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We assessed phylogenetic relationships among 48 of 53 genera of phyllostomid bats based on mitochondrial DNA (mtDNA) sequence data encompassing three adjacent genes (12S rRNA, tRNA^a^} 16S rRNA). We employed Bayesian methods to produce an mtDNA tree, to reanalyze the nuclear Recombination-Activating Gene-2 (.RAG2) sequence data, and to produce a tree of concatenated mtDNA and RAG2 data. We compared these gene trees with a recent total-evidence phylogeny based primarily on morphology. The congruence across all three trees (mtDNA, RAG2, total-evidence), was 16 of 55 nodes with identical content. The majority of incongruencies involved nodes that were weakly supported in the total-evidence tree. There was greater congruence between data sets from the mitochondrial and nuclear genomes, with 37 of 55 nodes identical in content. Analysis of the concatenated molecular data (about 4.0 kilobases) produced nearly identical branching patterns but with higher statistical support. Forty-eight of 55 generated clades received Bayesian posterior probabilities >0.95 and 42 had a probability of 1.00. The seven weakly-supported clades occurred in the middle or terminal part of the tree. We interpret the Bayesian posterior probability values as well as the observation that the total number of shared nodes (37 of 55) between the gene trees (support from two independent genomes) as strong evidence that these nodes, as identified, have a high probability of reflecting evolutionary relationships. We contend that digenomic congruence with concomitant statistical support is a robust statement in phylogeny reconstruction. Using the molecular and total-evidence trees and other information (e.g., karyotypes), we developed a higher-level classification for the family Phyllostomidae that includes 56 genera in 11 subfamilies: Macrotinae, Micronycterinae, Desmodontinae, Lonchorhininae, Phyllostominae, Glossophaginae, Lonchophyllinae, Carolliinae, Glyphonycterinae, Rhinophyllinae, and Stenodermatinae. Our arrangement differs substantially from previous classifications. For example, members of the traditional subfamily Phyllostominae are divided into five subfamilies. Front cover: Artwork by Fiona Reid depicting the five lineages of the former Phyllostominae that are representative of subfamilies in the classification proposed herein. Taxa (from left to right) are: Micronycteris hirsuta, Lonchorhina aurita, Trinycteris nicefori, Macrotus californicus, and Tonatia sauropkila.

Diversification among New World leaf-nosed bats : an evolutionary hypothesis and classification inferred from digenomic congruence of DNA sequence