Phylogenomic analyses data of the avian phylogenomics project.

Jarvis, Erich D

Mirarab, Siavash

Aberer, Andre J

Li, Bo

Houde, Peter

Li, Cai

Ho, Simon YW

Faircloth, Brant C

Nabholz, Benoit

Howard, Jason T

Suh, Alexander

Weber, Claudia C

da Fonseca, Rute R

Alfaro-Núñez, Alonzo

Narula, Nitish

Liu, Liang

Burt, Dave

Ellegren, Hans

Edwards, Scott V

Stamatakis, Alexandros

Mindell, David P

Cracraft, Joel

Braun, Edward L

Warnow, Tandy

Jun, Wang

Gilbert, M Thomas Pius

Zhang, Guojie

Avian Phylogenomics Consortium

United States

2015-12-08T03:17:31Z

2015

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.

http://www.ncbi.nlm.nih.gov/pubmed/25741440

38

2047-217X

https://hdl.handle.net/10161/11118

eng

Oxford University Press (OUP)

Gigascience

10.1186/s13742-014-0038-1

Avian genomes

Gene trees

Indels

Phylogenomics

Sequence alignments

Species tree

Transposable elements

Animals

Birds

Classification

DNA

DNA Transposable Elements

Genome

Genomics

Phylogeny

Sequence Alignment

Phylogenomic analyses data of the avian phylogenomics project.

Journal article

http://www.ncbi.nlm.nih.gov/pubmed/25741440

4

Basic Science Departments

Duke

Duke Institute for Brain Sciences

Institutes and Provost's Academic Units

Neurobiology

School of Medicine

University Institutes and Centers

Published online

4