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Abstract:One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two genetic markers: COI (mitochondrial) and DBY (nuclear) genes. The findings of this study strongly support the hypothesis of high genetic variability and identify at least six lineages within P. parnellii, some of which appear to be cryptic species. Keywords:Bats, COI, DBY, Neotropical America, Genetic diversity, Biogeography, Phylogeny, taxonomyPowered by TCPDF (www.tcpdf.org) Download source file (73.76 kB) Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae) Manuscript body INTRODUCTIONThe Neotropical region is home to the greatest diversity of bats in the world, and it is well known that this fauna awaits a number of basic lines of research, among which cryptic diversity stands as one of the most relevant. Thus, despite recent efforts to address the issue, not only in the Neotropics (Clare, 2011; Clare et al., 2011; Pavan et al., 2011; Larsen et al., 2012;Hernández-Dávila et al., 2012; Pavan et al., 2013; Velazco and Patterson, 2013; Parlos et al., 2014) but also in several other regions of the world (Mayer and von Helversen, 2001;Ibáñez et al., 2006;Furman et al., 2010;Raghuram et al., 2014; Bogdanowicz et al., 2015; Dammhahn et al., 2015;and Hassanin et al., 2015), cryptic species complexes have become a top priority for a number of international agendas.Pteronotus parnellii is investigated here as a special case in which to study cryptic species among Neotropical bats, considering that due to its wide distribution and low morphological differentiation, the family Mormoopidae is an excellent subject for this kind of analysis.The family has only two genera, Mormoops Leach, 1821 and Pteronotus Gray, 1838; both comprising insectivorous, gregarious, and strict cave-dwelling bats, which are found in a wide variety of habitats, ranging from tropical rainforests to arid regions, being particularly abundant in low dry forests throughout the Neotropics.The genus Mormoops has two species, Mormoops blainvillei Leach, 1821 which is distributed across the Greater Antilles and small adjacent islands, and M. megalophylla (Peters, 1864), with an extant distribution extending from Mexico to northwestern South America, and the West Indies. Pteronotus consists of a diverse group of six currently recognized species: P. davyi Gray, 1838; P. gymnonotus Naterer, 1843; P. parnellii (Gray, 1843) and P. personatus (Wagner, 1843), which are all distributed from Mexico to Brazil, and P. macleayi (Gray, 1843) and P. quadridens (Gundlach, 1840), which are known from the A...

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Recent historical and anthropogenic changes in the landscape causing habitat fragmentation can disrupt the connectivity of wild populations and pose a threat to the genetic diversity of multiple species. This study investigated the effect of habitat fragmentation on the structure and genetic diversity of the Mexican greater funnel-eared bat (Natalus mexicanus) throughout its distribution range in Mexico, whose natural habitat has decreased dramatically in recent years. Genetic structure and diversity were measured using the HVII hypervariable domain of the mitochondrial control region and ten nuclear microsatellite loci, to analyze historical and contemporary information, respectively. The mitochondrial and nuclear results pointed to a differential genetic structuring, derived mainly from philopatry in females. Our results also showed that genetic diversity was historically high and currently moderate; additionally, the contemporary gene flow between the groups observed was null. These findings confirm that the effects of habitat fragmentation have started to be expressed in populations and that forest loss is already building barriers to contemporary gene flow. The concern is that gene flow is a process essential to ensure that the genetic diversity of N. mexicanus populations (and probably of many other forest species) distributed in Mexico is preserved or increased in the long term by maintaining forest connectivity between locations.

Two sibling bare-backed bat species (Pteronotus fulvus and P. gymnonotus) have been traditionally differentiated by their size. However, intermediate specimens between the two species have been found in sympatric populations along southern Mexico and it has been suggested that they may be the outcome of a hybridization process between the two species. We used one mitochondrial (COI), three nuclear markers (PRKCL, STAT5A and RAG2) and 13 microsatellites to explore the evolutionary relationships between these two species and elucidate whether the intermediate morphotypes correspond to hybrid individuals. These markers have been analyzed in sympatric and allopatric populations of the two species plus the closely related species Pteronotus davyi. We confirmed the species-level differentiation of the three lineages (P. fulvus, P. davyi and P. gymnonotus), but the phylogenetic hypotheses suggested by the nuclear and mitochondrial markers were discordant. We confirm that the discordance between markers is due to genetic introgression through the mitochondrial capture of P. fulvus in P. gymnonotus populations. Such introgression was found in all P. gymnonotus specimens across its sympatric distribution range (Mexico to Costa Rica) and is related to expansion/retraction species distribution pulses associated with changes in forest distribution during the Quaternary climate cycles. Microsatellite analyses showed contemporary genetic contact between the two sympatric species and 3.0% of the samples studied were identified as hybrids. In conclusion, we found a historical and asymmetric genetic introgression (through mitochondrial capture) of P. fulvus into P. gymnonotus in Mexico and Central America and a limited contemporary gene exchange between the two species. However, no relationship was found between hybridization and the intermediate-sized specimens from southern Mexico, which might likely result from a clinal variation with latitude. These results confirm the need for caution when using forearm size to identify these species in the field and when differentiating them in the laboratory based on mitochondrial DNA alone.