Approximate Bayesian computation (ABC) techniques have seen rapid and accelerating development in biology, with applications including population genetics, systems biology, and community ecology (reviewed in Beaumont 2010;Csilléry et al. 2010). However, the approximations and model assumptions inherent in ABC can make model choice and parameter estimation problematic, and careful simulation-based validation and assessment of posterior predictive power are required (Gelman et al.

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.

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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.

Arboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades.

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.

The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.

Aim We investigate the Plio‐Pleistocene evolutionary history of one of the most abundant rodents in Afrotropical forests. Specifically, we ask how their diversification was influenced by climate change, topography and major rivers. Location Tropical Africa: Lower Guinea (including Cameroon volcanic line; CVL), Congolia, Albertine Rift (AR), Kenyan highlands (KH). Taxon Murine rodents of the Praomys jacksoni complex. Methods We used 849 genotyped individuals to describe the overall diversity and spatial genetic structure across a majority of their known distribution area. The combination of one mitochondrial and three nuclear markers was used to infer dated phylogenies using Bayesian and maximum likelihood approaches. Genetic structure was further assessed by multispecies coalescent species delimitation. Current and past distributions of particular taxa were predicted using environmental niche modelling. Results The complex is composed of five major genetic clades (proposed species). Two of them are restricted to specific habitat types (either montane forests of AR or wetlands in lowland forests along the Congo River), three others have wide geographic distributions and lower levels of ecological specialization. The earliest divergence is dated to the Plio‐Pleistocene boundary and is in accordance with the separation of AR forests and Guineo‐Congolian forests. Further diversification of the complex is associated with Pleistocene climate changes. Relatively stable refugia of suitable climatic conditions were identified in lowland Congolia (for two species currently distributed only in lowland forests) as well as in montane forests of CVL, AR, KH (playing the role of reservoirs of diversity). Large rivers, especially the Congo River, are important barriers to gene flow for most taxa, but probably were not the primary cause of differentiation. Main conclusions The evolutionary history of the complex was primarily affected by Pleistocene climate changes and diversification in forest refugia. There is little support for ecological parapatric speciation or the riverine barrier hypothesis.