Phylogenomic analyses data of the avian phylogenomics project.
Dataset type: Genomic
Data released on November 27, 2014
Aberer AJ; Alfaro-Nunez A; Braun EL; Burt DW; Cracraft J; da Fonseca RR; Edwards SV; Ellegren H; Faircloth BC; Gilbert MTP; Ho SYW; Houde P; Howard JT; Jarvis ED; Li C; Liu L; Mindell DP; Mirarab S; Nabholz B; Narula N; Stamatakis A; Suh A; Wang J; Warnow T; Weber CC; Zhang G (2014): Phylogenomic analyses data of the avian phylogenomics project. GigaScience Database. http://dx.doi.org/10.5524/101041
Determining the evolutionary relationships of modern 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 Neoagnathae and two of the five Palaegnoathae orders, and used the genomes to construct various genome-scale avian phylogenetic trees and perform comparative genomics analyses.
Here we release the datasets associated with the phylogenomic analyses, which include genome scale alignments, gene tree files (including binned supergene trees), species tree files (including timetrees), and loci sequence files including nucleotide, amino acid, indels, and transposable elements. We hope that this resource will serve future efforts in phylogenomics, evolutionary biology, and trait analyses.
Read the peer-reviewed publication(s):
Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451