DOI: 10.5061/dryad.s533p
title: Data from: Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity

description: The mechanisms underlying the high extant biodiversity in the Neotropics
 have been controversial since the 19th century. Support for the influence
 of period-specific changes on diversification often rests on detecting
 more speciation events during a particular period. The timing of
 speciation events may reflect the influence of incomplete taxon sampling,
 protracted speciation, and null processes of lineage accumulation. Here we
 assess the influence of these factors on the timing of speciation with new
 multilocus data for New World noctilionoid bats (Chiroptera:
 Noctilionoidea). Biogeographic analyses revealed the importance of the
 Neotropics in noctilionoid diversification, and the critical role of
 dispersal. We detected no shift in speciation rate associated with the
 Quaternary or pre-Quaternary periods, and instead found an increase in
 speciation linked to the evolution of the subfamily Stenodermatinae (∼18
 Ma). Simulations modeling constant speciation and extinction rates for the
 phylogeny systematically showed more speciation events in the Quaternary.
 Since recording more divergence events in the Quaternary can result from
 lineage accumulation, the age of extant sister species cannot be
 interpreted as supporting higher speciation rates during this period.
 Instead, analyzing the factors that influence speciation requires modeling
 lineage-specific traits and environmental, spatial, and ecological drivers
 of speciation.
description: Supplementary
 FiguresFigures S1–S9.
 Descriptions for the figures are contained in the file
 "Rojas_et_al_supplementary_material.docx"Rojas_et_al_supplementary_figures.pdfRojas_et_al_supplementary_materialDescriptions of figures S1–S9. Descriptions of Tables S1, S2 and S5. Tables S3, S4, S6 and S7.Rojas_et_al_Table_S1Species and GenBank accession numbers for each locus analyzed.Rojas_et_al_Table_S2Species, GenBank accession numbers, and collection number for each sequence generated for this study. Tissue samples were obtained from collections vouchered at the American Museum of Natural History (AMNH); the Field Museum of Natural History (FMNH); the Museo Universidad San Marcos (Lima, MUSM); the Museum of Texas Tech University (TTU, listed as TK); the Museum of Vertebrate Zoology (MVZ) of the University of California at Berkeley; the National Museum of Natural History (NMNH); and the Royal Ontario Museum (ROM). Stony Brook University (SBU) samples at the Dávalos lab are identified by collector number.Rojas_et_al_Table_S5Distribution of New World Noctilionoidea in Central and North America, South America, and the Antilles. Taxa were assigned to one or more of the three biogeographic regions based on their current distribution determined using the mammal distributions compiled by the IUCN (data downloaded on October 2013), and the literature since 2008. 1 = present, 0 = absent.Bayesian_majority-rule_treesBayesian majority-rule consensus tree data of noctilionoids for each independent locus. Further details are provided as comments in each NEXUS file.timing_speciationR script to quantify the number and timing of speciation events between extant sister species for the Quaternary and pre-Quaternary (Neogene + Paleogene) periods on a posterior sample of time-calibrated phylogenies. The code can be modified to accommodate older periods if necessary. The file "my_trees.nex" is a generic example that refers to any file including a posterior distribution of trees.