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Benda, Petr, Uvizl, Marek, Vallo, Peter, Reiter, Antonín, Uhrin, Marcel (2022): A revision of the Rhinolophus hipposideros group (Chiroptera: Rhinolophidae) with definition of an additional species from the Middle East. Acta Chiropterologica 24 (2): 269-298, DOI: 10.3161/15081109ACC2022.24.2.001

Many studies have demonstrated the importance of symbiotic microbial communities for the host with beneficial effects for nutrition, development, and the immune system. The majority of these studies have focused on bacteria residing in the gastrointestinal tract, while the fungal community has often been neglected. Gut anaerobic fungi of the class Neocallimastigomycetes are a vital part of the intestinal microbiome in many herbivorous animals and their exceptional abilities to degrade indigestible plant material means that they contribute significantly to fermentative processes in the enteric tract. Gorillas rely on a highly fibrous diet and depend on fermentative microorganisms to meet their daily energetic demands. To assess whether Neocallimastigomycetes occur in gorillas we analyzed 12 fecal samples from wild Western lowland gorillas (Gorilla gorilla gorilla) from Dzanga–Sangha Protected Areas, Central African Republic, and subjected potential anaerobic fungi sequences to phylogenetic analysis. The clone library contained ITS1 fragments that we related to 45 different fungi clones. Of these, 12 gastrointestinal fungi in gorillas are related to anaerobic fungi and our phylogenetic analyses support their assignment to the class Neocallimastigomycetes. As anaerobic fungi play a pivotal role in plant fiber degradation in the herbivore gut, gorillas might benefit from harboring these particular fungi with regard to their nutritional status. Future studies should investigate whether Neocallimastigomycetes are also found in other nonhuman primates with high fiber intake, which would also benefit from having such highly efficient fermentative microbes.

Noack's round-leaf bat Hipposideros cf. ruber is widely distributed in sub-Saharan Africa. Here, we present some aspects of its ecology from two caves in central Ghana. Our main objective was to assess the nightly and annual flight activity and to examine the influences of ambient temperature on flight activity. We tested the hypothesis that flight activity of the species is concentrated at certain periods of the night and the year using mist-netting data from 2,712 captured bats. We found no evidence for annual fluctuations in flight activity, probably due to no distinct seasonal limitation of food resources, no migration, and the lack of extreme environmental conditions in the study area. Our hypothesis of concentrated nightly flight activity was confirmed for one cave but not for the other. Flight activity was concentrated early in the night (20:00, 21:00 and 22:00 hours) at one cave, possibly to take advantage of locally available early active prey insects, while it was uniformly distributed throughout the night at the other. Lastly, we found a reduction in the flight activity of H. cf. ruber when there was a distinct drop in temperature over the night. We therefore suggest the reduction in flight activity may result from the direct effects of temperature on prey abundance as the bats responded by reducing activity to avoid excessive prey search costs.

Several house bat specimens superficially resembling the white-bellied house bat Scotophilus leucogaster (Cretzschmar, 1830), were recently captured in southwestern Ethiopia and southern South Sudan. These S . cf. leucogaster differed from typical S. leucogaster by their slightly smaller size and ventral coloration, conforming instead with the original description of S . altilis Allen, 1914. Scotophilus altilis is an overlooked taxon known from the Blue Nile region in Sudan that is currently considered a junior synonym of S . leucogaster . Phylogenetic analysis of mitochondrial cytochrome b gene ( cytb ) sequences revealed S . cf. leucogaster as a sister clade to S . leucogaster with a genetic distance of ca. 10%. Comparative specimens of questionable S . nigritellus de Winton, 1899 from northwestern Ethiopia and a wing biopsy sample of another S . cf. leucogaster from western Kenya also fell within this clade. Sequence data from two nuclear markers ( zfy and fgb7 ) corroborated the distinction of S . cf. leucogaster from S . leucogaster . Likewise, morphometric analysis of cranial data largely supported this distinction, as well as taxonomic affiliation with S . altilis based on comparison with the only available paratype specimen. The position of this paratype specimen within the new Scotophilus clade, inferred from analysis of a short fragment of cytb , confirmed its taxonomic identity. Based on the presented evidence, the overlooked East African taxon S. altilis should be resurrected as a full species within the genus Scotophilus .

