Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants
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{"title"=>"Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants", "type"=>"journal", "authors"=>[{"first_name"=>"Nadin", "last_name"=>"Rohland", "scopus_author_id"=>"6506138463"}, {"first_name"=>"David", "last_name"=>"Reich", "scopus_author_id"=>"7102313000"}, {"first_name"=>"Swapan", "last_name"=>"Mallick", "scopus_author_id"=>"24339060900"}, {"first_name"=>"Matthias", "last_name"=>"Meyer", "scopus_author_id"=>"35311551900"}, {"first_name"=>"Richard E.", "last_name"=>"Green", "scopus_author_id"=>"36023707900"}, {"first_name"=>"Nicholas J.", "last_name"=>"Georgiadis", "scopus_author_id"=>"7003307127"}, {"first_name"=>"Alfred L.", "last_name"=>"Roca", "scopus_author_id"=>"7005558848"}, {"first_name"=>"Michael", "last_name"=>"Hofreiter", "scopus_author_id"=>"6701450663"}], "year"=>2010, "source"=>"PLoS Biology", "identifiers"=>{"scopus"=>"2-s2.0-78650472000", "issn"=>"15449173", "pmid"=>"21203580", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)", "doi"=>"10.1371/journal.pbio.1000564", "pui"=>"360215990", "sgr"=>"78650472000"}, "id"=>"9deda0c6-f0a5-36e3-b98b-bf81a9fe08e0", "abstract"=>"To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American mastodon, and the woolly mammoth. Our data establish that the Asian elephant is the closest living relative of the extinct mammoth in the nuclear genome, extending previous findings from mitochondrial DNA analyses. We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants. Finally, we document a much larger effective population size in forest elephants compared with the other elephantid taxa, likely reflecting species differences in ancient geographic structure and range and differences in life history traits such as variance in male reproductive success.", "link"=>"http://www.mendeley.com/research/genomic-dna-sequences-mastodon-woolly-mammoth-reveal-deep-speciation-forest-savanna-elephants", "reader_count"=>348, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>26, "Librarian"=>1, "Researcher"=>94, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>83, "Student > Postgraduate"=>11, "Student > Master"=>41, "Other"=>25, "Student > Bachelor"=>36, "Lecturer"=>4, "Lecturer > Senior Lecturer"=>4, "Professor"=>16}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>26, "Librarian"=>1, "Researcher"=>94, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>83, "Student > Postgraduate"=>11, "Student > Master"=>41, "Other"=>25, "Student > Bachelor"=>36, "Lecturer"=>4, "Lecturer > Senior Lecturer"=>4, "Professor"=>16}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Agricultural and Biological Sciences"=>241, "Arts and Humanities"=>7, "Philosophy"=>1, "Chemistry"=>2, "Computer Science"=>4, "Earth and Planetary Sciences"=>7, "Environmental Science"=>42, "Biochemistry, Genetics and Molecular Biology"=>16, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>5, "Neuroscience"=>1, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>5, "Linguistics"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Social Sciences"=>{"Social Sciences"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>42}, "Arts and Humanities"=>{"Arts and Humanities"=>7}, "Chemistry"=>{"Chemistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>241}, "Computer Science"=>{"Computer Science"=>4}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Linguistics"=>{"Linguistics"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "Romania"=>1, "United States"=>12, "Japan"=>1, "United Kingdom"=>7, "United Arab Emirates"=>1, "Portugal"=>1, "Canada"=>3, "Sweden"=>1, "Netherlands"=>2, "Botswana"=>1, "Brazil"=>6, "Denmark"=>2, "Italy"=>1, "South Africa"=>3, "France"=>2, "Chile"=>1, "Australia"=>1, "Germany"=>2}, "group_count"=>13}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/810668"], "description"=>"<p>All quantities are expressed as a column-to-row ratio with a 90% credible interval. For example, the ratio of effective population sizes of forest to savanna populations = <i>N</i><sub>F</sub>/<i>N</i><sub>S</sub> is 3.58 (2.53–4.92). We do not include the <i>N</i><sub>Elephantid-Mastodon</sub> parameter ancestral to elephant-mastodon divergence as it is not estimated in a stable way. Abbreviations: F, forest elephant; S, savanna elephant; A, Asian elephant; M, woolly mammoth; Lox, <i>Loxodonta</i> (African forest plus savanna elephant); Eur, “Eurasian” (Asian elephant plus mammoth).