Phylogenomic analyses data of the avian phylogenomics project
Identifieur interne : 000B80 ( Pmc/Curation ); précédent : 000B79; suivant : 000B81Phylogenomic analyses data of the avian phylogenomics project
Auteurs : Erich D. Jarvis [États-Unis] ; Siavash Mirarab [États-Unis] ; Andre J. Aberer [Allemagne] ; Bo Li [République populaire de Chine, Danemark] ; Peter Houde [États-Unis] ; Cai Li [République populaire de Chine, Danemark] ; Simon Y W. Ho [Australie] ; Brant C. Faircloth [États-Unis] ; Benoit Nabholz [France] ; Jason T. Howard [États-Unis] ; Alexander Suh [Suède] ; Claudia C. Weber [Suède] ; Rute R. Da Fonseca [Danemark] ; Alonzo Alfaro-Nú Ez [Danemark] ; Nitish Narula [États-Unis, Japon] ; Liang Liu [États-Unis] ; Dave Burt [Royaume-Uni] ; Hans Ellegren [Suède] ; Scott V. Edwards [États-Unis] ; Alexandros Stamatakis [Allemagne] ; David P. Mindell [États-Unis] ; Joel Cracraft [États-Unis] ; Edward L. Braun [États-Unis] ; Tandy Warnow [États-Unis] ; Wang Jun [République populaire de Chine, Danemark, Arabie saoudite, Hong Kong] ; M Thomas Pius Gilbert [Danemark] ; Guojie Zhang [République populaire de Chine, Danemark]Source :
- GigaScience [ 2047-217X ] ; 2015.
Abstract
Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.
Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.
The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.
The online version of this article (doi:10.1186/s13742-014-0038-1) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13742-014-0038-1
PubMed: 25741440
PubMed Central: 4349222
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M Thomas Pius Gilbert<affiliation><nlm:aff id="Aff25">Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</nlm:aff>
<wicri:noCountry code="subfield">WA 6102 Australia</wicri:noCountry>
</affiliation>
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<wicri:regionArea>China National GeneBank, BGI-Shenzhen, Shenzhen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff5">College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Houde, Peter" sort="Houde, Peter" uniqKey="Houde P" first="Peter" last="Houde">Peter Houde</name>
<affiliation wicri:level="2"><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nouveau-Mexique</region>
</placeName>
<wicri:cityArea>Department of Biology, New Mexico State University, Las Cruces</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Li, Cai" sort="Li, Cai" uniqKey="Li C" first="Cai" last="Li">Cai Li</name>
<affiliation wicri:level="1"><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>China National GeneBank, BGI-Shenzhen, Shenzhen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name>
<affiliation wicri:level="4"><nlm:aff id="Aff8">School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia</nlm:aff>
<orgName type="university">Université de Sydney</orgName>
<country>Australie</country>
<placeName><settlement type="city">Sydney</settlement>
<region type="état">Nouvelle-Galles du Sud</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Faircloth, Brant C" sort="Faircloth, Brant C" uniqKey="Faircloth B" first="Brant C" last="Faircloth">Brant C. Faircloth</name>
<affiliation wicri:level="2"><nlm:aff id="Aff9">Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles</wicri:cityArea>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="Aff10">Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Louisiane</region>
</placeName>
<wicri:cityArea>Department of Biological Sciences, Louisiana State University, Baton Rouge</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Nabholz, Benoit" sort="Nabholz, Benoit" uniqKey="Nabholz B" first="Benoit" last="Nabholz">Benoit Nabholz</name>
<affiliation wicri:level="1"><nlm:aff id="Aff11">CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Howard, Jason T" sort="Howard, Jason T" uniqKey="Howard J" first="Jason T" last="Howard">Jason T. Howard</name>
<affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Suh, Alexander" sort="Suh, Alexander" uniqKey="Suh A" first="Alexander" last="Suh">Alexander Suh</name>
<affiliation wicri:level="1"><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Weber, Claudia C" sort="Weber, Claudia C" uniqKey="Weber C" first="Claudia C" last="Weber">Claudia C. Weber</name>
<affiliation wicri:level="1"><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Da Fonseca, Rute R" sort="Da Fonseca, Rute R" uniqKey="Da Fonseca R" first="Rute R" last="Da Fonseca">Rute R. Da Fonseca</name>
<affiliation wicri:level="1"><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Alfaro Nu Ez, Alonzo" sort="Alfaro Nu Ez, Alonzo" uniqKey="Alfaro Nu Ez A" first="Alonzo" last="Alfaro-Nú Ez">Alonzo Alfaro-Nú Ez</name>
<affiliation wicri:level="1"><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Narula, Nitish" sort="Narula, Nitish" uniqKey="Narula N" first="Nitish" last="Narula">Nitish Narula</name>
<affiliation wicri:level="2"><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nouveau-Mexique</region>
</placeName>
<wicri:cityArea>Department of Biology, New Mexico State University, Las Cruces</wicri:cityArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff13">Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Liu, Liang" sort="Liu, Liang" uniqKey="Liu L" first="Liang" last="Liu">Liang Liu</name>