Background Ghana is one of the six bat diversity hotspots on the African continent, yet its caves have not been fully explored for the bats they host. Research Aims We aimed to assess the species composition and diversity of five caves in central Ghana and identified those needing immediate conservation attention. Methods Using mist-nets, we captured bats over 102 full nights between October 2010 and July 2012 from the Upper Guinean forest and Savannah regions in central Ghana. Results A total of 10,226 bats belonging to nine species were recorded. PERMANOVA suggested significant variation in species composition among the caves. A SIMPER analysis revealed Coleura afra and Hipposideros jonesi to be the main discriminating species between caves, with a dominance of Hipposideros cf. ruber in all caves. The Bat Cave Vulnerability Index (BCVI) revealed Mframabuom cave from the Upper Guinean forest region as a high priority cave hosting threatened species, yet highly disturbed. The remaining caves were identified as medium priority caves. Conclusion The results of the study suggest the need for further research and an immediate conservation strategy as essential for approaching national conservation goals.

Evolutionary parallelism complicates taxonomy of the bat genus Scotophilus. This implies the necessity for a careful examination of morphologically similar species. Robbins' — or “nutlet” — house bat Scotophilus nucella is an insufficiently known taxon of the African rainforest zone based on just a handful of recorded specimens previously included in the nut-coloured house bat S. nux. Because its phylogenetic relationship to S. nux and other congeneric species is unknown, it was assessed using analysis of DNA sequences of single mitochondrial and nuclear genes. Based on the mitochondrial cytochrome b sequences, S. nucella was placed in sister position to S. nux. A genetic divergence of 7.8–9.4 % between them supports the recognition of S. nucella as a distinct species. Analysis of partial sequences of the nuclear zinc finger protein gene on the Y-chromosome corroborated the sister relationship of S. nucella and S. nux, while showing sufficient differences to consider them as two species. Mitocho...

Thirteen individuals of Noack's round-leaf bat, Hipposideros aff. ruber, were radio-tracked for 38 nights in an agricultural landscape in Kwamang, Ashanti Region, Ghana. Local convex hulls were used to estimate home range sizes of the bats. Based on 1,192 fixes, the mean (± SD) home range size was 36 ha ± 35 ha. Individual home range size ranged from six to 95 ha and frequently overlapped among individuals. The foraging area covered 50% of the home range while the core area formed 2%. The mean maximum foraging distance was 1.1 km, with individual distances up to 2.6 km, suggesting Hipposideros aff. ruber is capable of covering relatively long distances. Male bats returned to the cave more often than females during the night. Although the cave was the main roost, each bat also had individual night roosts on trees.

Made available in DSpace on 2018-12-11T16:53:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-05-21 Five of the 13 known species of Mammomonogamus have been described in members of the family Felidae, including domestic cats, making felids the most frequent hosts of Mammomonogamus. The occurrence of Mammomonogamus in felids is geographically scattered and information on the life cycle and other aspects of infections is lacking. The paucity of data opens the questions on possible conspecificity of some of the described species of Mammomonogamus and on the existence of possible reservoirs for infections in domestic cats in geographically isolated endemic foci of infection. To test such hypotheses, we compared sequences of mitochondrial and nuclear markers obtained from Mammomonogamus adults or eggs collected from domestic cats in three geographically distant localities. Based on morphology, geographic origin and site of infection, the worms examined can be referred to as Mammomonogamus ierei and Mammomonogamus auris. Phylogenetic analyses of both mitochondrial and ribosomal DNA markers showed monophyly of the genus Mammomonogamus and suggested the existence of at least two species in cats. Review of the literature, the existence of several species and the discontinuous geographic distribution of Mammomonogamus infections in domestic cats suggest an historical spillover of infection from wild reservoirs, presumably wild felids. Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 61242, Brno, Czech Republic Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1946/1, 612 42 Brno, Czech Republic Department of Virology, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert Einstein Allee 11, 89069, Ulm, Germany Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, Saint Kitts, West Indies Animal Island Paradise Hospital, Saipan, Northern Mariana Islands, USA Faculdade de Ciências Agrárias e Veterinárias da Universidade Estadual Paulista (UNESP) – Câmpus de Jaboticabal, Via de Acesso Prof. Paulo Donato Castelane, S/N – Vila Industrial, Jaboticabal – SP, 14884-900, Brazil Société d'Ornithologie de Polynésie, BP 7023–98719 Taravao, Tahiti, Polynésie Française Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic

