Article open access publication

Phylogenomic analyses data of the avian phylogenomics project

GigaScience, Oxford University Press (OUP), ISSN 2047-217X

Volume 4, 1, 2015

DOI:10.1186/s13742-014-0038-1, Dimensions: pub.1030179613, PMC: PMC4349222, PMID: 25741440,



  1. (1) Duke University Hospital, grid.189509.c
  2. (2) The University of Texas at Austin, grid.89336.37
  3. (3) Heidelberg Institute for Theoretical Studies, grid.424699.4
  4. (4) Xi'an Jiaotong University, grid.43169.39
  5. (5) University of Copenhagen, grid.5254.6, KU
  6. (6) Beijing Genomics Institute, grid.21155.32
  7. (7) New Mexico State University, grid.24805.3b
  8. (8) University of Sydney, grid.1013.3
  9. (9) Louisiana State University, grid.64337.35
  10. (10) University of California, Los Angeles, grid.19006.3e
  11. (11) Institut des Sciences de l'Evolution de Montpellier, grid.462058.d
  12. (12) Uppsala University, grid.8993.b
  13. (13) Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, 904-0495, Okinawa, Japan
  14. (14) University of Georgia, grid.213876.9
  15. (15) University of Edinburgh, grid.4305.2
  16. (16) Harvard University, grid.38142.3c
  17. (17) Karlsruhe Institute of Technology, grid.7892.4
  18. (18) University of California, San Francisco, grid.266102.1
  19. (19) American Museum of Natural History, grid.241963.b
  20. (20) University of Florida, grid.15276.37
  21. (21) King Abdulaziz University, grid.412125.1
  22. (22) Macau University of Science and Technology, grid.259384.1
  23. (23) University of Hong Kong, grid.194645.b
  24. (24) Curtin University, grid.1032.0


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.


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Field Citation Ratio (FCR): 6.87

Relative Citation ratio (RCR): 1.92

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