African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats

Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.

A systematic review on current approaches in bat virus discovered between 2018 and 2022

Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.

Southern Africa's Great Escarpment as an amphitheater of climate-driven diversification and a buffer against future climate change in bats

Hosting 1460 plant and 126 vertebrate endemic species, the Great Escarpment (hereafter, Escarpment) forms a semi-circular "amphitheater" of mountains girdling southern Africa from arid west to temperate east. Since arid and temperate biota are usually studied separately, earlier studies overlooked the biogeographical importance of the Escarpment as a whole. Bats disperse more widely than other mammalian taxa, with related species and intraspecific lineages occupying both arid and temperate highlands of the Escarpment, providing an excellent model to address this knowledge gap. We investigated patterns of speciation and micro-endemism from modeled past, present, and future distributions in six clades of southern African bats from three families (Rhinolophidae, Cistugidae, and Vespertilionidae) having different crown ages (Pleistocene to Miocene) and biome affiliations (temperate to arid). We estimated mtDNA relaxed clock dates of key divergence events across the six clades in relation both to biogeographical features and patterns of phenotypic variation in crania, bacula and echolocation calls. In horseshoe bats (Rhinolophidae), both the western and eastern "arms" of the Escarpment have facilitated dispersals from the Afrotropics into southern Africa. Pleistocene and pre-Pleistocene "species pumps" and temperate refugia explained observed patterns of speciation, intraspecific divergence and, in two cases, mtDNA introgression. The Maloti-Drakensberg is a center of micro-endemism for bats, housing three newly described or undescribed species. Vicariance across biogeographic barriers gave rise to 29 micro-endemic species and intraspecific lineages whose distributions were congruent with those identified in other phytogeographic and zoogeographic studies. Although Köppen-Geiger climate models predict a widespread replacement of current temperate ecosystems in southern Africa by tropical or arid ecosystems by 2070-2100, future climate Maxent models for 13 bat species (all but one of those analyzed above) showed minimal range changes in temperate species from the eastern Escarpment by 2070, possibly due to the buffering effect of mountains to climate change.

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.

A dataset on African bats' functional traits

Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.

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.

Ancestral African Bats Brought Their Cargo of Pathogenic Leptospira to Madagascar under Cover of Colonization Events

Madagascar is home to an extraordinary diversity of endemic mammals hosting several zoonotic pathogens. Although the African origin of Malagasy mammals has been addressed for a number of volant and terrestrial taxa, the origin of their hosted zoonotic pathogens is currently unknown. Using bats and Leptospira infections as a model system, we tested whether Malagasy mammal hosts acquired these infections on the island following colonization events, or alternatively brought these bacteria from continental Africa. We first described the genetic diversity of pathogenic Leptospira infecting bats from Mozambique and then tested through analyses of molecular variance (AMOVA) whether the genetic diversity of Leptospira hosted by bats from Mozambique, Madagascar and Comoros is structured by geography or by their host phylogeny. This study reveals a wide diversity of Leptospira lineages shed by bats from Mozambique. AMOVA strongly supports that the diversity of Leptospira sequences obtained from bats sampled in Mozambique, Madagascar, and Comoros is structured according to bat phylogeny. Presented data show that a number of Leptospira lineages detected in bat congeners from continental Africa and Madagascar are imbedded within monophyletic clades, strongly suggesting that bat colonists have indeed originally crossed the Mozambique Channel while infected with pathogenic Leptospira.

A new Pipistrelle bat from the oceanic Island of Príncipe (Western Central Africa)

We describe a population of pipistrelle-like bats from Príncipe Island (Gulf of Guinea, Western Central Africa) as a new species based on the molecular and morphological characteristics of six specimens collected more than 30 years ago. The description of this new species was not possible until the traditionally entangled systematics of the whole pipistrelle group was clarified in recent years with the inclusion of molecular techniques and adequate species sampling. In this new taxonomic framework, the new species was clearly included within the dark-winged group of the recently described genus Pseudoromicia. The pipistrelles from Príncipe Island present a moderately inflated skull in lateral view with inner upper incisors that are moderately bicuspids and a baculum distinctly long with expanded tips. Besides these morphological characters, the new bat species is distinguished by its dwarfism, being the smallest species recognized within the genus. The ecology and conservation status of this endemic island species are unknown and field studies are urgently needed to evaluate the situation and conservation threats to this new species in its natural habitat.

Integrative taxonomic analysis of new collections from the central Angolan highlands resolves the taxonomy of African pipistrelloid bats on a continental scale

Ten years ago, the genus-level and species-level taxonomy of African pipistrelloid bats was in a state of flux. In spite of advances in the past decade, gaps in collecting from species-rich regions like Angola have hampered efforts to revise this group. We report on new collections of pipistrelle-like bats from the poorly sampled central highlands of Angola (1000–1500 m a.s.l.) as well as comparative material from lower-lying areas of Eswatini and South Africa. Specimens identified as Neoromicia anchietae, collected 400–700 km east of the holotype locality in the western highlands of Angola, were genetically and morphologically distinctive from N. anchietae s.l. from South Africa and Eswatini. We describe herein this latter lineage as a distinct species from low-lying areas of south-eastern Africa, distinct from N. anchietae s.s., which is therefore restricted to the central and western Angolan highlands. We also identified shallow to deep genetic divergence between different African regions in other recognized pipistrelloid species, such as conspecificity between the long-eared species Laephotis angolensis from Angola and Laephotis botswanae from northern Botswana, northern Namibia and south-western Zambia. Our phylogeny supports a recently proposed generic classification of African pipistrelloid bats.

