TY - JOUR

T1 - Phylogenomic analyses data of the avian phylogenomics project

AU - Jarvis, Erich D

AU - Mirarab, Siavash

AU - Aberer, Andre J

AU - Li, Bo

AU - Houde, Peter

AU - Li, Cai

AU - Ho, Simon Y. W.

AU - Faircloth, Brant C.

AU - Nabholz, Benoit

AU - Howard, Jason T.

AU - Suh, Alexander

AU - Weber, Claudia C.

AU - Rodrigues da Fonseca, Rute Andreia

AU - Alfaro Nuñez, Luis Alonso

AU - Narula, Nitish

AU - Liu, Liang

AU - Burt, Dave

AU - Ellegren, Hans

AU - Edwards, Scott V.

AU - Stamatakis, Alexandros

AU - Mindell, David P.

AU - Cracraft, Joel

AU - Braun, Edward L.

AU - Warnow, Tandy

AU - Wang, Jun

AU - Gilbert, M. Thomas P.

AU - Zhang, Guojie

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1186/s13742-014-0038-1

DO - 10.1186/s13742-014-0038-1

M3 - Journal article

C2 - 25741440

VL - 4

JO - GigaScience

JF - GigaScience

SN - 2047-217X

M1 - 4

ER -