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.

Ultraconserved elements resolve phylogenetic relationships and biogeographic history of African-Malagasy bent-winged bats (Miniopterus)

African-Malagasy species of the bat genus Miniopterus are notable both for the dramatic increase in the number of newly recognized species over the last 15 years, as well as for the profusion of new taxa from Madagascar and the neighboring Comoros. Since 2007, seven new Malagasy Miniopterus species have been described compared to only two new species since 1936 from the Afrotropics. The conservative morphology of Miniopterus and limited geographic sampling in continental Africa have undoubtedly contributed to the deficit of continental species. In addition to uncertainty over species limits, phylogenetic relationships of Miniopterus remain mostly unresolved, particularly at deeper backbone nodes. Previous phylogenetic studies were based on limited taxon sampling and/or limited genetic sampling involving no more than five loci. Here, we conduct the first phylogenomic study of the Afrotropical Miniopteridae by analyzing up to 3772 genome-wide ultraconserved elements (UCEs) from historic and modern samples of 70 individuals from 25 Miniopterus species/lineages. We analyze multiple datasets of varying degrees of completeness (70, 90, and 100 percent complete) using partitioned concatenated maximum likelihood and multispecies coalescent methods. Our well-supported, species-level phylogenies resolved most (6/8 or 7/8) backbone nodes and strongly support for the first time the monophyly of the Malagasy radiation. We inferred the crown age of African Miniopteridae in the late Miocene (10.4 Ma), while the main lineages of Miniopterus appear to have contemporaneously diversified in two sister radiations in the Afrotropics and Madagascar. Species-level divergence of 23 of 25 African + Malagasy Miniopterus were estimated to have 95 % HPDs that overlap with the late Miocene (5.3-10.4 Ma). We present ancestral range estimates that unambiguously support a continental African radiation that originated in the Zambezian and Somalian/Ethiopian biogeographic regions, but we cannot rule out back colonization of Africa from Madagascar. The phylogeny indicates genetic support for up to seven new species.

Guild Vertical Stratification and Drivers of Bat Foraging in a Semi-Arid Tropical Region, Kenya

Africa faces significant challenges in reconciling economic and social development while preserving its natural resources. Little is known about the diverse bat community on the continent, particularly in drier ecosystems. A better understanding of the bat community will help improve and inform the management of these ecosystems. Our study aimed to provide detailed information on the main drivers of bat richness and activity at three different heights above the ground in a semi-arid region of Kenya. We assessed how bat activity varied with space and height using acoustic sampling and complementary methods. We sampled 48 sites at ground level and two sites on meteorological masts at 20 m and 35 m above the ground. We recorded more than 20 bat species, including one species of concern for conservation. Our models showed that the use of space varies with bat guild, creating trade-offs in the variables that affect their activity. Low-flying bat species are mostly associated with habitat variables, whereas high-flying species are more dependent on weather conditions. Our study highlights the richness of bat assemblages in semi-arid environments and emphasizes the need for management measures to protect bat diversity in the face of habitat degradation caused by climate change, land management, and development projects.

Nycteribiid bat flies (Arthropoda, Insecta, Diptera, Nycteribiidae) of Kenya

Bat flies (Diptera: Nycteribiidae and Streblidae) are hematophagous ectoparasites of bats characterized by viviparous pupiparity and generally high host specificity. Nycteribiid bat flies are wingless, morphologically constrained, and are most diverse in the Eastern Hemisphere. Africa hosts approximately 22% of global bat biodiversity and nearly one-third of all African bat species occur in Kenya, one of Africa's most bat-rich countries. However, records of nycteribiid bat fly diversity in Kenya remain sparse and unconsolidated. This paper combines all past species records of nycteribiid bat flies with records from a survey of 4,255 Kenyan bats across 157 localities between 2006 and 2015. A total of seven nycteribiid genera and 17 species are recorded, with seven species from the recent 'Bats of Kenya' surveys representing previously undocumented country records. Host associations and geographic distributions based on all available records are also described. This comprehensive species catalog addresses and further emphasizes the need for similar investigations of nycteribiid biodiversity across Africa.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Genetic, morphological and acoustic differentiation of African trident bats (Rhinonycteridae: Triaenops)

