Genetic diversity of neotropical Myotis (chiroptera: vespertilionidae) with an emphasis on South American species

Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore

Background

The Neotropics harbors the largest species richness of the planet; however, even in well-studied groups, there are potentially hundreds of species that lack a formal description, and likewise, many already described taxa are difficult to identify using morphology. Specifically in small mammals, complex morphological diagnoses have been facilitated by the use of molecular data, particularly from mitochondrial sequences, to obtain accurate species identifications. Obtaining mitochondrial markers implies the use of PCR and specific primers, which are largely absent for non-model organisms. Oxford Nanopore Technologies (ONT) is a new alternative for sequencing the entire mitochondrial genome without the need for specific primers. Only a limited number of studies have employed exclusively ONT long-reads to assemble mitochondrial genomes, and few studies have yet evaluated the usefulness of such reads in multiple non-model organisms.

Methods

We implemented fieldwork to collect small mammals, including rodents, bats, and marsupials, in five localities in the northern extreme of the Cordillera Central of Colombia. DNA samples were sequenced using the MinION device and Flongle flow cells. Shotgun-sequenced data was used to reconstruct the mitochondrial genome of all the samples. In parallel, using a customized computational pipeline, species-level identifications were obtained based on sequencing raw reads (Whole Genome Sequencing). ONT-based identifications were corroborated using traditional morphological characters and phylogenetic analyses.

Results

A total of 24 individuals from 18 species were collected, morphologically identified, and deposited in the biological collection of Universidad EAFIT. Our different computational pipelines were able to reconstruct mitochondrial genomes from exclusively ONT reads. We obtained three new mitochondrial genomes and eight new molecular mitochondrial sequences for six species. Our species identification pipeline was able to obtain accurate species identifications for up to 75% of the individuals in as little as 5 s. Finally, our phylogenetic analyses corroborated the identifications from our automated species identification pipeline and revealed important contributions to the knowledge of the diversity of Neotropical small mammals.

Discussion

This study was able to evaluate different pipelines to reconstruct mitochondrial genomes from non-model organisms, using exclusively ONT reads, benchmarking these protocols on a multi-species dataset. The proposed methodology can be applied by non-expert taxonomists and has the potential to be implemented in real-time, without the need to euthanize the organisms and under field conditions. Therefore, it stands as a relevant tool to help increase the available data for non-model organisms, and the rate at which researchers can characterize life specially in highly biodiverse places as the Neotropics.

Forecasting climate change impacts on neotropical Myotis: Insights from ecological niche models for conservation strategies

Myotis originated during the Oligocene in Eurasia and has become one of the most diverse bat genera, with over 140 species. In the case of neotropical Myotis, there is a high degree of phenotypic conservatism. This means that the taxonomic and geographic limits of several species are not well understood, which constrains detailed studies on their ecology and evolution and how to effectively protect these species. Similar to other organisms, bats may respond to climate change by moving to different areas, adapting to new conditions, or going extinct. Ecological niche models have become established as an efficient and widely used method for interpolating (and sometimes extrapolating) species' distributions and offer an effective tool for identifying species conservation requirements and forecasting how global environmental changes may affect species distribution. How species respond to climate change is a key point for understanding their vulnerability and designing effective conservation strategies in the future. Thus, here, we assessed the impacts of climate change on the past and future distributions of two phylogenetically related species, Myotis ruber and Myotis keaysi. The results showed that the species are influenced by changes in temperature, and for M. ruber, precipitation also becomes important. Furthermore, M. ruber appears to have been more flexible to decreases in temperature that occurred in the past, which allowed it to expand its areas of environmental suitability, unlike M. keaysi, which decreased and concentrated these areas. However, despite a drastic decrease in the spatial area of environmental suitability of these species in the future, there are areas of potential climate stability that have been maintained since the Pleistocene, indicating where conservation efforts need to be concentrated in the future.