Strongylid nematodes in large terrestrial herbivores such as great apes, equids, elephants, and humans tend to occur in complex communities. However, identification of all species within strongylid communities using traditional methods based on coproscopy or single nematode amplification and sequencing is virtually impossible. High-throughput sequencing (HTS) technologies provide opportunities to generate large amounts of sequence data and enable analyses of samples containing a mixture of DNA from multiple species/genotypes. We designed and tested an HTS approach for strain-level identification of gastrointestinal strongylids using ITS-2 metabarcoding at the MiSeq Illumina platform in samples from two free-ranging non-human primate species inhabiting the same environment, but differing significantly in their host traits and ecology. Although we observed overlapping of particular haplotypes, overall the studied primate species differed in their strongylid nematode community composition. Using HTS, we revealed hidden diversity in the strongylid nematode communities in non-human primates, more than one haplotype was found in more than 90% of samples and coinfections of more than one putative species occurred in 80% of samples. In conclusion, the HTS approach on strongylid nematodes, preferably using fecal samples, represents a time and cost-efficient way of studying strongylid communities and provides a resolution superior to traditional approaches.

Made available in DSpace on 2018-12-11T16:52:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01 Four species of Mammomonogamus are known from large African herbivores. A recent study demonstrated that a single Mammomonogamus species was shared by both western lowland gorillas (Gorilla gorilla gorilla) and African forest elephants (Loxodonta cyclotis) in Central African Republic, suggesting lower species diversity than previously described in literature. We examined more than 500 fecal samples collected from sympatric African forest elephants, western lowland gorillas, and African forest buffaloes (Syncerus caffer nanus) at four study sites across Central Africa and examined them by coproscopic methods to detect Mammomonogamus eggs, which were found at three of the study sites. Subsequently, sequences of 18S rDNA, 28S rDNA, and cox1 amplified from individual eggs were analyzed. Phylogenetic analyses of both nuclear and mitochondrial DNA revealed two clades: one formed by sequences originating from Gabonese buffaloes and the other comprising gorillas and elephants. The gorilla–elephant clade was further differentiated depending on the locality. We show the existence of at least two distinct species of Mammomonogamus, M. loxodontis in elephants and gorillas and M. nasicola in buffaloes. The available information on Mammomonogamus in African herbivores is reviewed. Department of Pathology and Parasitology Faculty of Veterinary Medicine University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1 Central European Institute for Technology (CEITEC) University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1946/1 Department of Virology Veterinary Research Institute, Hudcova 296/70 Institute of Vertebrate Biology Czech Academy of Sciences, Květná 8 Evolutionary Ecology and Conservation Genomics University of Ulm, Albert Einstein Allee 11 Institute of Parasitology Biology Centre of the Czech Academy of Sciences, Branišovská 31 Liberec Zoo, Lidové sady 425/1 WWF Dzanga-Sangha Protected Areas Projet Grands Singes Centre for Research and Conservation Royal Zoological Society of Antwerp, Koningin Astridplein 20–26 WWF Kudu-Zumbo Programme Universidade Estadual Paulista—UNESP Faculdade de Ciências Agrárias e Veterinárias Câmpus de Jaboticabal, Via de Acesso Prof. Paulo Donato Castelane, S/N Veterinary Medicine and Animal Science School UNESP—São Paulo State University, Rua Prof. Doutor Walter Mauricio Correa, S/N Universidade Estadual Paulista—UNESP Faculdade de Ciências Agrárias e Veterinárias Câmpus de Jaboticabal, Via de Acesso Prof. Paulo Donato Castelane, S/N Veterinary Medicine and Animal Science School UNESP—São Paulo State University, Rua Prof. Doutor Walter Mauricio Correa, S/N

