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Phylogenomic analyses data of the avian phylogenomics project
Duke Univ, Med Ctr, Howard Hughes Med Inst, Dept Neurobiol, Durham, NC 27710 USA.;Duke Univ, Med Ctr, Durham, NC 27710 USA..ORCID iD: 0000-0001-8931-5049
Univ Texas Austin, Dept Comp Sci, Austin, TX 78712 USA..
Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany..
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..
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2015 (English)In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 4, 4Article in journal (Refereed) Published
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Abstract [en]

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.

Place, publisher, year, edition, pages
2015. Vol. 4, 4
Keyword [en]
Avian genomes, Phylogenomics, Sequence alignments, Species tree, Gene trees, Indels, Transposable elements
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-271607DOI: 10.1186/s13742-014-0038-1ISI: 000365661800001PubMedID: 25741440OAI: oai:DiVA.org:uu-271607DiVA: diva2:892896
Available from: 2016-01-11 Created: 2016-01-11 Last updated: 2017-12-01Bibliographically approved

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Jarvis, Erich D.Suh, AlexanderEllegren, Hans

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