</p>", "links"=>[], "tags"=>["sizes"], "article_id"=>481036, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.t005", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_values_of_effective_population_sizes_estimated_by_MCMCcoal_/481036", "title"=>"Relative values of effective population sizes estimated by MCMCcoal.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-21 00:17:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/810636"], "description"=>"<p>All quantities are expressed as a column-to-row ratio with a 90% credible interval. For example, the ratio of forest-savanna population split time <i>T</i><sub>FS</sub> in years to African-Eurasian split time <i>T</i><sub>Lox-Eur</sub> is <i>Τ</i><sub>FS</sub>/<i>Τ</i><sub>Lox-Eur</sub> = 0.62 (0.45–0.79). We do not include the <i>T</i><sub>Elephantid-Mastodon</sub> parameter ancestral to elephant-mastodon divergence as it is not estimated in a stable way. Abbreviations: F, forest elephant; S, savanna elephant; A, Asian elephant; M, woolly mammoth; Lox, <i>Loxodonta</i> (African forest plus savanna elephant); Eur, “Eurasian” (Asian elephant plus mammoth).</p>", "links"=>[], "tags"=>["divergence", "times"], "article_id"=>480999, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.t004", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_values_of_population_divergence_times_estimated_by_MCMCcoal_/480999", "title"=>"Relative values of population divergence times estimated by MCMCcoal.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-21 00:16:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/810790"], "description"=>"<p>All estimates are from MCMCcoal and are scaled in coalescent units; that is, a demographic parameter times a mutation rate. Abbreviations: F, forest elephant; S, savanna elephant; A, Asian elephant; M, woolly mammoth; Lox, <i>Loxodonta</i> (African forest and savanna elephant); Eur, “Eurasian” (Asian elephant and mammoth).</p>", "links"=>[], "tags"=>["parameters"], "article_id"=>481158, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.t003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_demographic_parameters_from_MCMCcoal_/481158", "title"=>"Estimates of demographic parameters from MCMCcoal.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-21 00:19:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/810715"], "description"=>"<p>We calculated genetic divergences based on 549 sites that are polymorphic among the elephantids, normalizing by savanna-Asian elephant genetic divergence. Standard errors are from a Weighted Jackknife (calculated in this way, savanna-Asian genetic divergence has no uncertainty since it is used for normalization). The results show that savanna and forest elephants are sister groups (>4 standard deviations less diverged than savanna-Asian) and that Asian elephants and mammoths are also sister groups (>6 standard deviations less diverged than savanna-Asian).</p>", "links"=>[], "tags"=>["divergence", "heterozygosity", "estimates"], "article_id"=>481073, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.t001", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_divergence_and_heterozygosity_estimates_for_the_elephantids_/481073", "title"=>"Genetic divergence and heterozygosity estimates for the elephantids.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-21 00:17:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/810758"], "description"=>"<p>The outgroup is the mastodon. To calculate the rate of any class of sites, we used the product of the relevant allele frequencies; for example, the expected rate of a “12” site where 1 and 2 share the derived allele to the exclusion of 3 is (f<sub>1</sub>)(f<sub>2</sub>)(1−f<sub>3</sub>). Values are summed over 1,775 sites. Standard errors are from a Weighted Jackknife.</p><p>*<i>p</i> values for the Asian-mammoth divergence being less than that of forest-savanna are based on a Weighted Jackknife. The Incomplete Lineage Sorting analysis in the last column, which is based on rare “13” and “23” divergent site classes, shows that there is a significantly higher probability of forest and savanna elephant alleles being unrelated all the way back to the time of their common ancestry with the Eurasian elephantids than is the case for Asian elephants and mammoth.