A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
John E. McCormack,Michael G. Harvey,Brant C. Faircloth,Nicholas G. Crawford,Travis C. Glenn,Robb T. Brumfield +5 more
TLDR
This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families.Abstract:
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.read more
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Journal ArticleDOI
Whole-genome analyses resolve early branches in the tree of life of modern birds
Erich D. Jarvis,Siavash Mirarab,Andre J. Aberer,Bo Li,Bo Li,Bo Li,Peter Houde,Cai Li,Cai Li,Simon Y. W. Ho,Brant C. Faircloth,Benoit Nabholz,Jason T. Howard,Alexander Suh,Claudia C. Weber,Rute R. da Fonseca,Jianwen Li,Fang Zhang Zhang,Hui Li,Long Zhou,Nitish Narula,Nitish Narula,Liang Liu,Ganesh Ganapathy,Bastien Boussau,Shamsuzzoha Bayzid,Volodymyr Zavidovych,Sankar Subramanian,Toni Gabaldón,Salvador Capella-Gutierrez,Jaime Huerta-Cepas,Bhanu Rekepalli,Bhanu Rekepalli,Kasper Munch,Mikkel H. Schierup,Bent E. K. Lindow,Wesley C. Warren,David A. Ray,Richard E. Green,Michael William Bruford,Xiangjiang Zhan,Xiangjiang Zhan,Andrew Dixon,Shengbin Li,Ning Li,Yinhua Huang,Elizabeth P. Derryberry,Elizabeth P. Derryberry,Mads F. Bertelsen,Frederick H. Sheldon,Robb T. Brumfield,Claudio V. Mello,Claudio V. Mello,Peter V. Lovell,Morgan Wirthlin,Maria Paula Cruz Schneider,Francisco Prosdocimi,José Alfredo Samaniego,Amhed Missael Vargas Velazquez,Alonzo Alfaro-Núñez,Paula F. Campos,Bent O. Petersen,Thomas Sicheritz-Pontén,An Pas,Thomas L. Bailey,R. Paul Scofield,Michael Bunce,David M. Lambert,Qi Zhou,Polina L. Perelman,Amy C. Driskell,Beth Shapiro,Zijun Xiong,Yongli Zeng,Shiping Liu,Zhenyu Li,Binghang Liu,Kui Wu,Jin Xiao,Xiong Yinqi,Quiemei Zheng,Yong Zhang,Huanming Yang,Jian Wang,Linnéa Smeds,Frank E. Rheindt,Michael J. Braun,Jon Fjeldså,Ludovic Orlando,F. Keith Barker,Knud A. Jønsson,Warren E. Johnson,Klaus-Peter Koepfli,Stephen J. O'Brien,David Haussler,Oliver A. Ryder,Carsten Rahbek,Eske Willerslev,Gary R. Graves,Gary R. Graves,Travis C. Glenn,John E. McCormack,Dave Burt,Hans Ellegren,Per Alström,Scott V. Edwards,Alexandros Stamatakis,David P. Mindell,Joel Cracraft,Edward L. Braun,Tandy Warnow,Tandy Warnow,Wang Jun,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Guojie Zhang,Guojie Zhang +116 more
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Journal ArticleDOI
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Richard O. Prum,Richard O. Prum,Jacob S. Berv,Alex Dornburg,Alex Dornburg,Alex Dornburg,Daniel J. Field,Daniel J. Field,Jeffrey P. Townsend,Emily Moriarty Lemmon,Alan R. Lemmon +10 more
TL;DR: The results of the divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
Journal ArticleDOI
ASTRAL: genome-scale coalescent-based species tree estimation
Siavash Mirarab,Rezwana Reaz,Md. Shamsuzzoha Bayzid,Théo Zimmermann,M. S. Swenson,Tandy Warnow +5 more
TL;DR: ASTRAL is a fast method for estimating species trees from multiple genes that is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods.
Journal ArticleDOI
Fast coalescent-based computation of local branch support from quartet frequencies
Erfan Sayyari,Siavash Mirarab +1 more
TL;DR: This article proposes a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees and evaluates the precision and recall of the local PP on a wide set of simulated and biological datasets.
Journal ArticleDOI
MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics
Rémi Allio,Alex Schomaker-Bastos,Jonathan Romiguier,Francisco Prosdocimi,Benoit Nabholz,Frédéric Delsuc +5 more
TL;DR: MitoFinder, a user‐friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries, and shows that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA.
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