "Stanley F. Nelson", "Elaine A. Ostrander", "Tomàs Marques-Bonet", "Robert K. Wayne", "John Novembre"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004016.g006", "stats"=>{"downloads"=>5, "page_views"=>138, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Copy_number_variation_at_amylase_AMY2B_locus_/902783", "title"=>"Copy number variation at amylase (<i>AMY2B</i>) locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:38:19"}

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