Phylogeny and diversification of the largest avian radiation

Abstract

The order Passeriformes (''perching birds'') comprises extant species diversity comparable to that of living mammals. For over a decade, a single phylogenetic hypothesis based on DNA-DNA hybridization has provided the primary framework for numerous comparative analyses of passerine ecological and behavioral evolution and for tests of the causal factors accounting for rapid radiations within the group. We report here a strongly supported phylogenetic tree based on two single-copy nuclear gene sequences for the most complete sampling of passerine families to date. This tree is incongruent with that derived from DNA-DNA hybridization, with half of the nodes from the latter in conflict and over a third of the conflicts significant as assessed under maximum likelihood. Our historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. The revised history implied by these data will require reassessment of comparative analyses of passerine diversification and adaptation.M ajor lineages of the Ϸ5,739 species of passerine birds (1) have diversified on all continents and now occupy nearly all terrestrial ecosystems. The songbirds (oscines, suborder Passeri) alone comprise nearly half of all extant avian species and represent the largest identifiable radiation of birds (2), encompassing a staggering ecological and behavioral diversity. The foundation for understanding passerine diversification and for integrating the spatial, ecological, and temporal history of the group is a comprehensive and robust phylogenetic hypothesis. A decade ago, in a pioneering work, Sibley and Ahlquist (3) used DNA-DNA hybridization to produce the first large-scale phylogenetic hypothesis for passerine birds and suggested a specific temporal history for passerine diversification. Despite oftenvoiced concerns about the robustness of this phylogeny (colloquially termed the ''Tapestry'' after its appearance on the wall at an ornithological meeting), it has provided a framework for numerous historical analyses of passerine ecology (4), behavior (5), and diversification (6, 7), and continues to fuel the search for explanations of passerine diversity (8).Recently, studies have begun to contradict aspects of the DNA hybridization hypothesis for passerines (ref. 9; citations in ref. 10). These investigations, however, used relatively short gene sequences and, more importantly, limited taxon sampling across passerines; thus the phylogenetic, biogeographic, and temporal interpretations of the radiation were incomplete, and broad tests of the DNA hybridization tree were not possible. Here we analyze 4,126 aligned positions of the nuclear genes RAG-1 and -2 from 144 passerine species in 45 families, including representatives of all but one family recognized by current taxonomy (1). We find substantial support for many portions of the passerine tree, as well as quantitative evidence for the re...

Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds

“…Bayesian posterior probabilities were calculated for each node and are provided in the figure. Because all sampled taxa belong to the core corvoidea (sensu Barker et al, 2004), we were unable to independently provide an appropriate root for our phylogeny. We therefore rooted the phylogeny consistently with other studies having broader sampling (Sibley and Ahlquist, 1982, 1985, 1987Barker et al, 2002Barker et al, , 2004.…”

“…Because all sampled taxa belong to the core corvoidea (sensu Barker et al, 2004), we were unable to independently provide an appropriate root for our phylogeny. We therefore rooted the phylogeny consistently with other studies having broader sampling (Sibley and Ahlquist, 1982, 1985, 1987Barker et al, 2002Barker et al, , 2004. Once rooted (i.e., with Petroica at the base), our results for Pachycephalidae did not conflict with the results of these other studies in any significant ways, although our taxon sampling is very different.…”

“…Genetic data Ahlquist, 1987, 1990) have argued that M. lugubris belongs with birds of paradise (Paradisaidae), but no genetic work has been done testing the relationships of M. gigantea. We believe that the placement of M. gigantea deserves closer scrutiny (see also Barker et al, 2004).…”

“…Pachycephalid phylogenetics have been partially treated by other researchers (Mayr, 1963;Boles, 1979;Ahlquist, 1982, 1990;Dumbacher, 1994;Barker et al, 2004), but these treatments each include only a few of the 12 or so genera suspected to form a monophyletic family. The whistlers in the genus Pachycephala (about 33 of about 60 species in the family Pachycephalidae) form the core of the family.…”

Population genetics of the olive‐winged bulbul (Pycnonotus plumosus) in a tropical urban‐fragmented landscape

“…For each analysis, the short‐tailed babbler ( Pellorneum malaccense ) was used as the out‐group taxon, following recent phylogenetic studies showing babblers to be close relatives of bulbuls ( Pycnonotidae ) (Barker et al. 2004; Alström et al. 2013).…”