mtDNA perspective of chromosomal diversification and hybridization in Peters' tent-making bat (Uroderma bilobatum: Phyllostomidae)

Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes

Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.

Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia

Simple Summary

Disease prevention and appropriate wildlife management are among the major challenges in wildlife conservation. In the present study, we made a first assessment of the variability of major histocompatibility complex (MHC) genes in roe deer in Slovenia and evaluated local population adaptation by comparing MHC variability with neutral microsatellites. We discovered three new MHC DRB exon 2 alleles in addition to seven previously described in the literature. Moreover, we found evidence of historical positive selection, as selection analysis indicated that approx. 10% of the encoded amino acids were subjected to episodic positive selection. This study provides the basis for further research on immunogenetic variation in roe deer and highlights opportunities to incorporate genetic data into science-based population management.

Abstract

Disease control and containment in free-ranging populations is one of the greatest challenges in wildlife management. Despite the importance of major histocompatibility complex (MHC) genes for immune response, an assessment of the diversity and occurrence of these genes is still rare in European roe deer, the most abundant and widespread large mammal in Europe. Therefore, we examined immunogenetic variation in roe deer in Slovenia to identify species adaptation by comparing the genetic diversity of the MHC genes with the data on neutral microsatellites. We found ten MHC DRB alleles, three of which are novel. Evidence for historical positive selection on the MHC was found using the maximum likelihood codon method. Patterns of MHC allelic distribution were not congruent with neutral population genetic findings. The lack of population genetic differentiation in MHC genes compared to existing structure in neutral markers suggests that MHC polymorphism was influenced primarily by balancing selection and, to a lesser extent, by neutral processes such as genetic drift, with no clear evidence of local adaptation. Selection analyses indicated that approx. 10% of amino acids encoded under episodic positive selection. This study represents one of the first steps towards establishing an immunogenetic map of roe deer populations across Europe, aiming to better support science-based management of this important game species.

Consequences of Hybridization in Mammals: A Systematic Review

Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.

Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation

Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.

Systematics and Taxonomy of Tonatia saurophila Koopman & Williams, 1951 (Chiroptera, Phyllostomidae)

The Stripe-headed Round-eared bat, Tonatiasaurophila, includes three subspecies: Tonatiasaurophilasaurophila (known only from subfossil records in Jamaica), Tonatiasaurophilabakeri (distributed from southeastern Mexico to northern Colombia, Venezuela west and north of the Cordillera de Mérida, and northwestern Ecuador), and Tonatiasaurophilamaresi (distributed in Venezuela east and south of the Cordillera de Mérida, the Guianas, Trinidad and Tobago, northeastern Brazil, and along the upper Amazon basin in Colombia, Ecuador, Peru, and Bolivia). The last two subspecies are an attractive example to test predictions about the historical role of the Andes in mammalian diversification. Based on morphological descriptions, morphometric analyses, and phylogenetic reconstruction using the mitochondrial gene Cyt-b and the nuclear exon RAG2, this study evaluates the intraspecific relationships within Tonatiasaurophila and the taxonomic status of the taxon. The three subspecies of T.saurophila are recognizable as full species: Tonatiabakeri, Tonatiamaresi, and Tonatiasaurophila. The latter is restricted to its type locality and possibly is extinct. Tonatiabakeri, in addition to being larger than T.maresi, is morphologically distinguishable by possessing an acute apex at the posterior edge of the skull, a well-developed clinoid process, and relatively robust mandibular condyles, and by lacking a diastema between the canine and the first lower premolar. The genetic distance between T.bakeri and T.maresi is 7.65%.

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

Investigating Hybridization between the Two Sibling Bat Species Myotis myotis and M. blythii from Guano in a Natural Mixed Maternity Colony

Because they can form seasonal mixed-species groups during mating and maternal care, bats are exciting models for studying interspecific hybridization. Myotis myotis and M. blythii are genetically close and morphologically almost identical, but they differ in some aspects of their ecology and life-history traits. When they occur in sympatry, they often form large mixed maternity colonies, in which their relative abundance can vary across time due to a shift in the timing of parturition. For the first time, we used non-invasive genetic methods to assess the hybridization rate and colony composition in a maternity colony of M. myotis and M. blythii located in the French Alps. Bat guano was collected on five sampling dates spread across the roost occupancy period and was analysed for individual genotype. We investigated whether the presence of hybrids followed the pattern of one of the parental species or if it was intermediate. We identified 140 M. myotis, 12 M. blythii and 13 hybrids among 250 samples. Parental species appeared as genetically well-differentiated clusters, with an asymmetrical introgression towards M. blythii. By studying colony parameters (effective size, sex ratio and proportion of the three bat types) across the sampling dates, we found that the abundances of hybrid and M. blythii individuals were positively correlated. Our study provides a promising non-invasive method to study hybridization in bats and raises questions about the taxonomic status of the two Myotis species. We discuss the contribution of this study to the knowledge of hybrid ecology, and we make recommendations for possible future research to better understand the ecology and behaviour of hybrid individuals.

