Toward solving the global green-green dilemma between wind energy production and bat conservation

Wind energy production is growing rapidly worldwide in an effort to reduce greenhouse gas emissions. However, wind energy production is not environmentally neutral. Negative impacts on volant animals, such as bats, include fatalities at turbines and habitat loss due to land-use change and displacement. Siting turbines away from ecologically sensitive areas and implementing measures to reduce fatalities are critical to protecting bat populations. Restricting turbine operations during periods of high bat activity is the most effective form of mitigation currently available to reduce fatalities. Compensating for habitat loss and offsetting mortality are not often practiced, because meaningful offsets are lacking. Legal frameworks to prevent or mitigate the negative impacts of wind energy on bats are absent in most countries, especially in emerging markets. Therefore, governments and lending institutions are key in reconciling wind energy production with biodiversity goals by requiring sufficient environmental standards for wind energy projects.

Kenyan Free-Tailed Bats Demonstrate Seasonal Birth Pulse Asynchrony with Implications for Virus Maintenance

Ecological information on wildlife reservoirs is fundamental for research targeting prevention of zoonotic infectious disease, yet basic information is lacking for many species in global hotspots of disease emergence. We provide the first estimates of synchronicity, magnitude, and timing of seasonal birthing in Mops condylurus, a putative ebolavirus host, and a co-roosting species, Mops pumilus (formerly Chaerephon pumilus). We show that population-level synchronicity of M. condylurus birthing is wide (~ 8.5 weeks) and even wider in M. pumilus (> 11 weeks). This is predicted to promote the likelihood of filovirus persistence under conditions of bi-annual birthing (two births per year). Ecological features underlying the magnitude of the birth pulse-relative female abundance (higher than expected for M. condylurus and lower for M. pumilus, based on literature) and reproductive rate (lower than expected)-will have countering effects on birthing magnitude. Species-specific models are needed to interpret how identified birth pulse attributes may interact with other features of molossid ebolavirus ecology to influence infection dynamics. As a common feature of wildlife species, and a key driver of infection dynamics, detailed information on seasonal birthing will be fundamental for future research on these species and will be informative for bat-borne zoonoses generally.

The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

Frequent and intense human-bat interactions occur in buildings of rural Kenya

Simultaneous use of domestic spaces by humans and wildlife is little understood, despite global ubiquity, and can create an interface for human exposure to wildlife pathogens. Bats are a pervasive synanthropic taxon and are associated with several pathogens that can spill over and cause disease in humans. Urbanization has destroyed much natural bat habitat and, in response, many species increasingly use buildings as roosts. The purpose of this study was to characterize human interactions with bats in shared buildings to assess potential for human exposure to and spillover of bat-borne pathogens. We surveyed 102 people living and working in buildings used as bat roosts in Taita-Taveta county, Kenya between 2021 and 2023. We characterized and quantified the duration, intensity, and frequency of human-bat interactions occurring in this common domestic setting. Survey respondents reported living with bats in buildings year-round, with cohabitation occurring consistently for at least 10 years in 38% of cases. Human contact with bats occurred primarily through direct and indirect routes, including exposure to excrement (90% of respondents), and direct touching of bats (39% of respondents). Indirect contacts most often occurred daily, and direct contacts most often occurred yearly. Domestic animal consumption of bats was also reported (16% of respondents). We demonstrate that shared building use by bats and humans in rural Kenya leads to prolonged, frequent, and sometimes intense interactions between bats and humans, consistent with interfaces that can facilitate exposure to bat pathogens and subsequent spillover. Identifying and understanding the settings and practices that may lead to zoonotic pathogen spillover is of great global importance for developing countermeasures, and this study establishes bat roosts in buildings as such a setting.

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.

Roost selection by synanthropic bats in rural Kenya: implications for human-wildlife conflict and zoonotic pathogen spillover

Many wildlife species are synanthropic and use structures built by humans, creating a high-risk interface for human-wildlife conflict and zoonotic pathogen spillover. However, studies that investigate features of urbanizing areas that attract or repel wildlife are currently lacking. We surveyed 85 buildings used by bats and 172 neighbouring buildings unused by bats (controls) in southeastern Kenya during 2021 and 2022 and evaluated the role of microclimate and structural attributes in building selection. We identified eight bat species using buildings, with over 25% of building roosts used concurrently by multiple species. Bats selected taller cement-walled buildings with higher water vapour pressure and lower presence of permanent human occupants. However, roost selection criteria differed across the most common bat species: molossids selected structures like those identified by our main dataset whereas Cardioderma cor selected buildings with lower presence of permanent human occupants. Our results show that roost selection of synanthropic bat species is based on specific buildings attributes. Further, selection criteria that facilitate bat use of buildings are not homogeneous across species. These results provide information on the general mechanisms of bat-human contact in rural settings, as well as specific information on roost selection for synanthropic bats in urbanizing Africa.

