Timing and patterns of diversification in the Neotropical bat genus Pteronotus (Mormoopidae)

Historical biogeography of the Neotropical noctilionoid bats (Chiroptera: Noctilionoidea), revisited through a geographically explicit analysis

Biogeographic studies have generally relied on methods that use a few, large predefined areas, which may overlook fine-scale patterns. Here we test previous hypotheses about the biogeographic history of a diverse bat clade regarding its association with major Neotropical geological formations, particularly the Antilles, the South American Dry Diagonal, the Andes and the Panamanian land bridge, by applying a recently available method that uses actual distributions instead of predefined areas. We compiled and curated spatially explicit, georeferenced data of 173 bat species (Mammalia: Chiroptera: Noctilionoidea) from the online database Global Biodiversity Information Facility. By taking a previous comprehensive phylogeny as an evolutionary framework, we performed computationally intensive analyses using the Geographically-explicit Event Model. This method uses the observed species distributions to reconstruct the ancestral areas and biogeographic events at each phylogeny node. We found that sympatric speciation was the most frequently reconstructed event, and involved mainly the Panamanian Isthmus and northern South America (SA), but all sympatry reconstructions were different and specific to each node. Allopatric events were important in the Andes; vicariance caused both west/east and north/south disjunctions that went unnoticed previously. Founder events indicated bidirectional dispersal between the mainland and the Antilles since the Miocene, and across the incomplete Panamanian bridge and the SA Dry Diagonal since the early Pliocene. Overall, we found support for previous hypotheses on the influence of major Neotropical paleogeographic events in the diversification of the group, but additionally revealed multi-scale patterns that are embedded within the mainland and were previously overlooked. Our results highlight a trans-isthmian centre of diversification in the biogeographic history of Noctilionoidea including the Panamanian Isthmus and Northern SA.

MC. Molecular and morphological data suggest a new species of big-eared bat (Vespertilionidae: Corynorhinus) endemic to northeastern Mexico

Corynorhinus mexicanus is an insectivorous bat endemic to Mexico that inhabits the high and humid regions of the Sierra Madre Oriental (SMO), the Trans-Mexican Volcanic Belt (TMVB), and the Sierra Madre Occidental (SMOC). A previous study suggested that C. mexicanus could be a cryptic species complex due to the genetic divergence observed between specimens from the TMVB and SMOC. The present study implemented phylogenetic, population genetics, and morphological analyses to evaluate the hypothesis that C. mexicanus is a species complex. The phylogenetic analysis indicated that C. mexicanus is a polyphyletic species composed of three indirectly related lineages. The estimated divergence times for the lineages suggest that they first originated during the Pliocene, while the second and third shared a common ancestor with C. townsendii 1.55 million years ago, and diverged 600,000 years ago during the Middle Pleistocene. The population genetics analysis reveals the SMO lineage of C. mexicanus is an isolated genetic group and highly diverged from the rest of lineages (SMOC and TMVB). The morphological analyses showed variation in the skull and mandible associated with the lineages and sex of the specimens, highlighting a difference in mandible shape between the specimens of the SMO and the rest of C. mexicanus. The results of this study suggest the presence of an undescribed species of the genus Corynorhinus.

High genetic connectivity among large populations of Pteronotus gymnonotus in bat caves in Brazil and its implications for conservation

Bat caves in the Neotropical region harbor exceptional bat populations (> 100,000 individuals). These populations play a wider role in ecological interactions, are vulnerable due to their restriction to caves, and have a disproportionate conservation value. Current knowledge of bat caves in Brazil is still small. However, systematic monitoring of some bat caves in northeastern Brazil shows that they experience strong population fluctuations over short periods of time, suggesting large-scale movements between roosts and a much broader use of the landscape than previously considered. Spatio-temporal reproductive connectivity between distant populations would change our understanding of the use of roosts among bat species in Brazil, and important gaps in knowledge of long-distance bat movements in the country would be filled. Here, we used ddRADseq data to analyze the genetic structure of Pteronotus gymnonotus across nine bat caves over 700 km. Our results indicate the lack of a clear geographic structure with gene flow among all the caves analyzed, suggesting that P. gymnonotus uses a network of bat caves geographically segregated hundreds of kilometers apart. Facing strong anthropogenic impacts and an underrepresentation of caves in conservation action plans worldwide, the genetic connectivity demonstrated here confirms that bat caves are priority sites for bat and speleological conservation in Brazil and elsewhere. Moreover, our results demonstrate a warning call: the applied aspects of the environmental licensing process of the mining sector and its impact must be reviewed, not only in Brazil, but wherever this licensing process affects caves having exceptional bat populations.

Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group

Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.

Acoustic clue: bringing echolocation call data into the distribution dilemma of Pteronotus (Chiroptera: Mormoopidae) complexes in Central America

In Central America, the distributional limits and the contact zones of some Pteronotus species, such as the naked-backed bats and the lesser mustached bats, are unclear. To elucidate the distributional dilemma of the species groups Pteronotus fulvus + Pteronotus davyi and Pteronotus psilotis + Pteronotus personatus in Central America, we studied the acoustic variation of their echolocation calls along the range of possible contact zones and the existence of distinct phonic groups. We performed hierarchical k-means clustering on principal components (HCPC) using acoustic samples from Mexico, Honduras, El Salvador, Nicaragua and Costa Rica to describe the global acoustic diversity, possibly overlooking differences between species groups. We assessed whether those acoustic differences were related to the geographical distance and geographical location. We found evidence of sympatry for three phonic groups within each species complex, without a clear correspondence to the known distribution of species. The changes in frequency of their echolocation calls seem to follow a similar pattern to the geographical variation in body size of the species. Future studies in Central America should include an integrative sampling of individually captured, tagged and recorded bats to help in resolution of the distribution dilemma raised here.

Genetic Introgression and Morphological Variation in Naked-Back Bats (Chiroptera: Mormoopidae: Pteronotus Species) along Their Contact Zone in Central America

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.

HOST-SWITCHING EVENTS IN LITOMOSOIDES CHANDLER, 1931 (FILARIOIDEA: ONCHOCERCIDAE) ARE NOT RAMPANT BUT CLADE DEPENDENT

The genus Litomosoides Chandler, 1931, includes species that as adults occur in the thoracic and abdominal cavity of mammalian hosts and are presumably vectored by mites. The vertebrate hosts include a variety of Neotropical mammals such as phyllostomid and mormoopid bats; cricetid, sciurid, and hystricognath rodents; and didelphid marsupials. It has been suggested that Litomosoides is not a monophyletic group and that rampant horizontal transfer explains their presence in disparate groups of mammals. Herein we present a phylogenetic reconstruction including mitochondrial genes of 13 vouchered species. This phylogeny is used to reconstruct the evolutionary history of these parasites and the ancestral states of key characters used in species classification, namely, the configuration of the spicules. The historical association of these filarioids with 6 groups of mammals, as well as their ancestral geographic distributions, were reconstructed using Bayesian statistical approaches comparing alternative models of biogeography and evolution and fossil states in selected nodes of the phylogeny. The optimal reconstruction suggests a model of dispersal, extinction, and cladogenesis (DEC) driving the evolution of Litomosoides; the results suggest an origin of Litomosoides in South America and association of ancestors with phyllostomids, and strong evidence of at least 2 host-switching events: 1 of these involving cricetid rodents and the other mormoopid bats. The latter event included a simultaneous geographic expansion of the parasite lineage across South and North America. The host-switching event from phyllostomid bats into cricetid rodents occurred once these rodents diversified across South America; subsequent diversification of the latter clade resulted in 2 branches, each showing expansion of the parasites back into North America. This result suggests that both parasites and cricetid rodents established an association in South America, underwent diversification, and then dispersed into North America. Further, this clade of cricetid-dwelling species includes parasites featuring the "sigmodontis" spicule type. The identification of a single host-switching event involving the disparate lineages of Chiroptera and Rodentia offers a framework to reconstruct the gene evolution and diversification of this lineage after the host-switching event. This will help in predicting the ability of these parasites to infect sympatric mammals.