Confirming the presence of Lasiurusfrantzii (Peters, 1870) (Chiroptera, Vespertilionidae) in South America: more questions than answers

The western or desert red bat, Lasiurusfrantzii, is a cryptic insectivore species distributed in the Neotropics from Mexico south through Central America to Panama. L.frantzii was long considered a subspecies of the red bat, Lasiurusblossevillii, but recently it was elevated to full-species status based on genetic information. Here we present evidence of the presence of L.frantzii in the Andean Region of Colombia, confirming the species' presence in South America; the new record, from 3836 m a.s.l., is also the highest elevation known for the species. We suggest that L.frantzii might be widely distributed in trans-Andean areas of Colombia, Ecuador, Venezuela, and perhaps Peru and Bolivia. However, a review and exploration of additional morphological traits to identify the species are necessary because of the uncertainty of the distribution of L.frantzii.

Argentinean Myotis (Chiroptera, Vespertilionidae), including the description of a new species from the Yungas

Myotis is the most speciose genus of mammals in the world and recent taxonomic revisions have revealed an impressive diversity of species in South America. Even so, the phenotypic conservatism of some taxa makes taxonomic delimitation difficult. We perform a taxonomic review of Myotis from Argentina based on qualitative and quantitative morphological characters. Our results confirm the occurrence of 12 species (M. albescens, M. chiloensis, M. dinellii, M. izecksohni, M. keaysi, M. lavali, M. levis, M. nigricans, M. oxyotus, M. riparius, M. ruber, and M. cf. simus) and revealed an additional new species for the Yungas Forest. The new species is small to medium (forearm length ~ 35 mm) and can be distinguished from its congeners by a set of characters that includes forearm length, cranial measurements, discrete craniodental characters, and fur color. This review does not exhaust the need for new systematic studies with Argentinean Myotis, considering the possibility of occurrence of new species and the great morphological variation found for some complex taxa.

Catalogue of primary types of Neotropical Myotis (Chiroptera, Vespertilionidae)

Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Neotropical Myotis have an accentuated phenotypic conservatism, which makes species delimitation and identification difficult, hindering our understanding of the diversity, distribution, and phylogenetic relationships of taxa. To encourage new systematic reviews of the genus, a catalogue of the primary types and names is presented, current and in synonymy, for Neotropical Myotis. Currently 33 valid species (and three subspecies) are recognized, and their primary types are deposited in 12 scientific collections in the USA (30 types), Brazil (two types), England (two types), and France (one type). The names of 29 Neotropical Myotis species currently in synonymy were found. However, it is possible that some synonyms represent independent evolutionary lineages, considering recent results provided by taxonomic revisions.

Variation in the Myotis keaysi complex (Chiroptera, Vespertilionidae), with description of a new species from Ecuador

The genus Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Twenty-eight Neotropical species are currently recognized. In this study, we evaluate molecular and morphological variation in the M. keaysi complex, a high elevation clade of Neotropical myotine bats characterized by complex taxonomy and high morphological variation. A phylogeny inferred with cytochrome-b sequences recovered two clades composed of samples traditionally assigned to M. keaysi, with 9% of genetic divergence between them. These clades were also suggested as putative distinct species by molecular species delimitation methods. Qualitative and quantitative morphological analyses indicated a phenotypic discontinuity between specimens from central Andes (including the holotype of M. keaysi) and western lowlands of Ecuador, showing strong congruence between molecular and morphological approaches. We therefore describe a new species for the Tumbes-Choco-Magdalena region, documenting their external and cranial diagnostic characters by comparing them with other Neotropical species. In addition, we provide an emended diagnosis for our new concept of M. keaysi.

A new species of Myotis (Chiroptera, Vespertilionidae) from Uruguay

Abstract

The genus Myotis comprises a diverse group of vesper bats with worldwide distribution. Twenty-eight neotropical species are currently recognized. Based on a morphological approach, we describe a new species of Myotis from the Uruguayan Pampas grasslands, an ecoregion under high anthropogenic pressure with a largely unknown bat fauna. Qualitative and quantitative morphological analyses support the recognition of the new species and we present a set of external and cranial diagnostic characters by comparing them with other neotropical Myotis species. The new species reassembles Myotis riparius, but can be distinguished by a set of qualitative and quantitative morphological traits, including its clearly bicolored dorsal fur, tricolored ventral fur, a pelage on the dorsal surface of uropatagium, sagittal crest lower, braincase lower in lateral view and overall smaller size.

