DOI: 10.5061/dryad.d7wm37pxc
title: Data from: Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

description: Genetic structures, historical events, habitat preferences, and geographic
 barriers might result in distinct patterns in insular versus mainland
 populations. Comparison between these two biogeographic systems provides
 an opportunity to investigate the relative role of isolation in
 phylogeographic patterns and to elucidate the importance of evolution and
 demographic history in population structure. Herein we use a genotype by
 sequencing approach (GBS) to explore population structure within three
 species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri),
 which represent different ecological histories and geographical
 distributions in the genus to explore phylogeographic patterns and better
 understand the role of geographic barriers in their dispersal and gene
 flow. We tested the hypotheses that oceanic straits serve as barriers to
 dispersal in Caribbean bats and that isolated island populations are more
 likely to experience genetic drift and bottlenecks relative to highly
 connected ones, which should have different phylogeographic patterns. We
 show that population structures vary according to general habitat
 preferences, to levels of population isolation, and to historical
 fluctuations in climate. In our dataset, mainland geographic barriers
 played only a small role in isolation of lineages. However, oceanic
 straits posed a partial barrier to the dispersal for some populations
 within some species (M. milleri), but do not seem to disrupt gene flow in
 others (M. molossus). Lineages on distant islands undergo genetic
 bottlenecks more frequently than island lineages closer to the mainland,
 which have a greater exchange of haplotypes.
description: We obtained tissue samples from 54 M. molossus from South
 America, Middle America and the Lesser Antilles, 20 M. coibensis from
 South and Middle America, and 19 M. milleri from the Greater Antilles.
 Samples description and localities are described in Loureiro et al. (in
 press). Tissues samples included skeletal muscle, liver, heart, and kidney
 and were preserved in 95% ethanol or were frozen in liquid nitrogen upon
 collection of the specimen in the field. DNA extraction was conducted
 using Qiagen DNeasy extraction kit (Qiagen, Inc. Valencia, CA, USA)
 following standard protocols. Genomic DNA quality was checked by visual
 inspection on an agarose gel and the DNA concentration was measured using
 a Nanodrop spectrophotometer (Nanodrop Techinologies). We used 30 ul of
 DNA samples with concentrations higher than 100 ng/ul for library
 preparation and for the genotyping by sequencing approach following the
 protocol described by Elshire et al. (2011). All libraries were sequenced
 on an Illumina HiSeq 2000 in the Cornell Institute of Genomic Diversity
 (IGD). De novo genotyping was performed using the Universal Network-Enable
 Analysis Kit (UNEAK) pipeline, available on TASSEL 3.0 software (Bradbury
 et al., 2007). Quality control and filtering of the reference genotypes of
 each species sample were also conducted on TASSEL 3.0  (Loureiro et al.,
 in press). References Bradbury,
 P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y., Buckler,
 E.S., 2007. TASSEL: Software for association mapping of complex traits in
 diverse samples. Bioinformatics 23, 2633–2635.
 https://doi.org/10.1093/bioinformatics/btm308 Elshire,
 R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S.,
 Mitchell, S.E., 2011. A robust, simple genotyping-by-sequencing (GBS)
 approach for high diversity species. PLoS One 6, 1–10.
 https://doi.org/10.1371/journal.pone.0019379 Loureiro,
 L. O., Engstrom, M. D., Lim, B. K. (In press) Next Comparative
 phylogeography of mainland and insular species of Neotropical molossid
 bats (<i>Molossus</i>). Ecology and Evolution. Submitted on
 July 25, 2019. 43p. ECE-2019-06-00727.
description: Genotype by Sequencing data on three species of Molossus
 (Molossidae, Chiroptera)