The taxonomic status of Myotis nesopolus larensis (Chiroptera, Vespertilionidae) and new insights on the diversity of Caribbean Myotis

Myotis nesopolus currently comprises two subspecies. The nominate subspecies (M. n. nesopolus) occurs on the Caribbean islands of Curaçao and Bonaire, Netherlands Antilles, whereas M. n. larensis is known from mainland South America in northeastern Colombia and northwestern Venezuela. Our Maximum Likelihood phylogenetic analyses of cytochrome-b gene sequences recovered M. nesopolus as a paraphyletic group, with M. n. nesopolus and M. n. larensis as non-sister lineages. The haplotype network indicates that these two subspecies do not share any haplotypes and are in different evolutionary trajectories. Additionally, these two subspecies can be distinguished on the basis of qualitative and quantitative morphological traits. This pattern supports the recognition of M. nesopolus and M. larensis as full species. Our results also reveal that the assemblage of Caribbean Myotis do not form a monophyletic group. Caribbean species are phylogenetically close to mainland species from northern South America and Central America, suggesting that colonization of Caribbean islands happened multiple times.

Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world's largest bats (Mammalia: Chiroptera)

AIM

Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group.

LOCATION

Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands.

TAXON

Pteropus (Pteropodidae).

METHODS

To infer the biogeographic history of Pteropus, we sequenced up to 6169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognized Pteropus species and subspecies with 3 Acerodon outgroups using BEAST and subsequently estimated ancestral areas using models implemented in BioGeoBEARS.

RESULTS

Species-level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor with Acerodon; founder-event speciation out of Wallacea was a common inference. Pteropus species in Micronesia and the western Indian Ocean were also inferred to result from founder-event speciation.

MAIN CONCLUSIONS

Dispersal between regions of the IAA and the islands found therein fostered diversification of Pteropus throughout the IAA and beyond. Dispersal in Pteropus is far higher than in most other volant taxa studied to date, highlighting the importance of inter-island movement in the biogeographic history of this large clade of large bats.

Field key to the bats of Costa Rica and Nicaragua

With more than 1,400 species of bats described worldwide, the order Chiroptera is second only to rodents in ecological and taxonomic diversity. Bats play critically important roles in natural systems as seed and pollen dispersers, predators of invertebrates and vertebrates, and sanguinivores. The Central American countries of Costa Rica and Nicaragua have at least 123 species of bats (in nine families and 66 genera), or nearly 10% of the world's known species. Because of the importance of proper species identification for ecological and systematic studies and conservation efforts, we present a dichotomous key to the bats of this region. Our goal is the positive, in-hand identification of living bats that may be released unharmed after identification. Identifying Neotropical bats and understanding the taxonomic changes that affect the names used for the various species over time can be a challenge. This key includes the 123 species known to occur in Costa Rica and Nicaragua as well as three that are expected to occur in these countries but which have not yet been recorded. We provide illustrations of key characters useful for differentiating bats to species and updated taxonomic notes to assist the reader in assessing the literature.

Con más de 1,400 especies de murciélagos descritos en todo el mundo, el orden Chiroptera es el segundo más diverso después de los roedores respecto a taxonomía. Los murciélagos juegan papeles de importancia crítica en los sistemas naturales como dispersores de semillas, polinizadores, depredadores de vertebrados e invertebrados, así como hematófagos. Costa Rica y Nicaragua presentan al menos 123 especies de murciélagos (en 9 familias y 66 géneros), casi el 10% de las especies conocidas en el mundo. Debido a la importancia de la identificación precisa de las especies para los estudios ecológicos, sistemáticos y de conservación, presentamos una clave dicotómica para los murciélagos de esta región. Nuestro objetivo es la identificación correcta con los murciélagos in vivo y que se pueden liberar sin daño después de la identificación. La caracterización de los murciélagos neotropicales y el seguimiento del estatus taxonómico de cada especie puede ser un reto en el proceso de identificación. Esta clave incluye las 123 especies conocidas en Costa Rica y Nicaragua, así como 3 no registradas pero con distribución potencial. Proporcionamos ilustraciones de características claves útiles para diferenciar murciélagos al nivel de la especie y notas taxonómicas actualizadas para ayudar al lector a la identificación.