<affiliation wicri:level="1"><nlm:aff id="Aff14">Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Burt, Dave" sort="Burt, Dave" uniqKey="Burt D" first="Dave" last="Burt">Dave Burt</name>
<affiliation wicri:level="4"><nlm:aff id="Aff15">Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK</nlm:aff>
<orgName type="university">Université d'Édimbourg</orgName>
<country>Royaume-Uni</country>
<placeName><settlement type="city">Édimbourg</settlement>
<region type="country">Écosse</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Ellegren, Hans" sort="Ellegren, Hans" uniqKey="Ellegren H" first="Hans" last="Ellegren">Hans Ellegren</name>
<affiliation wicri:level="1"><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Edwards, Scott V" sort="Edwards, Scott V" uniqKey="Edwards S" first="Scott V" last="Edwards">Scott V. Edwards</name>
<affiliation wicri:level="2"><nlm:aff id="Aff16">Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA</nlm:aff>
<country>États-Unis</country>
<placeName><region type="state">Massachusetts</region>
</placeName>
<wicri:cityArea>Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name>
<affiliation wicri:level="1"><nlm:aff id="Aff3">Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff17">Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name>
<affiliation wicri:level="2"><nlm:aff id="Aff18">Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Biochemistry & Biophysics, University of California, San Francisco</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Cracraft, Joel" sort="Cracraft, Joel" uniqKey="Cracraft J" first="Joel" last="Cracraft">Joel Cracraft</name>
<affiliation wicri:level="2"><nlm:aff id="Aff19">Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">État de New York</region>
</placeName>
<wicri:cityArea>Department of Ornithology, American Museum of Natural History, New York</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Braun, Edward L" sort="Braun, Edward L" uniqKey="Braun E" first="Edward L" last="Braun">Edward L. Braun</name>
<affiliation wicri:level="2"><nlm:aff id="Aff20">Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Floride</region>
</placeName>
<wicri:cityArea>Department of Biology and Genetics Institute, University of Florida, Gainesville</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Warnow, Tandy" sort="Warnow, Tandy" uniqKey="Warnow T" first="Tandy" last="Warnow">Tandy Warnow</name>
<affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Computer Science, The University of Texas at Austin, Austin</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Jun, Wang" sort="Jun, Wang" uniqKey="Jun W" first="Wang" last="Jun">Wang Jun</name>
<affiliation wicri:level="1"><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>China National GeneBank, BGI-Shenzhen, Shenzhen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff21">Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff22">Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia</nlm:aff>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff23">Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Macau University of Science and Technology, Avenida Wai long, Taipa, Macau</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff24">Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong</nlm:aff>
<country xml:lang="fr">Hong Kong</country>
<wicri:regionArea>Department of Medicine, University of Hong Kong, Hong Kong</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Gilbert, M Thomas Pius" sort="Gilbert, M Thomas Pius" uniqKey="Gilbert M" first="M Thomas Pius" last="Gilbert">M Thomas Pius Gilbert</name>
<affiliation wicri:level="1"><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen</wicri:regionArea>
</affiliation>
<affiliation><nlm:aff id="Aff25">Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</nlm:aff>
<wicri:noCountry code="subfield">WA 6102 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Zhang, Guojie" sort="Zhang, Guojie" uniqKey="Zhang G" first="Guojie" last="Zhang">Guojie Zhang</name>
<affiliation wicri:level="1"><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>China National GeneBank, BGI-Shenzhen, Shenzhen</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="Aff26">Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">GigaScience</title>
<idno type="eISSN">2047-217X</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
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</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.</p>
</sec>
<sec><title>Findings</title>
<p>Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.</p>
</sec>
<sec><title>Conclusions</title>
<p>The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13742-014-0038-1) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<biblStruct><analytic><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name>
</author>
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<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Mirarab, S" uniqKey="Mirarab S">S Mirarab</name>
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<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Dickinson, Ec" uniqKey="Dickinson E">EC Dickinson</name>
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<biblStruct><analytic><author><name sortKey="Gill, F" uniqKey="Gill F">F Gill</name>
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</biblStruct>
