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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., We investigated genetic variation, clade membership, and phylogenetic relationships in the bat family Nycteridae with broad sampling across Africa. At least 16 deeply divergent monophyletic lineages were recovered in both gene tree and species tree analyses. Genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. A large number of clades are distributed wholly or partly in East Africa (10/16 clades), suggesting Nycteris diversity has been historically underestimated.

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.

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.

BackgroundFree-tailed bats of the genusOtomopsare poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species ofOtomopswere recognized in continental Africa:Otomops martiensseni(Matschie, 1897) in southern, central and western Africa, and the new speciesO. harrisoniRalph et al., 2015 in the northeast and in Yemen.MethodsWe collected additional samples ofOtomopsin Kenya and Rwanda where the ranges of these taxa approach one another to clarify their geographic ranges and taxonomic status. Mitochondrial and nuclear intron sequences served to identify and delimit species; we also documented their echolocation call variation and ectoparasite complements.ResultsOtomops martiensseni, the southern African species, was documented in northern Kenya in Marsabit National Park.O. harrisoni, the northeastern African–Arabian species, was documented in southern Kenya and in a cave in Musanze District, Rwanda. Moreover, individuals of both species were found together at the Musanze cave, establishing them in precise spatial and temporal sympatry. Analyses of mitochondrial and nuclear loci identify no evidence of admixture between these forms, although available samples limit the power of this analysis. Echolocation call differences are also apparent among the three localities we analyzed. Three orders of insects and two families of mites are newly reported as ectoparasites ofO. harrisoni.DiscussionOur results corroborate species rank forO. harrisoniand establish a zone of potential geographic overlap withO. martienssenispanning at least 800 km of latitude. The new records establish the species in sympatry in northern Rwanda and add an additional species to the bat faunas of both Kenya and Rwanda. Future studies are needed to understandOtomopsroosting requirements and movements, thereby explaining the paucity of known colonies and yielding better estimates of their conservation status. The discovery of mixed roosting associations in Rwanda invites further investigation.