Patterns of Bat Diversity in an Undisturbed Forest and Forest Mosaic Habitats of the Afromontane Forest Biome of Western Cameroon

Anthropogenic activities continue to degrade natural montane ecosystems globally. Bats communities are altered by these changes. We analyzed how bats are affected by human-induced habitat changes by comparing the bat species diversity and functional diversity in undisturbed forest habitats and disturbed forest habitats of the Afromontane biome of Cameroon. We recorded 244 individuals from 13 species in the undisturbed forest, while 233 individuals from 16 species were recorded in the disturbed forest. Bat diversity was higher in disturbed habitats (D = 0.84) than undisturbed habitats (D = 0.67). Jackknife 1 species richness estimator suggests 21.53 species for the disturbed forest and 19.30 in the undisturbed forest. Closed-space forager insectivorous bats made up nearly half of the species in the undisturbed forest, but this dropped to 25% in the disturbed forest, meanwhile, edge-space foragers increased in the disturbed forest. Bat community analyses by ordination revealed a distinct bat community composition between the two forest types, demonstrated as a significant difference in diversity between the two forest types. The distribution of Rousettus aegyptiacus, Myonycteris angolensis, Hipposideros cf. ruber, and Micropteropus pusillus contribute the most to the difference in bat community composition between the two forest types. Edge and open-space species were likely to benefit from additional resources provided by the disturbed area, by expanding their range and distribution. However, this may not compensate for the decline in the population of forest species caused by the loss of pristine forests, thus measures to conserve montane forest remnants should be of utmost significance.

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.

Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.

Diversity, distribution, and drivers of Polychromophilus infection in Malagasy bats

Background

Numerous studies have been undertaken to advance knowledge of apicomplexan parasites infecting vertebrates, including humans. Of these parasites, the genus Plasmodium has been most extensively studied because of the socio-economic and public health impacts of malaria. In non-human vertebrates, studies on malaria or malaria-like parasite groups have been conducted but information is far from complete. In Madagascar, recent studies on bat blood parasites indicate that three chiropteran families (Miniopteridae, Rhinonycteridae, and Vespertilionidae) are infected by the genus Polychromophilus with pronounced host specificity: Miniopterus spp. (Miniopteridae) harbour Polychromophilus melanipherus and Myotis goudoti (Vespertilionidae) is infected by Polychromophilus murinus. However, most of the individuals analysed in previous studies were sampled on the western and central portions of the island. The aims of this study are (1) to add new information on bat blood parasites in eastern Madagascar, and (2) to highlight biotic and abiotic variables driving prevalence across the island.

Methods

Fieldworks were undertaken from 2014 to 2016 in four sites in the eastern portion of Madagascar to capture bats and collect biological samples. Morphological and molecular techniques were used to identify the presence of haemosporidian parasites. Further, a MaxEnt modelling was undertaken using data from Polychromophilus melanipherus to identify variables influencing the presence of this parasite

Results

In total, 222 individual bats belonging to 17 species and seven families were analysed. Polychromophilus infections were identified in two families: Miniopteridae and Vespertilionidae. Molecular data showed that Polychromophilus spp. parasitizing Malagasy bats form a monophyletic group composed of three distinct clades displaying marked host specificity. In addition to P. melanipherus and P. murinus, hosted by Miniopterus spp. and Myotis goudoti, respectively, a novel Polychromophilus lineage was identified from a single individual of Scotophilus robustus. Based on the present study and the literature, different biotic and abiotic factors are shown to influence Polychromophilus infection in bats, which are correlated based on MaxEnt modelling.

Conclusions

The present study improves current knowledge on Polychromophilus blood parasites infecting Malagasy bats and confirms the existence of a novel Polychromophilus lineage in Scotophilus bats. Additional studies are needed to obtain additional material of this novel lineage to resolve its taxonomic relationship with known members of the genus. Further, the transmission mode of Polychromophilus in bats as well as its potential effect on bat populations should be investigated to complement the results provided by MaxEnt modelling and eventually provide a comprehensive picture of the biology of host-parasite interactions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03696-0.

Small mammals of a West African hotspot, the Ziama-Wonegizi-Wologizi transfrontier forest landscape

The Upper Guinea rainforest zone in West Africa is considered a biodiversity hotspot and contains important habitats for threatened and endemic mammals, yet this region remains poorly known particularly for small mammals. The aim of this study was to survey small mammals in a Liberian and Guinean cross-border conservation area, the Ziama-Wonegizi-Wologizi landscape. We recorded a total of 52 small mammal species, including 26 bats, 15 rodents, 10 shrews, one otter-shrew, of which one rodent species was new to science (Colomys sp. nov.). We also documented the first country records of the bats Chaerephon aloysiisabaudiae, Pseudoromicia brunnea and Pipistrellus inexspectatus from Guinea, and the shrews Crocidura douceti and Crocidura grandiceps from Liberia. Furthermore, we recorded the recently described bat Nycticeinops happoldorum from Wologizi and Ziama, and we documented the presence of Micropotamogale lamottei at Wologizi, which represents the fourth known locality for this globally threatened species. Finally, the forests of Wologizi and Ziama support numerous threatened species. The results of our survey demonstrate the importance of this region for small mammals and support the creation of a transboundary protected area that will encompass the entire forest landscape.