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Nexus file for: Molecular diversification of hummingbirds

Cite this dataset

McGuire, Jimmy (2022). Nexus file for: Molecular diversification of hummingbirds [Dataset]. Dryad.


The tempo of species diversification in large clades can reveal fundamental evolutionary mechanisms that operate on large temporal and spatial scales. Hummingbirds have radiated into a diverse assemblage of specialized nectarivores comprising 338 species, but their evolutionary history has not, until now, been comprehensively explored. We studied hummingbird diversification by estimating a time-calibrated phylogeny for 284 hummingbird species, demonstrating that hummingbirds invaded South America by ~22 million years ago, and subsequently diversified into nine principal clades. Using ancestral state reconstruction and diversification analyses, we (1) estimate the age of the crown-group hummingbird assemblage, (2) investigate the timing and patterns of lineage accumulation for hummingbirds overall and regionally, and (3) evaluate the role of Andean uplift in hummingbird speciation. Detailed analyses reveal disparate clade-specific processes that allowed for ongoing species diversification. One factor was significant variation among clades in diversification rates. For example, the nine principal clades of hummingbirds exhibit ~15-fold variation in net diversification rates, with evidence for accelerated speciation of a clade that includes the Bee, Emerald, and Mountain Gem groups of hummingbirds. A second factor was colonization of key geographic regions, which opened up new ecological niches. For example, some clades diversified in the context of the uplift of the Andes Mountains, whereas others were affected by the formation of the Panamanian land bridge. Finally, although species accumulation is slowing in all groups of hummingbirds, several major clades maintain rapid rates of diversification on par with classical examples of rapid adaptive radiation.


DNA sequences representing six genes (four nuclear and two mitochondrial) were obtained for 451 individual birds, including 436 hummingbirds representing 284 species. Our sampling includes 101 of 105 currently recognized trochilid genera (lacking only three monotypic genera, Anopetia, Hylonympha, and Sternoclyta, as well as the bitypic genus Augastes). We included 15 outgroup species spanning four avian orders.

Usage notes

Our preferred time-calibrated Bayesian phylogenetic analyses were performed using BEAST v1.7.1.


National Science Foundation, Award: DEB 0543556