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.

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 (Molossus). Ecology and Evolution. Submitted on July 25, 2019. 43p. ECE-2019-06-00727.

Genotype by Sequencing data on three species of Molossus (Molossidae, Chiroptera)