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{"title"=>"Hunting the extinct steppe bison (Bison priscus) mitochondrial genome in the Trois- Frères Paleolithic painted cave", "type"=>"journal", "authors"=>[{"first_name"=>"Marie Claude", "last_name"=>"Marsolier-Kergoat", "scopus_author_id"=>"6506166660"}, {"first_name"=>"Pauline", "last_name"=>"Palacio", "scopus_author_id"=>"55967662000"}, {"first_name"=>"Véronique", "last_name"=>"Berthonaud", "scopus_author_id"=>"6506476636"}, {"first_name"=>"Frédéric", "last_name"=>"Maksud", "scopus_author_id"=>"25648103700"}, {"first_name"=>"Thomas", "last_name"=>"Stafford", "scopus_author_id"=>"7004919386"}, {"first_name"=>"Robert", "last_name"=>"Bégouën", "scopus_author_id"=>"55919334500"}, {"first_name"=>"Jean Marc", "last_name"=>"Elalouf", "scopus_author_id"=>"7003605321"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"26083419", "scopus"=>"2-s2.0-84939229415", "sgr"=>"84939229415", "doi"=>"10.1371/journal.pone.0128267", "pui"=>"605585898", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"695d40ef-0c5f-38cc-ab31-fc21759a8ba0", "abstract"=>"Despite the abundance of fossil remains for the extinct steppe bison (Bison priscus), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Freres Paleolithic cave (Ariege, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by Bos DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded Bison priscus DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the Bison priscus mitochondrial genome as basal to the clade delineated by the genomes of the modern American Bison bison. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published Bison bison mitochondrial genomes, provides an additional resource for the study of Bovinae specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Freres cave.", "link"=>"http://www.mendeley.com/research/hunting-extinct-steppe-bison-bison-priscus-mitochondrial-genome-trois-fr%C3%A8res-paleolithic-painted-cav", "reader_count"=>29, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>9, "Arts and Humanities"=>4, "Veterinary Science and Veterinary Medicine"=>1, "Social Sciences"=>1, "Earth and Planetary Sciences"=>3, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>4}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "France"=>1}, "group_count"=>0}

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• http://doi.org/10.1038/ncomms13158
• http://doi.org/10.1016/j.quaint.2019.01.025
• http://doi.org/10.1186/s12915-016-0317-7
• http://doi.org/10.1016/j.quaint.2017.01.005
• http://doi.org/10.1098/rspb.2018.0214
• http://doi.org/10.1186/s12862-017-0894-2

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{"EMBL"=>1, "UNIPROT"=>13}

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Wikipedia | Further Information

