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Since the last systematic review ofChiroderma(big-eyed bats) more than two decades ago, we report on biodiversity surveys that expand the distribution and species diversity of this Neotropical genus. The Caribbean endemic speciesChiroderma improvisumis documented for the first time from Nevis in the northern Lesser Antilles. A broader geographic sampling for a molecular analysis identifies a paraphyletic relationship inChiroderma trinitatumwith respect toChiroderma doriae. Cis-Andean populations ofC. trinitatumare most closely related to the morphologically distinctive and allopatrically distributedC. doriaein the Cerrado and Atlantic Forest of Brazil and Paraguay. The sister taxon to this grouping includes trans-Andean populations ofC. trinitatum, which we recommend to elevate to species status asC. gorgasi. This is an example of a cryptic species becauseC. gorgasiwas previously considered morphologically similar toC. trinitatum, but more detailed examination revealed that it lacks a posterolabial accessory cusp on the lower second premolar and has a narrower breadth of the braincase. We provide an amended description ofChiroderma gorgasi.

We describe a new species of mastiff bat in the genus Molossus (Molossidae), which was previously confused with the common and widely distributed M. molossus, from Guyana and Ecuador based on morphological and molecular differences. It is diagnosed by the following set of morphological characteristics: bicolored dorsal pelage, rounded anterior arch of the atlas, triangular occipital bone, and smaller body and skull size. In a molecular phylogenetic analysis of mitochondrial and nuclear DNA, maximum likelihood and parsimony trees recovered eight clades in the genus and a polyphyletic relationship for the M. molossus species complex. The new species was recovered in a well-supported clade that can be genetically distinguished from other species in the genus by its high level of sequence divergence based on the mitochondrial CO1 gene (8.0–10.1%) and on the nuclear gene beta fibrinogen (1.0–3.1%). It is broadly sympatric with M. molossus sensu stricto in northern South America, but morphologically distinct and genetically divergent.

The majority (90%) of native terrestrial mammal species living in the Dominican Republic are bats, and two-thirds of these species are endemic to the Caribbean. However, recent molecular studies using DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene have suggested at least a 25% underestimation of biodiversity in bats throughout the world. A recent survey of bats in the Dominican Republic documented 15 of the 18 known species on the island of Hispaniola. Phylogenetic analysis of 132 individuals resulted in well-supported monophyletic species-level clades (maximal bootstrap values) with intraspecific variation ranging from 0% to 4.7% and interspecific variation ranging from 14.1% to 32.5%. A phylogeographic pattern separating the northern and southern Dominican Republic was recovered in 3 species of bats (Macrotus waterhousii, Pteronotus parnellii, and Pteronotus quadridens). The inclusion of broader geographic sampling across the Neotropics indicated that 3 widely distributed species (Eptesicus fuscus, Molossus molossus, and Monophyllus redmani) have high sequence divergence among insular or between insular and continental populations. Further systematic study is needed to identify morphologically cryptic species and their implications for conservation priorities in the Caribbean.

Historical events, habitat preferences, and geographic barriers might result in distinct genetic 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. 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 in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and 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., In this manuscript, we use the genotype‐by‐sequencing approach on three species of Mastiff bats with different ecological histories and geographical distributions to explore population genetics parameters and better understand the role of geographic barriers in the dispersal and gene flow in bats. Our analyses show that the population structure of each species varies according to environmental factors, levels of population isolation, and demographic histories. We show that oceanic straights seem to pose a partial barrier for some species and that more isolated lineages on islands tend to undergo genetic bottlenecks more than connected lineages closer to the mainland.

Mammals are one of the better known groups of animals, and in the Neotropics bats typically comprise about half of the mammalian species diversity. But, well resolved species-level phylogenies are still lacking for most taxa of bats. One broadly distributed genus is the mastiff bats, Molossus. Species within this genus are morphologically very similar, which results in a confusing and unstable taxonomy. In addition, low levels of genetic divergence among some clades make resolution of phylogenetic relationships difficult. Most authors recognize Molossus as being monophyletic, however, phylogenetic relationships within the genus remain poorly understood based on traditional Sanger sequencing of individual genes. We propose a more comprehensive framework based on large-scale genomic data derived from Next Generation Sequencing techniques to better understand evolutionary relationships within a group of closely related species with a rich taxonomic history. In this study, we utilized the NGS method of Genotype by Sequencing (GBS) to test the monophyly of the genus, understand evolutionary relationships within Molossus and investigate the genetic integrity of currently recognized species. Given that both de novo and reference genome pipelines are often used in the assembly of Single Nucleotide Polymorphism data from GBS, and that several tree inference methodologies have been proposed for SNP data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Our data provide the first high resolution phylogeny for the genus Molossus, bringing new insights into recognition of species boundaries and relationships among taxa. This study clarifies the taxonomy of Molossus and elevates the number of species in the genus from 11 to 14. We suggest the revalidation of the names M. nigricans, and M. fluminensis, which were synonymized under the name M. rufus; and M. bondae, previously synonymized under the name M. currentium. Different alignments and phylogenetic inferences produce consistent results, supporting use of SNP approach in addressing evolutionary questions on a macroevolutionary scale where the genetic distance among clades is low.

Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.