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

We investigate the biogeographic processes related to the origin and current patterns of distribution of the extant species of the genus Pteronotus. This clade of insectivorous bats is widely distributed in the Neotropical Region and has recently gone through a taxonomic update which increased more than twice its diversity. Using six molecular markers of 15 Pteronotus lineages ranging from Mexico to Central Brazil, we reconstruct a time-calibrated tree and infer molecular evolutionary rates for this bat genus. In addition, estimates of range evolution across phylogeny were obtained through statistical model testing among six different biogeographic models. The origin of the genus Pteronotus occurred approximately 16million years ago (Ma), with initial cladogenesis events being evenly distributed across the phylogeny. Divergence between most closely related species is recent, falling in the Pleistocene period less than 2.6Ma. Mainland lineages present congruent patterns of north versus south continent splitting while insular clades differ in their time of arrival in the Caribbean Islands. Temporal and geographic range estimates for early nodes of Pteronotus phylogeny suggest a central role of Neogene tectonic reorganizations of Central America in the group diversification process. Also, South American colonization by Pteronotus occurred early in the genus history. Founder-event speciation was an important mode of lineage splitting in Pteronotus, with two independent dispersal jumps having occurred to the Greater Antilles. Finally, Pleistocenic sea-level variation and climatic oscillations are possibly associated with divergence between sister-species and recent ages of MRCA for Pteronotus species.

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization.

Chromosomal polymorphism in mammals: an evolutionary perspective

Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.

Karyotype evolution in the horseshoe bat Rhinolophus sedulus by whole-arm reciprocal translocation (WART)

Robertsonian (centric) fusion or fission is one of the predominant modes of chromosomal rearrangement in karyotype evolution among mammals. However, in karyotypes composed of only bi-armed chromosomes, creation of new chromosomal arm combinations in one step is possible only via whole-arm reciprocal translocation (WART). Although this type of rearrangement has often been proposed to play an important role in chromosomal evolution, direct observations of WARTs remained rare, and, in most cases, were found in hybrids of chromosomal races in the genera Mus and Sorex. For the first time, we present the karyotype of the horseshoe bat species Rhinolophus sedulus (2n = 28, FNa = 52), where a WART between 2 metacentric autosomes was detected by G-banding and confirmed by FISH with painting probes of the vespertilionid bat Myotis myotis. Among the 6 specimens analyzed, 2 showed the heterozygous condition of the WART, 1 showed the presumed ancestral, and 3 specimens showed the derived homozygous state. As the existence of a hybrid zone at the sampling locality is thought to be rather improbable, the WART may indicate ongoing karyotype evolution in this taxon.

A cryptic species of the Tylonycteris pachypus complex (Chiroptera: Vespertilionidae) and its population genetic structure in southern China and nearby regions

Three distinct bamboo bat species (Tylonycteris) are known to inhabit tropical and subtropical areas of Asia, i.e., T. pachypus, T. robustula, and T. pygmaeus. This study performed karyotypic examinations of 4 specimens from southern Chinese T. p. fulvidus populations and one specimen from Thai T. p. fulvidus population, which detected distinct karyotypes (2n=30) compared with previous karyotypic descriptions of T. p. pachypus (2n=46) and T. robustula (2n=32) from Malaysia. This finding suggested a cryptic Tylonycteris species within T. pachypus complex in China and Thailand. Morphometric studies indicated the difficulty in distinguishing the cryptic species and T. p. pachypus from Indonesia apart from the external measurements, which might be the reason for their historical misidentification. Based on 623 bp mtDNA COI segments, a phylogeographic examination including T. pachypus individuals from China and nearby regions, i.e., Vietnam, Laos, and Cambodia, was conducted to examine the population genetic structure. Genealogical and phylogeographical results indicated that at least two diverged lineages existed in these regions (average 3.4 % of Kimura 2-parameter distances) and their population structure did not match the geographic pattern. These results suggested that at least two historical colonizations have occurred by the cryptic species. Furthermore, through integration of traditional and geometric morphological results, morphological differences on zygomatic arches, toothrows and bullae were detected between two lineages in China. Given the similarity of vegetation and climate of Guangdong and Guangxi regions, we suggested that such differences might be derived from their historical adaptation or distinct evolutionary history rather than the differences of habitats they occurred currently.

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.