</p>", "links"=>[], "tags"=>["lineage", "coalescing", "lineages", "forest-savanna"], "article_id"=>481113, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.t002", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Incomplete_lineage_sorting_More_deeply_coalescing_lineages_between_forest_savanna_than_Asian_mammoth_/481113", "title"=>"Incomplete lineage sorting: More deeply coalescing lineages between forest-savanna than Asian-mammoth.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-21 00:18:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/810450"], "description"=>"<p>Demographic model that is fit by MCMCcoal, in which all population splits are instantaneous (without subsequent gene flow), and all population sizes are assumed to be constant over intervals. Here, <i>T</i><sub>FS</sub> refers to forest-savanna elephant population divergence time, <i>T</i><sub>AM</sub> refers to Asian elephant-mammoth population divergence time, <i>T</i><sub>Lox-Eur</sub> refers to African-Eurasian population divergence time, and <i>T</i><sub>Elephantid-Mastodon</sub> refers to elephantid-mastodon population divergence time, presented here in millions of years. The <i>Ν</i> quantities refer to constant diploid effective population sizes ancestral to each of these splits (in thousands). For obtaining estimates of years and population sizes, we assume that the elephantids have an average of 31 years per generation, based on estimates of 17–20 years for females <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564-Sukumar1\" target=\"_blank\">[53]</a>,<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564-Moss1\" target=\"_blank\">[54]</a> and 40–49 years for males <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564-HollisterSmith1\" target=\"_blank\">[43]</a>,<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564-Rasmussen2\" target=\"_blank\">[55]</a>. A lower or higher number of years per generation would produce a proportionate effect on the population size estimates. For each parameter, two sets of numbers are shown. The upper set shows the range consistent with the fossil record, calibrating to an assumed African-Eurasian population split of <i>T</i><sub>Lox-Eur</sub> = 4.2–9 Mya (justified in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564.s014\" target=\"_blank\">Text S5</a>). For example for forest-savanna population divergence, this leads to <i>T</i><sub>FS</sub> = 2.6–5.6 Mya given that MCMCcoal estimates <i>T</i><sub>FS</sub><i>/T</i><sub>Lox-Eur</sub> = 62%. The lower set of numbers (in parentheses) provides MCMCcoal's 90% credible interval for the parameters as a fraction of the best estimate (e.g. 76%–126% for <i>T</i><sub>FS</sub>). In the main text, we conservatively quote a range that combines the uncertainty from the fossil record and from MCMCcoal (e.g. <i>T</i><sub>FS</sub> = 1.9–7.1 Mya).</p>", "links"=>[], "tags"=>["Evolutionary biology", "evolutionary biology/genomics", "evolutionary biology/paleontology"], "article_id"=>480810, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_model_for_the_history_of_the_Elephantidae_/480810", "title"=>"Demographic model for the history of the Elephantidae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-21 00:13:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/810333"], "description"=>"<p>(a) <i>Mastodon shotgun 454 sequencing.</i> We ligated 454-adaptors (green and blue) to the ends of the DNA molecules and sequenced the libraries on a Roche 454 GS. (b) <i>Bioinformatic analysis of shotgun 454 sequences.</i> To identify proboscidean sequence, we compared the sequences to databases consisting of the savanna elephant draft genome (loxAfr1), the human genome (hg18), the mouse genome (mm8), NCBI's nucleotide database of environmental samples (env), and NCBI's non-redundant nucleotide database (nr). The 454 sequences with a best match to loxAfr1 (in red) were aligned to loxAfr1. Alignments of at least 90 bp in length and with a similarity higher than 87% were used for primer design after filtering out known repeat elements (using the UCSC RepeatMasker database). Primers were based on loxAfr1 sequence flanking the mastodon sequence. (c) <i>Multiplex PCR and sequencing of the targeted loci in modern elephants and mammoth.