Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup
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{"title"=>"Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup", "type"=>"journal", "authors"=>[{"first_name"=>"Nadin", "last_name"=>"Rohland", "scopus_author_id"=>"6506138463"}, {"first_name"=>"Anna Sapfo", "last_name"=>"Malaspinas", "scopus_author_id"=>"36772368200"}, {"first_name"=>"Joshua L.", "last_name"=>"Pollack", "scopus_author_id"=>"57197027987"}, {"first_name"=>"Montgomery", "last_name"=>"Slatkin", "scopus_author_id"=>"7006682712"}, {"first_name"=>"Paul", "last_name"=>"Matheus", "scopus_author_id"=>"6602299107"}, {"first_name"=>"Michael", "last_name"=>"Hofreiter", "scopus_author_id"=>"6701450663"}], "year"=>2007, "source"=>"PLoS Biology", "identifiers"=>{"pmid"=>"17676977", "doi"=>"10.1371/journal.pbio.0050207", "sgr"=>"34548223646", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)", "scopus"=>"2-s2.0-34548223646", "issn"=>"15449173", "pui"=>"47328271"}, "id"=>"f1baa5df-8d01-3ee6-bad4-b95412ed3d4d", "abstract"=>"We have sequenced the complete mitochondrial genome of the extinct American mastodon (Mammut americanum) from an Alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle. The sequence we obtained is substantially different from previously reported partial mastodon mitochondrial DNA sequences. By comparing those partial sequences to other proboscidean sequences, we conclude that we have obtained the first sequence of mastodon DNA ever reported. Using the sequence of the mastodon, which diverged 24-28 million years ago (mya) from the Elephantidae lineage, as an outgroup, we infer that the ancestors of African elephants diverged from the lineage leading to mammoths and Asian elephants approximately 7.6 mya and that mammoths and Asian elephants diverged approximately 6.7 mya. We also conclude that the nuclear genomes of the African savannah and forest elephants diverged approximately 4.0 mya, supporting the view that these two groups represent different species. Finally, we found the mitochondrial mutation rate of proboscideans to be roughly half of the rate in primates during at least the last 24 million years.", "link"=>"http://www.mendeley.com/research/proboscidean-mitogenomics-chronology-mode-elephant-evolution-using-mastodon-outgroup", "reader_count"=>205, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>12, "Researcher"=>53, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>4, "Student > Master"=>23, "Other"=>8, "Student > Bachelor"=>17, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>17}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>12, "Researcher"=>53, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>4, "Student > Master"=>23, "Other"=>8, "Student > Bachelor"=>17, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>17}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Agricultural and Biological Sciences"=>133, "Arts and Humanities"=>7, "Philosophy"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>20, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>12, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>13}, "Arts and Humanities"=>{"Arts and Humanities"=>7}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>20}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>133}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Argentina"=>2, "United States"=>6, "Japan"=>1, "Malaysia"=>1, "Switzerland"=>1, "Costa Rica"=>1, "Lebanon"=>1, "Austria"=>1, "Botswana"=>1, "Denmark"=>1, "Brazil"=>3, "Mexico"=>2, "South Africa"=>2, "Italy"=>1, "Chile"=>3, "Germany"=>2}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/947720"], "description"=>"<p>The high correlation coefficient of this plot suggests that the sequence data are highly informative. However, it cannot be excluded that the accuracy of divergence time estimates could be further improved by additional sequence data. The graph corresponds to the whole genome analysis. The partitioned data give a slightly higher correlation coefficient of 0.89 (not shown).</p>", "links"=>[], "tags"=>["saturation", "ci", "width", "posterior"], "article_id"=>618053, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050207.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_Saturation_as_Determined_by_the_95_CI_Width_as_a_Function_of_Posterior_Mean_Time_/618053", "title"=>"Data Saturation as Determined by the 95% CI Width as a Function of Posterior Mean Time", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-07-24 02:14:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/466555", "https://ndownloader.figshare.com/files/466565", "https://ndownloader.figshare.com/files/466576", "https://ndownloader.figshare.com/files/466596", "https://ndownloader.figshare.com/files/466603", "https://ndownloader.figshare.com/files/466614", "https://ndownloader.figshare.com/files/466623", "https://ndownloader.figshare.com/files/466635", "https://ndownloader.figshare.com/files/466644", "https://ndownloader.figshare.com/files/466653"], "description"=>"<div><p>We have sequenced the complete mitochondrial genome of the extinct American mastodon <em>(Mammut americanum)</em> from an Alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle. The sequence we obtained is substantially different from previously reported partial mastodon mitochondrial DNA sequences. By comparing those partial sequences to other proboscidean sequences, we conclude that we have obtained the first sequence of mastodon DNA ever reported. Using the sequence of the mastodon, which diverged 24–28 million years ago (mya) from the Elephantidae lineage, as an outgroup, we infer that the ancestors of African elephants diverged from the lineage leading to mammoths and Asian elephants approximately 7.6 mya and that mammoths and Asian elephants diverged approximately 6.7 mya. We also conclude that the nuclear genomes of the African savannah and forest elephants diverged approximately 4.0 mya, supporting the view that these two groups represent different species. Finally, we found the mitochondrial mutation rate of proboscideans to be roughly half of the rate in primates during at least the last 24 million years.