Evidence for two karyotypic variants of the lesser horseshoe bat ( Rhinolophus hipposideros , Chiroptera, Mammalia) in Central Europe

Three different diploid chromosome numbers (2n = 54, 56 and 58) have been reported in the lesser horseshoe bat, Rhinolophus hipposideros. Asia Minor and the Middle East are inhabited by R. hipposideros specimens with 58 chromosomes. In Europe, specimens with 56 chromosomes have been recorded from several localities in the Czech Republic, Slovakia, Italy and Greece. Up to now, specimens with 54 chromosomes have been reported only from Spain and possibly from Switzerland. With the record of 54 chromosomes in specimens from Germany presented here, the distributional area of this variant is expanded into Central Europe. According to the cytogenetic data presently available, we presume that the European R. hipposideros population is divided into a western form (from Spain to Germany) with a 2n = 54 karyotype and an eastern form (from the Czech Republic to Greece) with a 2n = 56 karyotype. This study presents banded karyotypes for the 2n = 54 and 2n = 56 variants for the first time. In addition, chromosomal arm homology to the vespertilionid bat species Myotis myotis revealed by chromosome painting is reported. Whether the variants could represent separate species is also discussed.

Diversification and reproductive isolation: cryptic species in the only New World high-duty cycle bat, Pteronotus parnellii

BACKGROUND

Molecular techniques are increasingly employed to recognize the presence of cryptic species, even among commonly observed taxa. Previous studies have demonstrated that bats using high-duty cycle echolocation may be more likely to speciate quickly. Pteronotus parnellii is a widespread Neotropical bat and the only New World species to use high-duty cycle echolocation, a trait otherwise restricted to Old World taxa. Here we analyze morphological and acoustic variation and genetic divergence at the mitochondrial COI gene, the 7th intron region of the y-linked Dby gene and the nuclear recombination-activating gene 2, and provide extensive evidence that P. parnellii is actually a cryptic species complex.

RESULTS

Central American populations form a single species while three additional species exist in northern South America: one in Venezuela, Trinidad and western Guyana and two occupying sympatric ranges in Guyana and Suriname. Reproductive isolation appears nearly complete (only one potential hybrid individual found). The complex likely arose within the last ~6 million years with all taxa diverging quickly within the last ~1-2 million years, following a pattern consistent with the geological history of Central and northern South America. Significant variation in cranial measures and forearm length exists between three of the four groups, although no individual morphological character can discriminate these in the field. Acoustic analysis reveals small differences (5-10 kHz) in echolocation calls between allopatric cryptic taxa that are unlikely to provide access to different prey resources but are consistent with divergence by drift in allopatric species or through selection for social recognition.

CONCLUSIONS

This unique approach, considering morphological, acoustic and multi-locus genetic information inherited maternally, paternally and bi-parentally, provides strong support to conclusions about the cessation of gene flow and degree of reproductive isolation of these cryptic species.

Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats

Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7^th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of the genetic species concept but demonstrate that estimates of mitochondrial diversity alone do not accurately represent gene flow in these species and that contact/hybrid zones must be explored to evaluate reproductive isolation.

Neotropical bats: estimating species diversity with DNA barcodes

DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

Historical male-mediated introgression in horseshoe bats revealed by multilocus DNA sequence data

Instances of hybridization between mammalian taxa in the wild are rarely documented. To test for introgression between sibling species of horseshoe bat (Rhinolophus yunanensis and R. pearsoni) and two subspecies of the latter (R. p. pearsoni and R. p. chinensis), we sequenced two mtDNA and two ncDNA markers in individuals sampled from multiple localities within their overlapping ranges. The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions, and coalescent-based analyses suggested divergence occurred around 4 MYA. However, these relationships strongly conflicted with those recovered from two independent nuclear gene trees, in which R. yunanensis clustered with R. p. pearsoni to the exclusion of R. p. chinensis. This geographically widespread discordance is best explained by large-scale historical introgression of ncDNA from R. yunanensis to R. pearsoni by male-mediated exchange in mixed species colonies during Pleistocene glacial periods, when ranges may have contracted and overlapped more than at present. Further species tree-gene tree conflicts were detected between R. p. pearsoni and R. p. chinensis, also indicating past and/or current introgression in their overlapping regions. However, here the patterns point to asymmetric mtDNA introgression without ncDNA introgression. Analyses of coalescence times indicate this exchange has occurred subsequent to the divergence of these subspecies from their common ancestor. Our work highlights the importance of using multiple data sets for reconstructing phylogeographic histories and resolving taxonomic relationships.

Phylogeography of the common vampire bat (Desmodus rotundus): marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

BACKGROUND

The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat.

RESULTS

Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar.

CONCLUSIONS

We therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.

Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii

The two sibling bat species Myotis myotis and Myotis blythii occur in sympatry over wide areas of Southern and Central Europe. Morphological, ecological and previous genetic evidence supported the view that the two species constitute two well-differentiated groups, but recent phylogenetic analyses have shown that the two species share some mtDNA haplotypes when they occur in sympatry. In order to see whether some genetic exchange has occurred between the two species, we sequenced a highly variable segment of the mitochondrial control region in both species living in sympatry and in allopatry. We also analysed the nuclear diversity of 160 individuals of both species found in two mixed nursery colonies located north and south of the Alps. MtDNA analysis confirmed that European M. blythii share multiple, identical or very similar haplotypes with M. myotis. Since allopatric Asian M. blythii presents mtDNA sequences that are very divergent from those of the two species found in Europe, we postulate that the mitochondrial genome of the European M. blythii has been replaced by that of M. myotis. The analysis of nuclear diversity shows a strikingly different pattern, as both species are well differentiated within mixed nursery colonies (F(ST) = 0.18). However, a Bayesian analysis of admixture reveals that the hybrids can be frequently observed, as about 25% of sampled M. blythii show introgressed genes of M. myotis origin. In contrast, less than 4% of the M. myotis analysed were classified as non-parental genotypes, revealing an asymmetry in the pattern of hybridization between the two species. These results show that the two species can interbreed and that the hybridization is still ongoing in the areas of sympatry. The persistence of well-differentiated nuclear gene pools, in spite of an apparent replacement of mitochondrial genome in European M. blythii by that of M. myotis, is best explained by a series of introgression events having occurred repeatedly during the recent colonization of Europe by M. blythii from Asia. The sharp contrast obtained from the analysis of mitochondrial and nuclear markers further points to the need to cautiously interpret results based on a single class of genetic markers.

SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT

We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson-Dobzhansky-Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these "morphologically cryptic genetic species" are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F(1)s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is "reproductively isolated species." Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen-based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.

Molecular systematics of Vampyressine bats (Phyllostomidae: Stenodermatinae) with comparison of direct and indirect surveys of mitochondrial DNA variation

Approximately 29 species in seven genera (Chiroderma, Mesophylla, Platyrrhinus, Uroderma, Vampyressa, Vampyriscus, and Vampyrodes) compose the Subtribe Vampyressina, a group of New World leaf-nosed bats (Phyllostomidae) specialized in fruit-eating. A recent study of restriction-site variability within the mitochondrial ND3-ND4 gene region contrasts with other molecular data, including sequence data from other mitochondrial genes, by suggesting that the monotypic genus Ectophylla (E. alba) also is member of the group and is related closely to Mesophylla. In this study, we address possible explanations for why the restriction-site data appear to contradict other molecular data by performing phylogenetic analysis of DNA sequence variation (direct survey) in the ND3-ND4 region and cytochrome b gene and by re-assessing ND3-ND4 restriction-site variability in the known sequences (indirect survey). Results from analysis of sequence data reject the Ectophylla-Mesophylla hypothesis (P<0.001) and suggest four primary lineages within Vampyressina: (1) Mesophylla-Vampyressa; (2) Chiroderma-Vampyriscus; (3) Platyrrhinus-Vampyrodes; and (4) Uroderma. We also find no support for the Ectophylla-Mesophylla hypothesis in our re-analysis of ND3-ND4 restriction-site variability, and suggest the differences between molecular studies have a methodological basis.

Molecular phylogeny of funnel-eared bats (Chiroptera: Natalidae), with notes on biogeography and conservation

Two assumptions have framed previous systematic and biogeographic studies of the family Natalidae: that it comprises a few widespread species, and that extant lineages originated in Mexico and/or Central America. This study analyzes new sequence data from the mitochondrial cytochrome b and the nuclear Rag2, to clarify species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b coincide with published morphological characters, and show that the family includes at least eight species. One newly recognized species is known to live from a single locality in Jamaica, suggesting immediate conservation measures and underscoring the urgency of taxonomic revision. Among the three genera, Chilonatalus and Natalus form a clade, to the exclusion of Nyctiellus. This phylogeny and the geographic distribution of natalids, both extant and extinct, are hardly compatible with a Middle American origin for the group. Instead, extant natalids appear to have originated in the West Indies. The threat of Caribbean hurricanes early in their evolutionary history might account for the specialized cave roosting that characterizes all natalids, even continental species.

Exploring population genetic structure in three species of Lesser Antillean bats

We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe-induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected in Ardops nichollsi (P = 0.718), but could be rejected in B. cavernarum (P < 0.001) and Artibeus jamaicensis (P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using an amova and was rejected in each species [Ardops nichollsi (P = 0.697); B. cavernarum (P = 0.598); Artibeus jamaicensis (P = 0.763)]. In B. cavernarum and Artibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly in Artibeus jamaicensis (PW < 0.01; PSE = 0.04), but cannot be rejected in B. cavernarum (PW = 0.81; PSE = 0.79). A conservative interpretation of the molecular data is that island populations of Artibeus jamaicensis, although isolated geographically, are not isolated genetically.