We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in theRNA-dependent RNA polymerase(RdRp) andspikegenes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3′ end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E.IMPORTANCEThe ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl- terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

The yellow-bellied Scotophilus dinganii is the only African house bat species reported to occur in the Arabian Peninsula. Formerly, the Arabian house bats were referred to similar-looking white-bellied S. leucogaster, which differs from S. dinganii mainly by the colour of ventral pelage. We reassessed the taxonomic status of house bats from southwestern Yemen using genetic and morphological analyses. The Yemeni specimens clustered within two distantly related mitochondrial lineages of African Scotophilus: East African S. aff. dinganii, which is a paraphyletic group to S. dinganii s.str. from South Africa, and West African S. leucogaster. This taxonomic assignation was based on published sequences of reference museum specimens. Differences in external and cranial measurements also indicated the presence of two distinct taxa in Yemen. The Yemeni and comparative Ethiopian populations of S. aff. dinganii showed close morphological similarity to the type specimen of S. nigrita colias from Kenya. Because the Yemeni and Ethiopian yellow-bellied house bats cannot be synonymized with S. dinganii, the designation S. colias is tentatively suggested for this particular East African and Yemeni lineage of the S. dinganii complex. However, final correspondence of this name with the respective populations or applicability of some of other available names must yet be explored. Based on environmental differences of the Yemeni localities of origin, S. colias appears to be ecologically delimited to mountainous habitats, while S. leucogaster to harsh lowland deserts. This is consistent with known habitats of African populations of both species.Key words: cytochrome b, phylogeny, cranial morphometrics, Scotophilus dinganii, Scotophilus leucogaster.

SUMMARYSyngamid strongylids of the genusMammomonogamusundoubtedly belong among the least known nematodes with apparent zoonotic potential and the real diversity of the genus remains hard to evaluate without extensive molecular data. Eggs ofMammomonogamussp. are frequently found in feces of African forest elephants (Loxodonta cyclotis) and western lowland gorillas (Gorilla gorilla gorilla) in Dzanga-Sangha Protected Areas. Using sedimentation-based coproscopic techniques, we found the eggs ofMammomonogamusin 19·7% elephant and 54·1% gorilla fecal samples with 8–55 and 1–24 eggs per gram of fecal sediment for elephants and gorillas, respectively. We used a combination of light microscopy, scanning electron microscopy and analysis of cytochromecoxidase subunit I (cox1) and a partial sequence of 18S rDNA isolated from single eggs to test the hypothesis of possibleMammomonogamusconspecificity in gorillas and elephants. Whereas 18S rDNA sequences were identical in both gorillas and elephants, we distinguished seven different haplotypes within thecox1. Two haplotypes were found in both gorillas and elephants suggesting sharing ofMammomonogamus.Assignment of the parasite toM. loxodontisis proposed. Provided sequences represent the first genomic data onMammomonogamusspp.

We screened fecal specimens of 4,758 bats from Ghana and 272 bats from 4 European countries for betacoronaviruses. Viruses related to the novel human betacoronavirus EMC/2012 were detected in 46 (24.9%) of 185 Nycteris bats and 40 (14.7%) of 272 Pipistrellus bats. Their genetic relatedness indicated EMC/2012 originated from bats.

Due to the combination of general morphological similarity among representatives of particular populations and/or taxa, the taxonomy of the Myotis mystacinus morphogroup is traditionally considered to be one of the most complex topics of bat systematics. We used a combination of genetic and morphological approaches to identify which taxa of the morphogroup inhabit the broader Caucasus region (i.e. the territory between Crimea, Southern Russia, Northern Anatolia, and Northern Iran, incl.) and to define the relationships of these taxa to other Palaearctic populations of the morphogroup. Based on the genetic identification (complete sequence of the cytochrome b gene) of 56 specimens of the morphogroup originating from the region and the subsequent morphological comparison of more than 100 museum specimens, five species were shown to occur in the Caucasus region: Myotis mystacinus s.str., M. davidii, M. alcathoe, M. hyrcanicus, and M. brandtii. While the intraspecific positions of the Caucasian populations of M. mystacinus and M. davidii remain unresolved, the populations of M. brandtii belong to the nominotypical form of this species, and the populations of M. alcathoe represent an endemic subspecies, which is here newly described; M. hyrcanicus is regarded a monotypic species.