</i> We show the protocol for the first of four rounds of the project (<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000564#pbio.1000564.s009\" target=\"_blank\">Table S3</a> provides details of the further rounds). A total of 213 primer pairs were randomly divided into 5 multiplex primer mixes with 41–44 primer pairs per mix. These mixes were used for the first step of the two-step multiplex PCR approach, for each of the 5 samples (La, <i>Loxodonta africana</i>; Lc, <i>L. cyclotis</i>; Em 1, <i>Elephas maximus</i> 1; Em 2, <i>E. maximus</i> 2; Mp, <i>Mammuthus primigenius</i>). Dilutions of these products were used as templates to amplify the loci individually in the second step (shown for <i>L. africana</i>), resulting in 213 distinct products per sample. These products were quantified, normalized, and merged into one pool per sample. A 454 library was prepared and sequenced on 1/16<sup>th</sup> of a picotiter plate of a Roche 454 GS.</p>", "links"=>[], "tags"=>["obtaining", "overlapping", "dna", "elephantids"], "article_id"=>480695, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000564.g001", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strategy_for_obtaining_overlapping_DNA_from_four_elephantids_and_a_mastodon_/480695", "title"=>"Strategy for obtaining overlapping DNA from four elephantids and a mastodon.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-21 00:11:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/404575", "https://ndownloader.figshare.com/files/404586", "https://ndownloader.figshare.com/files/404598", "https://ndownloader.figshare.com/files/404610", "https://ndownloader.figshare.com/files/404616", "https://ndownloader.figshare.com/files/404626", "https://ndownloader.figshare.com/files/404632", "https://ndownloader.figshare.com/files/404640", "https://ndownloader.figshare.com/files/404644", "https://ndownloader.figshare.com/files/404651", "https://ndownloader.figshare.com/files/404658", "https://ndownloader.figshare.com/files/404662", "https://ndownloader.figshare.com/files/404666", "https://ndownloader.figshare.com/files/404673"], "description"=>"<div><p>To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American mastodon, and the woolly mammoth. Our data establish that the Asian elephant is the closest living relative of the extinct mammoth in the nuclear genome, extending previous findings from mitochondrial DNA analyses. We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants. Finally, we document a much larger effective population size in forest elephants compared with the other elephantid taxa, likely reflecting species differences in ancient geographic structure and range and differences in life history traits such as variance in male reproductive success.</p></div>", "links"=>[], "tags"=>["genomic", "dna", "sequences", "mastodon", "woolly", "mammoth", "speciation", "Savanna", "elephants"], "article_id"=>139955, "categories"=>["Evolutionary Biology"], "users"=>["Nadin Rohland", "David Reich", "Swapan Mallick", "Matthias Meyer", "Richard E. Green", "Nicholas J. Georgiadis", "Alfred L. Roca", "Michael Hofreiter"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000564.s001", "https://dx.doi.org/10.1371/journal.pbio.1000564.s002", "https://dx.doi.org/10.1371/journal.pbio.1000564.s003", "https://dx.doi.org/10.1371/journal.pbio.1000564.s004", "https://dx.doi.org/10.1371/journal.pbio.1000564.s005", "https://dx.doi.org/10.1371/journal.pbio.1000564.s006", "https://dx.doi.org/10.1371/journal.pbio.1000564.s007", "https://dx.doi.org/10.1371/journal.pbio.1000564.s008", "https://dx.doi.org/10.1371/journal.pbio.1000564.s009", "https://dx.doi.org/10.1371/journal.pbio.1000564.s010", "https://dx.doi.org/10.1371/journal.pbio.1000564.s011", "https://dx.doi.org/10.1371/journal.pbio.1000564.s012", "https://dx.doi.org/10.1371/journal.pbio.1000564.s013", "https://dx.doi.org/10.1371/journal.pbio.1000564.s014"], "stats"=>{"downloads"=>14, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_DNA_Sequences_from_Mastodon_and_Woolly_Mammoth_Reveal_Deep_Speciation_of_Forest_and_Savanna_Elephants/139955", "title"=>"Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-12-21 02:45:55"}

PMC Usage Stats | Further Information

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