<biblStruct><analytic><author><name sortKey="Hillier, Lw" uniqKey="Hillier L">LW Hillier</name>
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<author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name>
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</biblStruct>
<biblStruct><analytic><author><name sortKey="Warren, Wc" uniqKey="Warren W">WC Warren</name>
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<author><name sortKey="Clayton, Df" uniqKey="Clayton D">DF Clayton</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mccormack, Je" uniqKey="Mccormack J">JE McCormack</name>
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</biblStruct>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Gigascience</journal-id>
<journal-id journal-id-type="iso-abbrev">Gigascience</journal-id>
<journal-title-group><journal-title>GigaScience</journal-title>
</journal-title-group>
<issn pub-type="epub">2047-217X</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25741440</article-id>
<article-id pub-id-type="pmc">4349222</article-id>
<article-id pub-id-type="publisher-id">38</article-id>
<article-id pub-id-type="doi">10.1186/s13742-014-0038-1</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Data Note</subject>
</subj-group>
</article-categories>
<title-group><article-title>Phylogenomic analyses data of the avian phylogenomics project</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes"><name><surname>Jarvis</surname>
<given-names>Erich D</given-names>
</name>
<address><email>jarvis@neuro.duke.edu</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Mirarab</surname>
<given-names>Siavash</given-names>
</name>
<address><email>smirarab@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Aberer</surname>
<given-names>Andre J</given-names>
</name>
<address><email>andre.aberer@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Bo</given-names>
</name>
<address><email>libo@genomics.org.cn</email>
</address>
<xref ref-type="aff" rid="Aff4"></xref>
<xref ref-type="aff" rid="Aff5"></xref>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Houde</surname>
<given-names>Peter</given-names>
</name>
<address><email>phoude@nmsu.edu</email>
</address>
<xref ref-type="aff" rid="Aff7"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Cai</given-names>
</name>
<address><email>licai@genomics.cn</email>
</address>
<xref ref-type="aff" rid="Aff4"></xref>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ho</surname>
<given-names>Simon Y W</given-names>
</name>
<address><email>simon.ho@sydney.edu.au</email>
</address>
<xref ref-type="aff" rid="Aff8"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Faircloth</surname>
<given-names>Brant C</given-names>
</name>
<address><email>brant@faircloth-lab.org</email>
</address>
<xref ref-type="aff" rid="Aff9"></xref>
<xref ref-type="aff" rid="Aff10"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nabholz</surname>
<given-names>Benoit</given-names>
</name>
<address><email>benoit.nabholz@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff11"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Howard</surname>
<given-names>Jason T</given-names>
</name>
<address><email>howard@neuro.duke.edu</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Suh</surname>
<given-names>Alexander</given-names>
</name>
<address><email>Alexander.Suh@ebc.uu.se</email>
</address>
<xref ref-type="aff" rid="Aff12"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Weber</surname>
<given-names>Claudia C</given-names>
</name>
<address><email>claudia.weber@ebc.uu.se</email>
</address>
<xref ref-type="aff" rid="Aff12"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>da Fonseca</surname>
<given-names>Rute R</given-names>
</name>
<address><email>rute.r.da.fonseca@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Alfaro-Núñez</surname>
<given-names>Alonzo</given-names>
</name>
<address><email>alonzoalfaro@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Narula</surname>
<given-names>Nitish</given-names>
</name>
<address><email>nitishnarula19@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff7"></xref>
<xref ref-type="aff" rid="Aff13"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liu</surname>
<given-names>Liang</given-names>
</name>
<address><email>lliu@uga.edu</email>
</address>
<xref ref-type="aff" rid="Aff14"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Burt</surname>
<given-names>Dave</given-names>
</name>
<address><email>dave.burt@roslin.ed.ac.uk</email>
</address>
<xref ref-type="aff" rid="Aff15"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ellegren</surname>
<given-names>Hans</given-names>
</name>
<address><email>Hans.Ellegren@ebc.uu.se</email>
</address>
<xref ref-type="aff" rid="Aff12"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Edwards</surname>
<given-names>Scott V</given-names>
</name>
<address><email>sedwards@fas.harvard.edu</email>
</address>
<xref ref-type="aff" rid="Aff16"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stamatakis</surname>
<given-names>Alexandros</given-names>
</name>
<address><email>Alexandros.Stamatakis@h-its.org</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
<xref ref-type="aff" rid="Aff17"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mindell</surname>
<given-names>David P</given-names>
</name>