Background Habitat types can affect vector and pathogen distribution and transmission dynamics. The prevalence and genetic diversity of Plasmodium spp. in two eastern chimpanzee populations—Kalinzu Forest Reserve, Uganda and Issa Valley, Tanzania—inhabiting different habitat types was investigated. As a follow up study the effect of host sex and age on infections patterns in Kalinzu Forest Reserve chimpanzees was determined. Methods Molecular methods were employed to detect Plasmodium DNA from faecal samples collected from savanna-woodland (Issa Valley) and forest (Kalinzu Forest Reserve) chimpanzee populations. Results Based on a Cytochrome-b PCR assay, 32 out of 160 Kalinzu chimpanzee faecal samples were positive for Plasmodium DNA, whilst no positive sample was detected in 171 Issa Valley chimpanzee faecal samples. Sequence analysis revealed that previously known Laverania species (Plasmodium reichenowi, Plasmodium billbrayi and Plasmodium billcollinsi) are circulating in the Kalinzu chimpanzees. A significantly higher proportion of young individuals were tested positive for infections, and switching of Plasmodium spp. was reported in one individual. Amongst the positive individuals sampled more than once, the success of amplification of Plasmodium DNA from faeces varied over sampling time. Conclusion The study showed marked differences in the prevalence of malaria parasites among free ranging chimpanzee populations living in different habitats. In addition, a clear pattern of Plasmodium infections with respect to host age was found. The results presented in this study contribute to understanding the ecological aspects underlying the malaria infections in the wild. Nevertheless, integrative long-term studies on vector abundance, Plasmodium diversity during different seasons between sites would provide more insight on the occurrence, distribution and ecology of these pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1476-2) contains supplementary material, which is available to authorized users.

Crimean Congo hemorrhagic fever virus (CCHFV) is a highly virulent tick-borne pathogen that causes hemorrhagic fever in humans. The geographic range of human CCHF cases largely reflects the presence of ticks. However, highly similar CCHFV lineages occur in geographically distant regions. Tick-infested migratory birds have been suggested, but not confirmed, to contribute to the dispersal. Bats have recently been shown to carry nairoviruses distinct from CCHFV. In order to assess the presence of CCHFV in a wide range of bat species over a wide geographic range, we analyzed 1,135 sera from 16 different bat species collected in Congo, Gabon, Ghana, Germany, and Panama. Using a CCHFV glycoprotein-based indirect immunofluorescence test (IIFT), we identified reactive antibodies in 10.0% (114/1,135) of tested bats, pertaining to 12/16 tested species. Depending on the species, 3.6%–42.9% of cave-dwelling bats and 0.6%–7.1% of foliage-living bats were seropositive (two-tailed t-test, p = 0.0447 cave versus foliage). 11/30 IIFT-reactive sera from 10 different African bat species had neutralizing activity in a virus-like particle assay. Neutralization of full CCHFV was confirmed in 5 of 7 sera. Widespread infection of cave-dwelling bats may indicate a role for bats in the life cycle and geographic dispersal of CCHFV.

Two metrically defined subspecies have traditionally been recognised within the Palaearctic distribution range of the Egyptian fruit bat Rousettus aegyptiacus ;t he largerR. a. aegyptiacus in Egypt and the northern part of the Middle East and the smaller R. a. arabicus in the southern Middle East. An extensive material of R. aegyptiacus from all parts of this area, i.e. the Levant (incl. Turkey and Cyprus), Egypt (incl. Sinai), northern Sudan, Yemen, Oman, Iran, and Pakistan, as well as comparative samples from its sub-Saharan range, were tested using both morphological and genetic approaches in order to revise the species' taxonomic status. The results indicated two possible processes, depending on the method used. Genetic analysis of the mitochondrial genome (nd1 and cytb) indicated low variation (< 2.0% of genetic distance) and lack of geographical structure while morphometric analysis indicated significant metric differences. Two basic size morphotypes were found within the Palaearctic range, with a rather mosaic-like geographical distribution and a lack of clear size distinction between the two categories, though intermediate types were detected. Thus, we suggest that all Palaearctic populations of R. aegyptiacus represent one form, the nominotypical subspecies, which is uniform in genetic traits but plastic in metric traits.