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.

Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies

Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.

The published complete mitochondrial genome of Eptesicus serotinus is a chimera of Vespertilio sinensis and Hypsugo alaschanicus (Mammalia: Chiroptera)

The mitogenome of Eptesicus serotinus (Serotine bat) was published in 2013 with GenBank accession number KF111725 and NCBI Reference Sequence number NC_022474. This sequence was placed with Vespertilio sinensis (Asian parti-colored bat) in a COI gene tree but with Hypsugo alashanicus (Alashanian pipistrelle) in a cytochrome b gene tree. Direct comparison of mitogenomes showed that 92.4% of this mitogenome is similar to Vespertilio sinensis, 5.9% to Hypsugo alaschanicus, and that 1.6% of the mitogenome could not be attributed to either species, or any other species. This mitogenome has been re-used in at least 17 phylogenies. Our findings suggest that mitogenomes are best verified with multiple gene trees, followed by direct comparison of sequences. We conclude that greater vigilance is warranted to ensure that problematic sequences do not enter the scientific record, and are not re-used in subsequent studies.

Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis) - A Genomics Approach

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here. https://doi.org/10.25387/g3.12173385

Genetic variation and relationships among Afrotropical species of Myotis (Chiroptera: Vespertilionidae)

The genus Myotis is nearly cosmopolitan and the second-most speciose genus of mammals, but its Afrotropical members are few and poorly known. We analyzed phylogenetic and phylogeographic relationships of six of the eight known Afrotropical species using Cytb and sequences from four nuclear introns. Using Bayesian and maximum-likelihood approaches to generate single-locus, concatenated, and species trees, we confirmed prior evidence that the clade containing Afrotropical Myotis also contains both Palearctic and Indomalayan members. Additionally, we demonstrate that M. bocagii is sister to the Indian Ocean species M. anjouanensis, that this group is sister to M. tricolor and the Palearctic M. emarginatus, and find evidence suggesting that M. welwitschii is the earliest-diverging Afrotropical species and sister to the remainder. Although M. tricolor and M. welwitschii are both currently regarded as monotypic, both mitochondrial and nuclear data sets document significant, largely concordant geographic structure in each. Evidence for the distinction of two lineages within M. tricolor is particularly strong. On the other hand, geographic structure is lacking in M. bocagii, despite the current recognition of two subspecies in that species. Additional geographic sampling (especially at or near type localities), finer-scale sampling (especially in zones of sympatry), and integrative taxonomic assessments will be needed to better document this radiation and refine its nomenclature.

New data on the bats (Chiroptera) of Martinique island (Lesser Antilles), with an emphasis on sexual dimorphism and sex ratios

For deciphering the biodiversity of native mammals on the island of Martinique (Lesser Antilles), bats (Chiroptera) were netted in various localities during the course of two separate studies spanning 2004–2015. A total of 2613 individuals were caught in ground-level mist nets at 79 localities. In this study, we concentrate on 1859 captures of nine species of bats caught at 24 capture-rich localities. We provide sex-ratio values, forearm and body weight measurements for each taxon. The order of decreasing abundance in captures was Artibeus jamaicensis, Sturnira angeli, Brachyphylla cavernarum, Monophyllus plethodon, Myotis martiniquensis, Molossus molossus, Ardops nichollsi, Pteronotus davyi and Tadarida brasiliensis. Our results suggest a strong sex-bias in capture rates, with males much more abundant for Ardops and Monophyllus, whereas females are more abundant for Molossus, Pteronotus and Sturnira. A clear sexual dimorphism exists with larger females in Ardops and Pteronotus, whereas males are larger in Molossus, Monophyllus and Sturnira. Reproductive females (pregnant, lactating) were found almost exclusively during the dry season (January to June) for A. jamaicensis, M. plethodon and S. angeli.

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.