<address><email>dpmindell@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff18"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cracraft</surname>
<given-names>Joel</given-names>
</name>
<address><email>jlc@amnh.org</email>
</address>
<xref ref-type="aff" rid="Aff19"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Braun</surname>
<given-names>Edward L</given-names>
</name>
<address><email>ebraun68@ufl.edu</email>
</address>
<xref ref-type="aff" rid="Aff20"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Warnow</surname>
<given-names>Tandy</given-names>
</name>
<address><email>warnow@illinois.edu</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Jun</surname>
<given-names>Wang</given-names>
</name>
<address><email>wangj@genomics.org.cn</email>
</address>
<xref ref-type="aff" rid="Aff4"></xref>
<xref ref-type="aff" rid="Aff21"></xref>
<xref ref-type="aff" rid="Aff22"></xref>
<xref ref-type="aff" rid="Aff23"></xref>
<xref ref-type="aff" rid="Aff24"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Gilbert</surname>
<given-names>M Thomas Pius</given-names>
</name>
<address><email>mtpgilbert@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff6"></xref>
<xref ref-type="aff" rid="Aff25"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Zhang</surname>
<given-names>Guojie</given-names>
</name>
<address><email>zhanggj@genomics.cn</email>
</address>
<xref ref-type="aff" rid="Aff4"></xref>
<xref ref-type="aff" rid="Aff26"></xref>
</contrib>
<contrib contrib-type="author"><collab>The Avian Phylogenomics Consortium</collab>
</contrib>
<aff id="Aff1"><label></label>
Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</aff>
<aff id="Aff2"><label></label>
Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</aff>
<aff id="Aff3"><label></label>
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</aff>
<aff id="Aff4"><label></label>
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</aff>
<aff id="Aff5"><label></label>
College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061 China</aff>
<aff id="Aff6"><label></label>
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</aff>
<aff id="Aff7"><label></label>
Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</aff>
<aff id="Aff8"><label></label>
School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia</aff>
<aff id="Aff9"><label></label>
Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA</aff>
<aff id="Aff10"><label></label>
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA</aff>
<aff id="Aff11"><label></label>
CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier, France</aff>
<aff id="Aff12"><label></label>
Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</aff>
<aff id="Aff13"><label></label>
Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan</aff>
<aff id="Aff14"><label></label>
Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA</aff>
<aff id="Aff15"><label></label>
Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK</aff>
<aff id="Aff16"><label></label>
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA</aff>
<aff id="Aff17"><label></label>
Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany</aff>
<aff id="Aff18"><label></label>
Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA</aff>
<aff id="Aff19"><label></label>
Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA</aff>
<aff id="Aff20"><label></label>
Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA</aff>
<aff id="Aff21"><label></label>
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark</aff>
<aff id="Aff22"><label></label>
Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia</aff>
<aff id="Aff23"><label></label>
Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China</aff>
<aff id="Aff24"><label></label>
Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong</aff>
<aff id="Aff25"><label></label>
Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</aff>
<aff id="Aff26"><label></label>
Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark</aff>
</contrib-group>
<pub-date pub-type="epub"><day>12</day>
<month>2</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>12</day>
<month>2</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<volume>4</volume>
<elocation-id>4</elocation-id>
<history><date date-type="received"><day>26</day>
<month>11</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>16</day>
<month>12</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© Jarvis et al.; licensee BioMed Central. 2015</copyright-statement>
<license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><sec><title>Background</title>
<p>Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.</p>
</sec>
<sec><title>Findings</title>
<p>Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.</p>
</sec>
<sec><title>Conclusions</title>
<p>The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13742-014-0038-1) contains supplementary material, which is available to authorized users.</p>
</sec>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Avian genomes</kwd>
<kwd>Phylogenomics</kwd>
<kwd>Sequence alignments</kwd>
<kwd>Species tree</kwd>
<kwd>Gene trees</kwd>
<kwd>Indels</kwd>
<kwd>Transposable elements</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2015</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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