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.

Our good neighbors: Understanding ecosystem services provided by insectivorous bats in Rwanda

Bats are prodigious consumers of agricultural and forest pests, and are, therefore, a natural asset for agricultural productivity, suppressing populations of such pests. This study provides baseline information of diet of 143 bats belonging to eight insectivorous bat species from agricultural areas of Rwanda while evaluating the effectiveness of bats as pest suppressors. Using DNA metabarcoding to analyze bat fecal pellets, 85 different insect species were detected, with 60% (n = 65), 64% (n = 11) and 78% (n = 9) found to be agricultural pests from eastern, northern and western regions, respectively. Given the high percentages of agricultural pests detected, we submit that Rwandan insectivorous bats have the capacity for biocontrol of agricultural pests. Rwandan bat populations should be protected and promoted since they may foster higher crop yields and sustainable livelihoods.

No Substantial Histopathologic Changes in Mops condylurus Bats Naturally Infected with Bombali Virus, Kenya

We found similar mild perivascular inflammation in lungs of Bombali virus-positive and -negative Mops condylurus bats in Kenya, indicating the virus is well-tolerated. Our findings indicate M. condylurus bats may be a reservoir host for Bombali virus. Increased surveillance of these bats will be important to reduce potential virus spread.

A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats

BACKGROUND AND METHODS

To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.

RESULTS

Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.

CONCLUSIONS

Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.

Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data

BACKGROUND

The recognition and delineation of morphologically indistinguishable cryptic species can have broad implications for wildlife conservation, disease ecology and accurate estimates of biodiversity. Parasites are intriguing in the study of cryptic speciation because unique evolutionary pressures and diversifying factors are generated by ecological characteristics of host-parasite relationships, including host specificity. Bat flies (Diptera: Nycteribiidae and Streblidae) are obligate, hematophagous ectoparasites of bats that generally exhibit high host specificity. One rare exception is Penicillidia fulvida (Diptera: Nycteribiidae), an African bat fly found in association with many phylogenetically distant hosts. One explanation for P. fulvida's extreme polyxeny is that it may represent a complex of host-specific yet cryptic species, an increasingly common finding in molecular genetic studies of supposed generalist parasites.

METHODS

A total of 65 P. fulvida specimens were collected at 14 localities across Kenya, from bat species representing six bat families. Mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear 28S ribosomal RNA (rRNA) sequences were obtained from 59 specimens and used to construct Bayesian and maximum likelihood phylogenies. Analysis of molecular variance was used to determine how genetic variation in P. fulvida was allocated among host taxa.

RESULTS

The 28S rRNA sequences studied were invariant within P. fulvida. Some genetic structure was present in the COI sequence data, but this could be more parsimoniously explained by geography than host family.

CONCLUSIONS

Our results support the status of P. fulvida as a rare example of a single bat fly species with primary host associations spanning multiple bat families. Gene flow among P. fulvida utilizing different host species may be promoted by polyspecific roosting behavior in bats, and host preference may also be malleable based on bat assemblages occupying shared roosts. The proclivity of generalist parasites to switch hosts makes them more likely to vector or opportunistically transmit pathogens across host species boundaries. Consequently, the presence of polyxenous bat flies is an important consideration to disease ecology as bat flies become increasingly known to be associated with bat pathogens.

The future of zoonotic risk prediction

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya, 2019

Previously identified only in Sierra Leone, Guinea, and southeastern Kenya, Bombali virus–infected Mops condylurus bats were recently found »750 km away in western Kenya. This finding supports the role of M. condylurus bats as hosts and the potential for Bombali virus circulation across the bats’ range in sub-Saharan Africa.

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.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

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.

Volunteer based approach to dog vaccination campaigns to eliminate human rabies: Lessons from Laikipia County, Kenya

BACKGROUND

An estimated 59,000 people die from rabies annually, with 99% of those deaths attributable to bites from domestic dogs (Canis lupus familiaris). This preventable Neglected Tropical Disease has a large impact across continental Africa, especially for rural populations living in close contact with livestock and wildlife. Mass vaccinations of domestic dogs are effective at eliminating rabies but require large amounts of resources, planning, and political will to implement. Grassroots campaigns provide an alternative method to successful implementation of rabies control but remain understudied in their effectiveness to eliminate the disease from larger regions.