Speciation with Gene Flow in North American Myotis Bats

Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification. In this investigation, we aim to infer the recent phylogenetic history of a clade of western long-eared bats while evaluating a number of different models that parameterize gene flow in a variety of ways. We utilize PHRAPL, a new tool for phylogeographic model selection, to compare the fit of a broad set of demographic models that include divergence, migration, or both among Myotis evotis, $M$. thysanodes and M. keenii. A genomic data set consisting of 808 loci of ultraconserved elements was used to explore such models in three steps using an incremental design where each successive set was informed by, and thus more focused than, the previous set of models. Specifically, the three steps were to (i) assess whether gene flow should be modeled and identify the best topologies, (ii) infer directionality of migration using the best topologies, and (iii) estimate the timing of gene flow. The best model (AIC model weight ${\sim}0.98$) included two divergence events (($M$. evotis, $M$. thysanodes), M. keenii) accompanied by gene flow at the initial stages of divergence. These results provide a striking example of speciation-with-gene-flow in an evolutionary lineage. [Myotis bats; PHRAPL; P2C2M; phylogeographic model selection; speciation with gene flow.].

Mitochondrial genome of Pteronotus personatus (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations

We described the complete mitochondrial genome (mitogenome) of the Wagner's mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.

Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest

Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied, particularly for taxa that are difficult to sample such as bats. Aiming to estimate the amount of cryptic diversity among bats of a Neotropical montane cloud forest in Talamanca Range-south-east Central America-, we performed a 15-night sampling campaign, which resulted in 90 captured bats belonging to 8 species. We sequenced their mitochondrial cytochrome c oxidase subunit I (COI) and screened their inter- and intraspecific genetic variation. Phylogenetic relations with conspecifics and closely related species from other geographic regions were established using Maximum Likelihood and Bayesian inference methods, as well as median-joining haplotype networks. Mitochondrial lineages highly divergent from hitherto characterized populations (> 9% COI dissimilarity) were found in Myotis oxyotus and Hylonycteris underwoodi. Sturnira burtonlimi and M. keaysi also showed distinct mitochondrial structure with sibling species and/or populations. These results suggest that mountains in the region hold a high degree of endemicity potential that has previously been ignored in bats. They also warn of the high extinction risk montane bats may be facing due to climatic change, particularly in isolated mountain systems like Talamanca Range.

Review of genetic diversification of bats in the Caribbean and biogeographic relationships to Neotropical species based on DNA barcodes

DNA barcoding is helping in discovering high levels of cryptic species and an underestimation of biodiversity in many groups of organisms. Although mammals are arguably the most studied and one of the least speciose taxonomic classes, the rate of species discovery is increasing and biased for small mammals on islands. An earlier study found bats in the Caribbean as a taxonomic and geographic deficiency in the International Barcode of Life initiative to establish a genetic reference database to enable specimen identification to species. Recent surveys in Dominican Republic, Jamaica, and Martinique have documented and barcoded half of the 58 bat species known from the Caribbean. I analyze all available barcode data of Caribbean bats to investigate biogeography and cryptic species in the Neotropical region. Analysis of the mitochondrial DNA gene cytochrome c oxidase subunit 1 results in a phylogenetic tree with all but one species as well-supported and reciprocally monophyletic. With a broader sampling across the Neotropics, there are also divergent lineages that exhibit biogeographic structuring: (i) a phylogenetic split between northern and southern Dominican Republic in three species, (ii) two taxa with cryptic species associated with higher degree of island endemism, (iii) populations of two widely distributed species with deep divergence between the Caribbean and North and Central America, and (iv) one species in the Caribbean with affinities to taxa in South America.

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.

