Phylogenetic relationships among the 14 manakin genera were inferred from DNA sequence data obtained from both mitochondrial and nuclear DNA loci. Phylogenetic analysis resulted in a well-supported hypothesis that corroborates a sister relationship between tyrant-manakins and the "core" manakins (Antilophia, Chiroxiphia, Corapipo, Dixiphia, Heterocercus, Ilicura, Lepidothrix, Manacus, Masius, Machaeropterus, Pipra, and Xenopipo). Our data strongly support these core manakin genera as a monophyletic group. Consistent with previous work, we find two major clades within the core manakins, although the placement of the genus Xenopipo with regards to these two clades is ambiguous. Generic relationships within these clades are generally well resolved. Although we find some concordance between our study and a previous manakin phylogeny based on syringeal characters, we note several fundamental differences between the phylogenies. Thus, we offer a new phylogenetic hypothesis for Pipridae.
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We thank D. J. Mennill for assistance in the field. We are grateful to R. Blanco and the Ministerio del Ambiente y Energía of Costa Rica for granting our research permits and to the curators and collection managers of the Louisiana State University Museum of Natural Science Collection of Genetic Resources for their generous provision of tissue samples. The Hill lab made helpful comments on the manuscript. Our research was funded by the Natural Sciences and Engineering Research Council of Canada, Sigma-Xi, the American Ornithologists’ Union, the Wilson Ornithological Society, the Explorer’s Club, the American Museum of Natural History, and Auburn University Graduate Research Grants (to SMD), as well as NSF grant IBN 0235778 (to GEH and HLM).