METHODOLOGY/PRINCIPAL FINDINGS

We report on the development, implementation, and effectiveness of a grassroots mass dog rabies vaccination campaign in Kenya, the Laikipia Rabies Vaccination Campaign. During 2015-2017, a total of 13,155 domestic dogs were vaccinated against rabies in 17 communities covering approximately 1500 km2. Based on an estimated population size of 34,275 domestic dogs, percent coverages increased across years, from 2% in 2015 to 24% in 2017, with only 3 of 38 community-years of vaccination exceeding the 70% target. The average cost of vaccinating an animal was $3.44 USD with in-kind contributions and $7.44 USD without in-kind contributions.

CONCLUSIONS/SIGNIFICANCE

The evolution of the Laikipia Rabies Vaccination Campaign from a localized volunteer-effort to a large-scale program attempting to eliminate rabies at the landscape scale provides a unique opportunity to examine successes, failures, and challenges facing grassroots campaigns. Success, in the form of vaccinating more dogs across the study area, was relatively straightforward to achieve. However, lack of effective post-vaccination monitoring and education programs, limited funding, and working in diverse community types appeared to hinder achievement of 70% coverage levels. These results indicate that grassroots campaigns will inevitably be faced with a philosophical question regarding the value of local impacts versus their contributions to a larger effort to eliminate rabies at the regional, country, or global scale.

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.

Bombali Virus in Mops condylurus Bat, Kenya

Bombali virus (genus Ebolavirus) was identified in organs and excreta of an Angolan free-tailed bat (Mops condylurus) in Kenya. Complete genome analysis revealed 98% nucleotide sequence similarity to the prototype virus from Sierra Leone. No Ebola virus–specific RNA or antibodies were detected from febrile humans in the area who reported contact with bats.

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.

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.

An annotated checklist of mammals of Kenya

Kenya has a rich mammalian fauna. We reviewed recently published books and papers including the six volumes of Mammals of Africa to develop an up-to-date annotated checklist of all mammals recorded from Kenya. A total of 390 species have been identified in the country, including 106 species of rodents, 104 species of bats, 63 species of even-toed ungulates (including whales and dolphins), 36 species of insectivores and carnivores, 19 species of primates, five species of elephant shrews, four species of hyraxes and odd-toed ungulates, three species of afrosoricids, pangolins, and hares, and one species of aardvark, elephant, sirenian and hedgehog. The number of species in this checklist is expected to increase with additional surveys and as the taxonomic status of small mammals (e.g., bats, shrews and rodents) becomes better understood.

On the taxonomic status and distribution of African species of Otomops (Chiroptera: Molossidae)

Background

Free-tailed bats of the genus Otomops are poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species of Otomops were recognized in continental Africa: Otomops martiensseni (Matschie, 1897) in southern, central and western Africa, and the new species O. harrisoniRalph et al., 2015 in the northeast and in Yemen.

Methods

We collected additional samples of Otomops in 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.

Results

Otomops 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 of O. harrisoni.

Discussion

Our results corroborate species rank for O. harrisoni and establish a zone of potential geographic overlap with O. martiensseni spanning 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 understand Otomops roosting 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.

Testing the Sensory Drive Hypothesis: Geographic variation in echolocation frequencies of Geoffroy's horseshoe bat (Rhinolophidae: Rhinolophus clivosus)

Geographic variation in sensory traits is usually influenced by adaptive processes because these traits are involved in crucial life-history aspects including orientation, communication, lineage recognition and mate choice. Studying this variation can therefore provide insights into lineage diversification. According to the Sensory Drive Hypothesis, lineage diversification may be driven by adaptation of sensory systems to local environments. It predicts that acoustic signals vary in association with local climatic conditions so that atmospheric attenuation is minimized and transmission of the signals maximized. To test this prediction, we investigated the influence of climatic factors (specifically relative humidity and temperature) on geographic variation in the resting frequencies of the echolocation pulses of Geoffroy's horseshoe bat, Rhinolophus clivosus. If the evolution of phenotypic variation in this lineage tracks climate variation, human induced climate change may lead to decreases in detection volumes and a reduction in foraging efficiency. A complex non-linear interaction between relative humidity and temperature affects atmospheric attenuation of sound and principal components composed of these correlated variables were, therefore, used in a linear mixed effects model to assess their contribution to observed variation in resting frequencies. A principal component composed predominantly of mean annual temperature (factor loading of -0.8455) significantly explained a proportion of the variation in resting frequency across sites (P < 0.05). Specifically, at higher relative humidity (around 60%) prevalent across the distribution of R. clivosus, increasing temperature had a strong negative effect on resting frequency. Climatic factors thus strongly influence acoustic signal divergence in this lineage, supporting the prediction of the Sensory Drive Hypothesis. The predicted future increase in temperature due to climate change is likely to decrease the detection volume in echolocating bats and adversely impact their foraging efficiency.