Repeated long-distance dispersal and convergent evolution in hazel

Closely related species with a worldwide distribution provide an opportunity to understand evolutionary and biogeographic processes at a global scale. Hazel (Corylus) is an economically important genus of tree and shrub species found in temperate regions of Asia, North America and Europe. Here we use multiple nuclear and chloroplast loci to estimate a time-calibrated phylogenetic tree of the genus Corylus. We model the biogeographic history of this group and the evolutionary history of tree and shrub form. We estimate that multiple Corylus lineages dispersed long distances between Europe and Asia and colonised North America from Asia in multiple independent events. The geographic distribution of tree versus shrub form of species appears to be the result of 4–5 instances of convergent evolution in the past 25 million years. We find extensive discordance between our nuclear and chloroplast trees and potential evidence for chloroplast capture in species with overlapping ranges, suggestive of past introgression. The important crop species C. avellana is estimated to be closely related to C. maxima, C. heterophylla var. thunbergii and the Colurnae subsection. Our study provides a new phylogenetic hypothesis or Corylus and reveals how long-distance dispersal can shape the distribution of biodiversity in temperate plants.

A coalescent-based estimator of genetic drift, and acoustic divergence in the Pteronotus parnellii species complex

Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested null hypothesis to explain trait divergence is genetic drift. Here we derive FST values from multi-locus coalescent isolation-with-migration models, and couple them with estimates of quantitative trait divergence, or PST, to test drift as the evolutionary process responsible for phenotypic divergence in island populations of the Pteronotus parnellii species complex. Compared to traditional comparisons of PST to FST, the migration-based estimates of FST are unidirectional instead of bidirectional, simultaneously integrate variation among loci and individuals, and posterior densities of PST and FST can be compared directly. We found the evolution of higher call frequencies is inconsistent with genetic drift for the Hispaniolan population, despite many generations of isolation from its Puerto Rican counterpart. While the Hispaniolan population displays dimorphism in call frequencies, the higher frequency of the females is incompatible with sexual selection. Instead, cultural drift toward higher frequencies among Hispaniolan females might explain the divergence. By integrating Bayesian coalescent and trait analyses, this study demonstrates a powerful approach to testing genetic drift as the default evolutionary mechanism of trait differentiation between populations.

Multifactorial processes underlie parallel opsin loss in neotropical bats

The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts, and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave-sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone.

Bats are famous for using their hearing to explore their environments, yet fewer people are aware that these flying mammals have both good night and daylight vision. Some bats can even see in color thanks to two light-sensitive proteins at the back of their eyes: S-opsin which detects blue and ultraviolet light and L-opsin which detects green and red light. Many species of bat, however, are missing one of these proteins and cannot distinguish any colors; in other words, they are completely color-blind.

Some bat species found in Central and South America have independently lost their ability to see blue-ultraviolet light and have thus also lost their color vision. These bats have diverse diets – ranging from insects to fruits and even blood – and being able to distinguish color may offer an advantage in many of their activities, including hunting or foraging. The vision genes in these bats, therefore, give scientists an opportunity to explore how a seemingly important trait can be lost at the molecular level.

Sadier, Davies et al. now report that S-opsin has been lost more than a dozen times during the evolutionary history of these Central and South American bats. The analysis used samples from 55 species, including animals caught from the wild and specimens from museums. As with other proteins, the instructions encoded in the gene sequence for S opsin need to be copied into a molecule of RNA before they can be translated into protein. As expected, S-opsin was lost several times because of changes in the gene sequence that disrupted the formation of the protein. However, at several points in these bats’ evolutionary history, additional changes have taken place that affected the production of the RNA or the protein, without an obvious change to the gene itself. This finding suggests that other studies that rely purely on DNA to understand evolution may underestimate how often traits may be lost. By capturing ‘evolution in action’, these results also provide a more complete picture of the molecular targets of evolution in a diverse set of bats.

Chromosomal Evolution in Chiroptera

Chiroptera is the second largest order among mammals, with over 1300 species in 21 extant families. The group is extremely diverse in several aspects of its natural history, including dietary strategies, ecology, behavior and morphology. Bat genomes show ample chromosome diversity (from 2n = 14 to 62). As with other mammalian orders, Chiroptera is characterized by clades with low, moderate and extreme chromosomal change. In this article, we will discuss trends of karyotypic evolution within distinct bat lineages (especially Phyllostomidae, Hipposideridae and Rhinolophidae), focusing on two perspectives: evolution of genome architecture, modes of chromosomal evolution, and the use of chromosome data to resolve taxonomic problems.