Vallo, P., Benda, P., Cervený, J. & Koubek, P. (2012). Conflicting mitochondrial and nuclear paraphyly in small-sized West African house bats (Vespertilionidae). —Zoologica Scripta, 42, 1–12. Hybridization between species may result in introgression of mitochondrial DNA from one species to another. Phylogenetic inference, therefore, may not recover true evolutionary relationships. In bats, there are only a few reported cases of introgressive hybridization. House bats are a genus with obscure phylogeny and taxonomy, caused mainly by morphological similarity. We undertook a detailed analysis of small-sized West African house bats (Scotophilus), tentatively identified as S. nigritellus, to clarify relationships between two sympatric colour forms. These forms were recovered in paraphyletic position to each other in both mitochondrial and nuclear phylogenies, signifying that they are two distinct species. While the yellow-bellied form could be assigned beyond doubt to S. nigritellus s. str., the white-bellied form may be an as yet undescribed species. Moreover, the white-bellied form clustered as a sister mitochondrial lineage to another species, Scotophilus leucogaster. These sister lineages differed by only 2.6–2.8% sequence divergence, which lies within the intraspecific range for this genus. Two nuclear markers, however, contradicted the sister relationship, showing them instead to be distantly related. The apparent conflict between the mitochondrial and nuclear signals suggests that past hybridization may have occurred between these morphologically distinct species.

The entodiniomorphid ciliate Troglodytella abrassarti is a colonic mutualist of great apes. Its host specificity makes it a suitable model for studies of primate evolution. We explored molecular diversity of T. abrassarti with regard to large geographical distribution and taxonomic diversity of its most common host, the chimpanzee. We found a very low diversification of T. abrassarti in chimpanzees across Africa. Distribution of two types of T. abrassarti supports evolutionary separation of the Western chimpanzee, P. t. verus, from populations in Central and East Africa. Type I T. abrassarti is probably a derived form, which corresponds with the Central African origin of chimpanzees and a founder event leading to P. t. verus. Exclusivity of the respective types of T. abrassarti to Western and Central/Eastern chimpanzees corroborates the difference found between an introduced population of presumed Western chimpanzees on Rubondo Island and an autochthonous population in mainland Tanzania. The identity of T. abrassarti from Nigerian P. t. ellioti and Central African chimpanzees suggests their close evolutionary relationship. Although this contrasts with published mtDNA data, it corroborates current opinion on the exclusive position of P. t. verus within the chimpanzee phylogeny. The type of T. abrassarti occurring in Central and East African common chimpanzee was confirmed also in bonobos. This may point to the presence of an ancestral Type II found throughout the Lower Guinean rainforest dating back to the common Pan ancestor. Alternatively, the molecular uniformity of T. abrassarti may imply a historical overlap of the species' distribution ranges.

Two species are currently recognised within the genus Asellia, a typical inhabitant of arid areas of northern Africa and south-western Asia. Most of the distribution range of the genus is covered by Asellia tridens, while the other species, A. patrizii, is restricted to Ethiopia, Eritrea and several Red Sea islands. We analysed the morphological variation in an extensive set of Asellia samples covering the range of the genus, including most of the available type material. In a representative subset of samples, we employed molecular genetic analysis to infer the phylogenetic relationships within the broadly distributed A. tridens. Morphological comparisons revealed four distinct morphotypes. Except for the endemic A. patrizii, almost all African Asellia were found to belong to the same morphotype as most of the Middle Eastern specimens. This morphotype was unambiguously identified as A. tridens. Two other morphotypes of tentative A. tridens were further recognised based on skull shape differences; one in the southern Arabian region of Dhofar, the other in Socotra and Somalia. Phylogenetic analysis of complete sequences of the mitochondrial cytochrome b gene yielded three main monophyletic groups, which corresponded to the morphotypes revealed for A. tridens. Significant genetic divergences reaching over 5% and 12%, respectively, were discovered between them. Based on the morphological and molecular data obtained, we propose a split of the current A. tridens into three separate species: A. tridens in northern Africa and most of the Middle East, A. italosomalica in Socotra and Somalia, and Asellia sp. nov. in southern Arabia. Molecular dating, along with the available paleontological information and geological history of the Arabian Peninsula, supports an Arabian origin of the contemporary Asellia. While profound divergence of the Socotran form may be linked to the split of Socotra from the southern Arabian coast in the Middle Miocene, the low sequence variation of Asellia in most of Africa and the Middle East suggests a relatively recent colonisation of this vast area during the Pleistocene. The newly described form from southern Arabia most likely represents a relic of aridisation during the Miocene-Pliocene transition.

