A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Abstract

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our 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.

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

“…(2015), reads passing the high chastity CASAVA filter were assembled as follows. After merging overlapping reads (Rokyta, Lemmon, Margres, & Aronow, 2012), reads were assembled using A. carolinensis references derived from the Vertebrate v1 probe design (Lemmon et al., 2012).…”

Mammal madness: is the mammal tree of life not yet resolved?

“…Even for molecular data, different data types require different phylogenetic models [14], each of which has its own limitations [10]. Whole genome analyses have promised to revolutionize our understanding of animal evolutionary history, but some claims for the robust resolution of difficult nodes with phylogenomic data are underpinned by problematic analyses and/or poor data [10,19,20]. Despite these difficulties, there is consensus over the main topology [4][5][6] even though a few local polytomies are still unresolved (e.g.…”

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

“…Continental vicariance of Madagascar and Australasia far preceded diversification of phasianoids [30] and modern birds in general [31][32][33], meaning Margaroperdix and Anurophasis ancestors must have crossed permanent marine barriers. How did these 'non-vagile' phasianoids come to inhabit their present insular distributions?…”