The phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) has been investigated using several different molecular datasets. These studies differed widely in taxonomic and locus sampling, and their results tended to lack resolution of internal nodes and were themselves largely incongruent. To address this, we assembled a data set of 5 loci (up to 3.5 kbp from 12S rDNA, 16S rDNA, tDNA-valine, cytochrome b, and the nuclear gene c-mos) for 43 species of megachiropterans and 6 microchiropteran outgroups. We analyzed these data with direct optimization under equal costs for substitutions and indels. We used POY in a parallel setting, and searches consisted of replicated swapping + refinements (ratcheting, tree fusing, and iterative pass optimization). Our results indicate that Megachiroptera and all recognized genera (including Pteropus) are monophyletic, and that Melonycteris is the sister group of the clade containing all the other genera. Clades previously proposed using molecular data, as well as many new and traditional groups, were well-supported, and various sources suggest that the degree of conflict with morphological data may be considerably less marked than previously supposed. Analysis of individual loci suffer 70% loss in the number of compatible groups recovered across all analyses with respect to combined analyses. Our results indicate that, within Megachiroptera, nectarivory and cave-dwelling originated several times, but echolocation (used for obstacle detection) evolved only once. Megachiropterans likely originated in SE Asia-Melanesia, and colonized Africa at least four times.
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