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Sökning: onr:"swepub:oai:DiVA.org:uu-271607" > Phylogenomic analys...

Phylogenomic analyses data of the avian phylogenomics project

Jarvis, Erich D. (författare)
Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA.;Duke Univ, Med Ctr, Durham, NC 27710 USA.
Mirarab, Siavash (författare)
Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA.
Aberer, Andre J. (författare)
Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany.
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Li, Bo (författare)
BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Xi An Jiao Tong Univ, Coll Med & Forens, Xian 710061, Peoples R China.;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.
Houde, Peter (författare)
New Mexico State Univ, Dept Biol, Las Cruces, NM 88003 USA.
Li, Cai (författare)
BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.
Ho, Simon Y. W. (författare)
Univ Sydney, Sch Biol Sci, Sydney, NSW 2006, Australia.
Faircloth, Brant C. (författare)
Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA.;Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA.
Nabholz, Benoit (författare)
Univ Montpellier 2, CNRS, UMR 5554, Inst Sci Evolut Montpellier, Montpellier, France.
Howard, Jason T. (författare)
Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA.;Duke Univ, Med Ctr, Durham, NC 27710 USA.
Suh, Alexander (författare)
Uppsala universitet,Evolutionsbiologi
Weber, Claudia C. (författare)
Uppsala universitet,Evolutionsbiologi
da Fonseca, Rute R. (författare)
Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.
Alfaro-Nunez, Alonzo (författare)
Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.
Narula, Nitish (författare)
New Mexico State Univ, Dept Biol, Las Cruces, NM 88003 USA.;Okinawa Inst Sci & Technol Onna Son, Biodivers & Biocomplex Unit, Okinawa 9040495, Japan.
Liu, Liang (författare)
Univ Georgia, Dept Stat, Athens, GA 30602 USA.;Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA.
Burt, Dave (författare)
Univ Edinburgh, Roslin Inst, Dept Genom & Genet, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Roslin EH25 9RG, Midlothian, Scotland.
Ellegren, Hans (författare)
Uppsala universitet,Evolutionsbiologi
Edwards, Scott V. (författare)
Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.;Harvard Univ, Museum Comparat Zool, Cambridge, MA 02138 USA.
Stamatakis, Alexandros (författare)
Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany.;Karlsruhe Inst Technol, Dept Informat, Inst Theoret Informat, D-76131 Karlsruhe, Germany.
Mindell, David P. (författare)
Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94158 USA.
Cracraft, Joel (författare)
Amer Museum Nat Hist, Dept Ornithol, New York, NY 10024 USA.
Braun, Edward L. (författare)
Univ Florida, Dept Biol, Gainesville, FL 32611 USA.;Univ Florida, Genet Inst, Gainesville, FL 32611 USA.
Warnow, Tandy (författare)
Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA.
Jun, Wang (författare)
BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark.;King Abdulaziz Univ, Princess Al Jawhara Ctr Excellence Res Hereditary, Jeddah 21589, Saudi Arabia.;Macau Univ Sci & Technol, Taipa 999078, Peoples R China.;Univ Hong Kong, Dept Med, Hong Kong, Hong Kong, Peoples R China.
Gilbert, M. Thomas Pius (författare)
Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Curtin Univ, Dept Environm & Agr, Trace & Environm DNA Lab, Perth, WA 6102, Australia.
Zhang, Guojie (författare)
BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.;Univ Copenhagen, Dept Biol, Ctr Social Evolut, DK-2100 Copenhagen, Denmark.
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Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA;Duke Univ, Med Ctr, Durham, NC 27710 USA. Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA. (creator_code:org_t)
2015-02-12
2015
Engelska.
Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 4
Relaterad länk:
https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
https://academic.oup...
https://urn.kb.se/re...
https://doi.org/10.1...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
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  • Background: 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. Findings: 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. Conclusions: 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Evolutionsbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Evolutionary Biology (hsv//eng)

Nyckelord

Avian genomes
Phylogenomics
Sequence alignments
Species tree
Gene trees
Indels
Transposable elements

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