Phylogenomic analyses data of the avian phylogenomics project.
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.


RESULTS
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.
Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA.
Erich D
ED
Jarvis
Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA.
Siavash
S
Mirarab
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Andre J
AJ
Aberer
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Bo
B
Li
Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA.
Peter
P
Houde
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Cai
C
Li
School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia.
Simon Y W
SY
Ho
Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA ; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA.
Brant C
BC
Faircloth
CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II, Montpellier, France.
Benoit
B
Nabholz
Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA.
Jason T
JT
Howard
Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
Alexander
A
Suh
Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
Claudia C
CC
Weber
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Rute R
RR
da Fonseca
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Alonzo
A
Alfaro-Núñez
Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA ; Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan.
Nitish
N
Narula
Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA.
Liang
L
Liu
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.
Dave
D
Burt
Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden.
Hans
H
Ellegren
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA.
Scott V
SV
Edwards
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany ; Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany.
Alexandros
A
Stamatakis
Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA.
David P
DP
Mindell
Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA.
Joel
J
Cracraft
Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA.
Edward L
EL
Braun
Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA.
Tandy
T
Warnow
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark ; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China ; Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong.
Wang
W
Jun
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark ; Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia.
M Thomas Pius
MT
Gilbert
China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Guojie
G
Zhang
D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D002965:Classification / Q000379:methods; D004247:DNA / Q000737:chemistry; D004251:DNA Transposable Elements; D016678:Genome; D023281:Genomics; D010802:Phylogeny; D016415:Sequence Alignment
D004251:DNA Transposable Elements; D004247:DNA
Avian genomes; Gene trees; Indels; Phylogenomics; Sequence alignments; Species tree; Transposable elements