DOI: 10.5061/dryad.77c1h
title: Data from: Timeframes of speciation, reticulation, and hybridization in the Bulldog bat explained through phylogenetic analyses of all genetic transmission elements

description: Phylogenetic comparisons of the different mammalian genetic transmission
 elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for
 understanding the process of speciation in nature. Through such
 comparisons the unique inheritance pathways of each genetic element and
 gender-biased processes can link genomic structure to the evolutionary
 process, especially among lineages which have recently diversified, in
 which genetic isolation may be incomplete. Bulldog bats of the genus
 Noctilio are an exemplar lineage, being a young clade, widely distributed,
 and exhibiting unique feeding ecologies. In addition, currently recognized
 species are paraphyletic with respect to the mtDNA gene tree and contain
 morphologically identifiable clades that exhibit mtDNA divergences as
 great as among many species. To test taxonomic hypotheses and understand
 the contribution of hybridization to the extant distribution of genetic
 diversity in Noctilio, we used phylogenetic, coalescent stochastic
 modeling, and divergence time estimates using sequence data from
 cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as
 well as evolutionary reconstructions based on amplified fragment length
 polymorphisms (AFLP) data. No evidence of ongoing hybridization between
 the two currently recognized species was identified. However, signatures
 of an ancient mtDNA capture were recovered in which an mtDNA lineage of
 one species was captured early in the noctilionid radiation. Among
 subspecific mtDNA clades, which were generally coincident with morphology
 and statistically definable as species, signatures of ongoing
 hybridization were observed in sex chromosome sequences and AFLP.
 Divergence dating of genetic elements corroborates the diversification of
 extant Noctilio beginning about three million years ago, with ongoing
 hybridization between mitochondrial lineages separated by 2.5 million
 years. The time-frame of species' divergence within Noctilio supports
 the hypothesis that shifts in the dietary strategies of gleaning insects
 (N. albiventris) or fish (N. leporinus) are among the most rapid instances
 of dietary evolution observed in mammals. This study illustrates the
 complex evolutionary dynamics shaping gene pools in nature, how
 comparisons of genetic elements can serve for understanding species
 boundaries, and the complex considerations for accurate taxonomic
 assignment.
description: Online Appendix
 1Online Appendix 1: List
 of Noctilio samples, museum numbers and localities used in the study.
 Superscript numbers 1 – 4 following N. albiventris and 1 – 2 following N.
 leporinus refers to the mitochondrial clade identified in the study,
 Albiventris 1 – 4 and Leporinus 1 – 2, respectively. Abbreviations of each
 museum code are described in the materials and method
 section.Noctilio_manuscript_AppendixOnlineUpdated_7May2013.pdfSupplementary MaterialTable S1-S3; Figure S1-S2Noctilio Manuscript_Supplementary_Tables_Figures_References_7May2013.pdf