</p> </div>", "links"=>[], "tags"=>["proboscidean", "chronology", "mastodon", "outgroup"], "article_id"=>151958, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0050207.sg001", "https://dx.doi.org/10.1371/journal.pbio.0050207.sg002", "https://dx.doi.org/10.1371/journal.pbio.0050207.sg003", "https://dx.doi.org/10.1371/journal.pbio.0050207.sd001", "https://dx.doi.org/10.1371/journal.pbio.0050207.sd002", "https://dx.doi.org/10.1371/journal.pbio.0050207.sd003", "https://dx.doi.org/10.1371/journal.pbio.0050207.st001", "https://dx.doi.org/10.1371/journal.pbio.0050207.st002", "https://dx.doi.org/10.1371/journal.pbio.0050207.st003", "https://dx.doi.org/10.1371/journal.pbio.0050207.st004"], "stats"=>{"downloads"=>53, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Proboscidean_Mitogenomics_Chronology_and_Mode_of_Elephant_Evolution_Using_Mastodon_as_Outgroup/151958", "title"=>"Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-07-24 00:32:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/947654"], "description"=>"<p>Colored bars indicate the posterior probabilities for each respective topology. Blue indicates a <i>Mammuthus–Elephas</i> sister group relationship, green indicates a <i>Mammuthus–Loxodonta</i> sister group relationship, and yellow indicates an <i>Elephas–Loxodonta</i> sister group relationship. Black bars show the length of the respective genes in base pairs.</p>", "links"=>[], "tags"=>["Evolutionary biology"], "article_id"=>617994, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050207.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_by_Gene_Topology_/617994", "title"=>"Gene-by-Gene Topology", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-07-24 02:13:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/947402"], "description"=>"<p>The scale bar shows centimeters.</p>", "links"=>[], "tags"=>["mastodon", "sequencing", "mtdna"], "article_id"=>617740, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050207.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Appearance_and_Location_of_Origin_of_the_Mastodon_Tooth_IK_99_8211_237_Used_for_Sequencing_of_the_mtDNA_Genome_/617740", "title"=>"Appearance and Location of Origin of the Mastodon Tooth (IK-99–237) Used for Sequencing of the mtDNA Genome", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-07-24 02:09:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/947519"], "description"=>"<p>The six points correspond to the ratio between species of Elephantidae (first two points), between Elephantidae and <i>Mammut,</i> between Proboscidea and (<i>Dugong, Procavia</i>), between Uranotheria and <i>Bos,</i> and between Mammalia and <i>Struthio</i>. The corresponding divergence times for proboscideans are given in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-t002\" target=\"_blank\">Table 2</a>. Dugong and hyrax diverged from Proboscidea 65 mya [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b005\" target=\"_blank\">5</a>,<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b009\" target=\"_blank\">9</a>]. We used 105 mya for the Uranotheria–ruminant split ([<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b009\" target=\"_blank\">9</a>] and citations therein). The mammalian–bird divergence was set to 313 mya (the mean value of the confidence interval of [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b062\" target=\"_blank\">62</a>]; but see also [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b063\" target=\"_blank\">63</a>,<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050207#pbio-0050207-b065\" target=\"_blank\">65</a>]). The arrows indicate the points of interest. The uncertainty of the divergence times is not taken into account because the goal was to show the general trend.</p>", "links"=>[], "tags"=>["transitions"], "article_id"=>617854, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050207.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ratio_of_the_Number_of_Transitions_to_the_Number_of_Transversions_/617854", "title"=>"Ratio of the Number of Transitions to the Number of Transversions", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-07-24 02:10:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/947890"], "description"=>"<p>Phylogeny and Divergence Times Determined by This Study for the Four Proboscidean Species Analyzed</p>", "links"=>[], "tags"=>["divergence", "times", "proboscidean"], "article_id"=>618223, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "Anna-Sapfo Malaspinas", "Joshua L Pollack", "Montgomery Slatkin", "Paul Matheus", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050207.g005", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_and_Divergence_Times_Determined_by_This_Study_for_the_Four_Proboscidean_Species_Analyzed_/618223", "title"=>"Phylogeny and Divergence Times Determined by This Study for the Four Proboscidean Species Analyzed", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-07-24 02:17:03"}

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Relative Metric

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