Rolling-circle transposons catalyze genomic innovation in a mammalian lineage

Rolling-circle transposons (Helitrons) are a newly discovered group of mobile DNA widespread in plant and invertebrate genomes but limited to the bat family Vespertilionidae among mammals. Little is known about the long-term impact of Helitron activity because the genomes where Helitron activity has been extensively studied are predominated by young families. Here, we report a comprehensive catalog of vetted Helitrons from the 7× Myotis lucifugus genome assembly. To estimate the timing of transposition, we scored presence/absence across related vespertilionid genome sequences with estimated divergence times. This analysis revealed that the Helibat family has been a persistent source of genomic innovation throughout the vespertilionid diversification from approximately 30–36 Ma to as recently as approximately 1.8–6 Ma. This is the first report of persistent Helitron transposition over an extended evolutionary timeframe. These findings illustrate that the pattern of Helitron activity is akin to the vertical persistence of LINE retrotransposons in primates and other mammalian lineages. Like retrotransposition in primates, rolling-circle transposition has generated lineage-specific variation and accounts for approximately 110 Mb, approximately 6% of the genome of M. lucifugus. The Helitrons carry a heterogeneous assortment of host sequence including retroposed messenger RNAs, retrotransposons, DNA transposons, as well as introns, exons and regulatory regions (promoters, 5′-untranslated regions [UTRs], and 3′-UTRs) of which some are evolving in a pattern suggestive of purifying selection. Evidence that Helitrons have contributed putative promoters, exons, splice sites, polyadenylation sites, and microRNA-binding sites to transcripts otherwise conserved across mammals is presented, and the implication of Helitron activity to innovation in these unique mammals is discussed.

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera)

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear Rag 2 (1148 bp) genes were used to assess the evolutionary history of the cosmopolitan bat genus Myotis, based on a worldwide sampling of over 88 named species plus 7 species with uncertain nomenclature. Phylogenetic reconstructions of this comprehensive taxon sampling show that most radiation of species occurred independently within each biogeographic region. Our molecular study supports an early divergence of species from the New World, where all Nearctic and Neotropical species plus a lineage from the Palaearctic constitute a monophyletic clade, sister to the remaining Old World taxa. The major Old World clade includes all remaining Eurasian taxa, most Oriental species, one Oceanian, and all Ethiopian species. Another lineage, including M. latirostris from Taiwan, appears at the base of these two major biogeographic clades and, because it bears nyctalodont molars, could be considered as a distinct genus. However, this molar configuration is also found in crown-group species, indicating that these dental characters are variable in the genus Myotis and may confound interpretation of the fossil record. Molecular datings suggest an origin of all recent Myotis in the early Miocene (about 21MYA with 95% highest posterior density interval 23-20MYA). This period was characterized by a global climatic cooling that reduced the availability of tropical habitats and favoured the development of more temperate vegetation. This sharp climatic change might have triggered the evolution of Myotis in the Northern continents, because Myotis ancestors seem to have been well adapted and successful in such temperate habitats. Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

Hidden diversity in Senegalese bats and associated findings in the systematics of the family Vespertilionidae

INTRODUCTION

The Vespertilionidae is the largest family of bats, characterized by high occurrence of morphologically convergent groups, which impedes the study of their evolutionary history. The situation is even more complicated in the tropics, where certain regions remain under-sampled.

RESULTS

Two hundred and thirteen vespertilionid bats from Senegal (West Africa) were studied with the use of non-differentially stained karyotypes and multi-locus sequence data analysed with maximum likelihood and Bayesian methods. These bats were identified as 10 different taxa, five of which were distinctive from their nominate species (Pipistrellus hesperidus, Nycticeinops schlieffenii, Scotoecus hirundo, Neoromicia nana and N. somalica), based on both karyotypes and molecular data. These five cryptic taxa are unrelated, suggesting that these West African populations have long been isolated from other African regions. Additionally, we phylogenetically analysed 166 vespertilionid taxa from localities worldwide using GenBank data (some 80% of the genera of the family) and 14 representatives of closely related groups, together with our Senegalese specimens. The systematic position of several taxa differed from previous studies and the tribes Pipistrellini and Vespertilionini were redefined. The African Pipistrellus rueppellii was basal to the Pipistrellus/Nyctalus clade and the Oriental species Glischropus tylopus was basal to the East Asian pipistrelles within the tribe Pipistrellini. The African genus Neoromicia was confirmed to be diphyletic. Based on GenBank data, Eptesicus was polyphyletic, with the Asian E. nasutus and E. dimissus both supported as phylogenetically distinct from the Eptesicus clade. The subfamily Scotophilinae was confirmed as one of the basal branches of Vespertilionidae.

CONCLUSIONS

New taxa and new systematic arrangements show that there is still much to resolve in the vespertilionids and that West Africa is a biogeographic hotspot with more diversity to be discovered.