Rhinonycteridae (trident bats) are a small Palaeotropical family of insectivorous bats allied to Hipposideridae. Their taxonomy has been in a state of flux. Here, we use mitochondrial and nuclear sequences to evaluate species relationships, confirming the monophyly of both Triaenops and Paratriaenops. Although most Triaenops afer specimens are recovered as a group, mitochondrial analyses strongly support some Kenyan individuals as members of Triaenops persicus. Analyses of four nuclear introns (ACOX2, COPS7A, RODGI and STAT5A) strongly support the mitochondrial topology. Morphometric analysis of the skull, external morphology and echolocation calls confirm that the Triaenops from the Rift Valley in Kenya (Nakuru, Baringo and Pokot counties) are distinct from typical T. afer in coastal (Kilifi and Kwale counties) or interior (Laikipia and Makueni counties) colonies. We interpret these analyses to indicate that two species of Triaenops occur in East Africa: T. afer in coastal regions along the Indian Ocean and in the highlands of central Kenya and Ethiopia, and T. persicus in the Rift Valley of Kenya. Although they appear widely disjunct from Middle Eastern populations, Kenyan T. persicus might be more widely distributed in the Rift Valley; they are somewhat differentiated from Middle Eastern populations in terms of both cranial morphology and vocalizations.

A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species

Vespertilionidae (class Mammalia) constitutes the largest family of bats, with ~500 described species. Nonetheless, the systematic relationships within this family are poorly known, especially among the pipistrelle-like bats of the tribes Vespertilionini and Pipistrellini. Perhaps as a result of their drab pelage and lack of obvious morphological characters, the genus and species limits of pipistrelle-like bats remain poorly resolved, particularly in Africa, where more than one-fifth of all vesper bat species occur. Further exacerbating the problem is the accelerating description of new species within these groups. In this study, we attempt to resolve the systematic relationships among the pipistrelle-like bats of sub-Saharan Africa and Madagascar and provide a more stable framework for future systematic efforts. Our systematic inferences are based on extensive genetic and morphological sampling of > 400 individuals covering all named genera and the majority of described African pipistrelle-like bat species, focusing on previously unstudied samples of East African bats. Our study corroborates previous work by identifying three African genera in Pipistrellini (Pipistrellus, Scotoecus and Vansonia), none of which is endemic to Africa. However, the situation is more complex in Vespertilionini. With broad taxonomic sampling, we confirm that the genus Neoromicia is paraphyletic, a situation that we resolve by assigning the species of Neoromicia to four genera. Neoromicia is here restricted to Neoromicia zuluensis and allied taxa. Some erstwhile Neoromicia species are transferred into an expanded Laephotis, which now includes both long-eared and short-eared forms. We also erect two new genera, one comprising a group of mostly forest-associated species (many of which have white wings) and the other for the genetically and morphologically unique banana bat. All four of these genera, as recognized here, are genetically distinct, have distinctive bacular morphologies and can be grouped by cranial morphometrics. We also demonstrate that the genus Nycticeinops, until now considered monospecific, includes both Afropipistrellus and the recently named Parahypsugo, thus representing the fifth African genus in Vespertilionini. A sixth genus, Hypsugo, is mostly extra-limital to sub-Saharan Africa. Finally, we describe three new species of pipistrelle-like bats from Kenya and Uganda, uncovered during the course of systematic bat surveys in the region. Such surveys are greatly needed across tropical Africa to uncover further bat diversity.

A phylogeny for African Pipistrellus species with the description of a new species from West Africa (Mammalia: Chiroptera)

Pipistrelloid bats are among the most poorly known bats in Africa, a status no doubt exacerbated by their small size, drab brown fur and general similarity in external morphology. The systematic relationships of these bats have been a matter of debate for decades, and despite some recent molecular studies, much confusion remains. Adding to the confusion has been the recent discovery of numerous new species. Using two mitochondrial genes, we present a phylogeny for this group that supports the existence of three main clades in Africa: Pipistrellus, Neoromicia and the recently described Parahypsugo. However, the basal branches of the tree are poorly supported. Using an integrative taxonomic approach, we describe a new species of Pipistrellus sp. nov. from West Africa, which has been cited as Pipistrellus cf. grandidieri in the literature. We demonstrate that it is not closely related to Pipistrellus grandidieri from East Africa, but instead is sister to Pipistrellus hesperidus. Furthermore, the species Pi. grandidieri appears to be embedded in the newly described genus Parahypsugo, and is therefore better placed in that genus than in Pipistrellus. This has important taxonomic implications, because a new subgenus (Afropipistrellus) described for Pi. grandidieri predates Parahypsugo and should therefore be used for the entire “Parahypsugo” clade. The Upper Guinea rainforest zone, and particularly the upland areas in the south-eastern Guinea—northern Liberia border region may represent a global hotspot for pipistrelloid bats and should receive increased conservation focus as a result.

Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae)

The Old World leaf-nosed bats (Hipposideridae) are aerial and gleaning insectivores that occur throughout the Paleotropics. Both their taxonomic and phylogenetic histories are confused. Until recently, the family included genera now allocated to the Rhinonycteridae and was recognized as a subfamily of Rhinolophidae. Evidence that Hipposideridae diverged from both Rhinolophidae and Rhinonycteridae in the Eocene confirmed their family rank, but their intrafamilial relationships remain poorly resolved. We examined genetic variation in the Afrotropical hipposiderids Doryrhina, Hipposideros, and Macronycteris using relatively dense taxon-sampling throughout East Africa and neighboring regions. Variation in both mitochondrial (cyt-b) and four nuclear intron sequences (ACOX2, COPS, ROGDI, STAT5) were analyzed using both maximum likelihood and Bayesian inference methods. We used intron sequences and the lineage delimitation method BPP—a multilocus, multi-species coalescent approach—on supported mitochondrial clades to identify those acting as independent evolutionary lineages. The program StarBEAST was used on the intron sequences to produce a species tree of the sampled Afrotropical hipposiderids. All genetic analyses strongly support generic monophyly, with Doryrhina and Macronycteris as Afrotropical sister genera distinct from a Paleotropical Hipposideros; mitochondrial analyses interpose the genera Aselliscus, Coelops, and Asellia between these clades. Mitochondrial analyses also suggest at least two separate colonizations of Africa by Asian groups of Hipposideros, but the actual number and direction of faunal interchanges will hinge on placement of the unsampled African-Arabian species H.megalotis. Mitochondrial sequences further identify a large number of geographically structured clades within species of all three genera. However, in sharp contrast to this pattern, the four nuclear introns fail to distinguish many of these groups and their geographic structuring disappears. Various distinctive mitochondrial clades are consolidated in the intron-based gene trees and delimitation analyses, calling into question their evolutionary independence or else indicating their very recent divergence. At the same time, there is now compelling genetic evidence in both mitochondrial and nuclear sequences for several additional unnamed species among the Afrotropical Hipposideros. Conflicting appraisals of differentiation among the Afrotropical hipposiderids based on mitochondrial and nuclear loci must be adjudicated by large-scale integrative analyses of echolocation calls, quantitative morphology, and geometric morphometrics. Integrative analyses will also help to resolve the challenging taxonomic issues posed by the diversification of the many lineages associated with H.caffer and H.ruber.

Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals.

IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South-East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species-ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well-resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male-biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species-rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.

Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics

Background

The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history.

Results

We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups.

Conclusions

Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1485-1) contains supplementary material, which is available to authorized users.

New records of bats and terrestrial small mammals from the Seli River in Sierra Leone before the construction of a hydroelectric dam

Sierra Leone is situated at the western edge of the Upper Guinean Forests in West Africa, a recognised biodiversity hotspot which is increasingly threatened by habitat degradation and loss through anthropogenic impacts. The small mammal fauna of Sierra Leone is poorly documented, although bats and rodents account for the majority of mammalian diversity. Based on morphological, genetic and echolocation data, we recorded 30 bat (Chiroptera), three shrew (Soricomorpha) and eleven rodent (Rodentia) species at the Seli River in the north of the country in 2014 and 2016, during a baseline study for the Bumbuna Phase II hydroelectric project. In 2016, 15 bat species were additionally documented at the western fringe of the Loma Mountains, a recently established national park and biodiversity offset for the Bumbuna Phase I dam. Three bat species were recorded for the first time in Sierra Leone, raising the total number for the country to 61. Further, two bat species are threatened and endemic to the Upper Guinean Forest and several taxa of small mammals are poorly known or represent undescribed species. Overall, the habitats of the project area supported a species-rich small mammal fauna including species of global conservation concern. Suitable mitigation measures and/or offsets are necessary to maintain biodiversity and ecosystems in a region that is under high human pressure.

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.