Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genus Accipiter) are not monophyletic. Here, we combine a large new dataset obtained from ultraconserved elements, generated from whole genome sequencing of 134 species, with publicly available legacy markers (i.e. a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 237 extant or recently extinct species. Our densely sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly of Accipiter and provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups.
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We present the complete genome sequences of 87 species of hawks from 39 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.more » « less
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Sarcoramphus papa is a New World Vulture found predominantly in tropical lowland forests stretching from southern Mexico to northern Argentina. We present the whole genome sequence of this species. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR19167646) and assembled genome (GCA_027580115).more » « less
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Abstract We reconstruct the species-level phylogenetic relationship among toucans, toucan-barbets, New World barbets using phylogenomic data to assess the monophyly and relationships at the family, generic, and specific levels. Our analyses confirmed (1) the monophyly of toucans (Aves: Ramphastidae), toucan-barbets (Aves: Semnornithidae), and New World barbets (Aves: Capitonidae) and that the toucan-barbets are sister to the toucans, an arrangement suggested, but poorly supported, in previously published phylogenies; (2) the paraphyly of lowland Selenidera toucanets with respect to Andigena mountain-toucans; and (3) evidence of some mitonuclear discordance, suggesting introgression or incomplete lineage sorting. For example, mitonuclear conflict in the phylogenetic placement of Ramphastos vitellinus subspecies suggests that Amazonian populations of Ramphastos vitellinus ariel may have introgressed mitogenomes derived from other Amazonian vitellinus taxa. To reconstruct the phylogenetic history of toucans, toucan-barbets, and New World barbets, we included all species-level taxa from the three families, with the addition of outgroups from the two major clades of Old World barbets (Megalaimidae and Lybiidae). We analyzed a combination of UCE sequences and whole mitochondrial genome sequences to reconstruct phylogenetic trees.