• {"title"=>"Steppe bison", "url"=>"http://en.wikipedia.org/wiki/Steppe_bison", "timestamp"=>"2019-02-11T13:30:28Z"}
• {"title"=>"Bovid hybrid", "url"=>"http://en.wikipedia.org/wiki/Bovid_hybrid", "timestamp"=>"2018-12-24T09:10:40Z"}
• {"title"=>"Bison", "url"=>"http://en.wikipedia.org/wiki/Bison", "timestamp"=>"2019-03-01T19:49:27Z"}
• {"title"=>"European bison", "url"=>"http://en.wikipedia.org/wiki/European_bison", "timestamp"=>"2019-03-14T15:17:08Z"}
• {"title"=>"Quaternary extinction event", "url"=>"http://en.wikipedia.org/wiki/Quaternary_extinction_event", "timestamp"=>"2019-03-15T21:58:23Z"}
• {"title"=>"Amerikanischer Bison", "url"=>"http://de.wikipedia.org/wiki/Amerikanischer_Bison", "timestamp"=>"2019-02-17T09:43:40Z"}
• {"title"=>"Wisent", "url"=>"http://de.wikipedia.org/wiki/Wisent", "timestamp"=>"2019-03-09T19:09:56Z"}
• {"title"=>"バイソン属", "url"=>"http://ja.wikipedia.org/wiki/バイソン属", "timestamp"=>"2019-03-03T12:31:06Z"}
• {"title"=>"ステップバイソン", "url"=>"http://ja.wikipedia.org/wiki/ステップバイソン", "timestamp"=>"2018-12-08T14:35:46Z"}
• {"title"=>"ヨーロッパバイソン", "url"=>"http://ja.wikipedia.org/wiki/ヨーロッパバイソン", "timestamp"=>"2018-12-08T09:19:40Z"}
• {"title"=>"オーロックス", "url"=>"http://ja.wikipedia.org/wiki/オーロックス", "timestamp"=>"2018-12-07T14:06:24Z"}
• {"title"=>"アメリカバイソン", "url"=>"http://ja.wikipedia.org/wiki/アメリカバイソン", "timestamp"=>"2019-03-03T12:33:34Z"}
• {"title"=>"西伯利亞野牛", "url"=>"http://zh.wikipedia.org/wiki/西伯利亞野牛", "timestamp"=>"2019-02-21T06:58:38Z"}
• {"title"=>"스텝들소", "url"=>"http://ko.wikipedia.org/wiki/스텝들소", "timestamp"=>"2019-02-02T05:20:22Z"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/2119323"], "description"=>"<p>(A) Uncalibrated (B.P.) and calibrated (calBP) age of the bone sample. The calBP data correspond to 95.4% (2 σ) confidence interval of the sample age using IntCal13 calibration curve. (B) Characterization of the dated material.</p>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451509, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128267.g003", "stats"=>{"downloads"=>2, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Radiocarbon_and_stable_isotopes_data_for_the_SGE2_bison_sample_/1451509", "title"=>"Radiocarbon and stable isotopes data for the SGE2 bison sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 02:54:37"}
• {"files"=>["https://ndownloader.figshare.com/files/2119322"], "description"=>"<p>DNA extracts were analyzed for a fragment of the mitochondrial cytB gene using primers encompassing a 63-bp sequence where <i>Bos</i> (<i>Bos taurus</i>, <i>Bos primigenius</i>) and <i>Bison</i> (<i>Bison bison</i>, <i>Bison bonasus</i>) reference genomes display 5 differences. The cloned PCR products were sequenced and identified as <i>Bos</i> or <i>Bison</i> according to the number of differences with the reference genomes (see text for details).</p>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451508, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128267.g002", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_analysis_of_the_samples_for_Bovinae_sequences_/1451508", "title"=>"PCR analysis of the samples for <i>Bovinae</i> sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 02:54:37"}
• {"files"=>["https://ndownloader.figshare.com/files/2119325"], "description"=>"<p>The numbers indicated in parentheses after the species name refer to the number of genomes examined for that species (which is equal to 1 by default). The tree with the highest log-likelihood is shown drawn to scale, with branch lengths established from the number of substitutions per site. The same topology was obtained with the Minimum Evolution (ME) and Neighbor-Joining (NJ) methods. The percentages of trees in which the associated taxa clustered together with the ML method are displayed next to the branches (these bootstrap values were determined with 1000 replicates). These percentages were also equal to 100 with the ME and the NJ methods. Photography of painted and engraved bison by Robert Bégouën.</p>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451511, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128267.g005", "stats"=>{"downloads"=>3, "page_views"=>162, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_Likelihood_phylogenetic_tree_of_complete_mitochondrial_genomes_of_Bison_and_Bos_species_/1451511", "title"=>"Maximum Likelihood phylogenetic tree of complete mitochondrial genomes of <i>Bison</i> and <i>Bos</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 02:54:37"}
• {"files"=>["https://ndownloader.figshare.com/files/2119326", "https://ndownloader.figshare.com/files/2119327", "https://ndownloader.figshare.com/files/2119328", "https://ndownloader.figshare.com/files/2119329", "https://ndownloader.figshare.com/files/2119330", "https://ndownloader.figshare.com/files/2119331", "https://ndownloader.figshare.com/files/2119332"], "description"=>"<div><p>Despite the abundance of fossil remains for the extinct steppe bison (<i>Bison priscus</i>), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Frères Paleolithic cave (Ariège, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by <i>Bos</i> DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded <i>Bison priscus</i> DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the <i>Bison priscus</i> mitochondrial genome as basal to the clade delineated by the genomes of the modern American <i>Bison bison</i>. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published <i>Bison bison</i> mitochondrial genomes, provides an additional resource for the study of <i>Bovinae</i> specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Frères cave.</p></div>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451512, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0128267.s001", "https://dx.doi.org/10.1371/journal.pone.0128267.s002", "https://dx.doi.org/10.1371/journal.pone.0128267.s003", "https://dx.doi.org/10.1371/journal.pone.0128267.s004", "https://dx.doi.org/10.1371/journal.pone.0128267.s005", "https://dx.doi.org/10.1371/journal.pone.0128267.s006", "https://dx.doi.org/10.1371/journal.pone.0128267.s007"], "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Hunting_the_Extinct_Steppe_Bison_Bison_priscus_Mitochondrial_Genome_in_the_Trois_Fr_res_Paleolithic_Painted_Cave/1451512", "title"=>"Hunting the Extinct Steppe Bison (<i>Bison priscus</i>) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-17 02:54:37"}
• {"files"=>["https://ndownloader.figshare.com/files/2119324"], "description"=>"<p>(A) Size distribution of the 3,851 unique Illumina reads. (B) Coverage for each position of the SGE2seq sequence obtained by merging the sequences of Illumina reads and PCR fragments.</p>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451510, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128267.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_sequences_used_to_assemble_the_Bison_priscus_mitochondrial_genome_/1451510", "title"=>"Characteristics of the sequences used to assemble the <i>Bison priscus</i> mitochondrial genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 02:54:37"}
• {"files"=>["https://ndownloader.figshare.com/files/2119321"], "description"=>"<p>(A) Geographic localization of the Trois-Frères cave. (B) Topography of the cave showing the site (white ellipse) where the samples were collected in the <i>Salle du Grand Éboulis</i>. (C-E) The samples considered for DNA extraction in the present study. SGE1: ulna distal fragment; SGE2: rib; SGE3: humerus fragment; SGE5, vertebra.</p>", "links"=>[], "tags"=>["European Paleolithic caves", "steppe bison sequence", "Bison priscus DNA", "Bison priscus mitochondrial genome", "pcr", "ere", "American Bison bison", "Ari ège France", "Extinct Steppe Bison", "steppe bison", "mitochondrial genome sequence", "Bison bison mitochondrial genomes"], "article_id"=>1451507, "categories"=>["Biological Sciences"], "users"=>["Marie-Claude Marsolier-Kergoat", "Pauline Palacio", "Véronique Berthonaud", "Frédéric Maksud", "Thomas Stafford", "Robert Bégouën", "Jean-Marc Elalouf"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128267.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_cave_site_and_bone_samples_/1451507", "title"=>"Overview of the cave site and bone samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 02:54:37"}

PMC Usage Stats | Further Information

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Relative Metric

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

F1000Prime