The yellow-bellied Scotophilus dinganii is the only African house bat species reported to occur in the Arabian Peninsula. Formerly, the Arabian house bats were referred to similar-looking white-bellied S. leucogaster, which differs from S. dinganii mainly by the colour of ventral pelage. We reassessed the taxonomic status of house bats from southwestern Yemen using genetic and morphological analyses. The Yemeni specimens clustered within two distantly related mitochondrial lineages of African Scotophilus: East African S. aff. dinganii, which is a paraphyletic group to S. dinganii s.str. from South Africa, and West African S. leucogaster. This taxonomic assignation was based on published sequences of reference museum specimens. Differences in external and cranial measurements also indicated the presence of two distinct taxa in Yemen. The Yemeni and comparative Ethiopian populations of S. aff. dinganii showed close morphological similarity to the type specimen of S. nigrita colias from Kenya. Because the Ye...

Two mitochondrial lineages of bats that are morphologically attributed to Hipposideros ruber have been shown to occur sympatrically in southeastern Senegal. We studied genetic diversity in these bats in the Niokolo Koba National Park using sequences of mitochondrial cytochrome b gene to determine the taxonomic status of the two genetic forms, and included skull morphology for comparison. Detailed multidimensional analysis of skull measurements indicated slight morphological differences between the two genetic forms. Exploration of peak frequency of the constant-frequency echolocation signals in a local population of Hipposideros aff. ruber was not available for both groups. Phylogenetic comparison with other available West African representatives of H. aff. ruber revealed paraphyletic relationship of the two Senegalese forms, with the less abundant form from Senegal forming a monophyletic group with that from Benin. Based on genetic divergence and sympatric occurrence, the two forms from Senegal might represent cryptic species. However, absence of nuclear gene flow between them is yet to be investigated to demonstrate their reproductive isolation.

Hipposideros spp. bats harbor a coronavirus that shares common ancestry with human viruses., We tested 12 bat species in Ghana for coronavirus (CoV) RNA. The virus prevalence in insectivorous bats (n = 123) was 9.76%. CoV was not detected in 212 fecal samples from Eidolon helvum fruit bats. Leaf-nosed bats pertaining to Hipposideros ruber by morphology had group 1 and group 2 CoVs. Virus concentrations were

The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the two reciprocally monophyletic lineages expected, corresponding to the two species, we recovered four distinct lineages with deep internal divergences. Two sister clades within a lineage of bats of H. caffer represent respectively the nominotypical form H. c. caffer, restricted to Southern Africa, and H. c. tephrus, inhabiting the Maghreb, West Africa and the Arabian Peninsula. Geographical isolation and deep genetic divergence suggest species status of both the forms. Another lineage comprises specimens of both morphotypes from West and East Africa. It probably represents a distinct species but its taxonomic assignation remains obscure. A Central African lineage of H. ruber comprises two sister clades, which become sympatric in Cameroon. Their status has to be clarified with additional evidence, since nuclear gene flow might be taking place. A further divergent lineage with H. ruber morphotype, most probably representing another distinct species, is restricted to West Africa. Although all three genetic forms of H. ruber may correspond to named taxa, their proper taxonomic assignation has to be assessed by comparison with type material.

SUMMARYAnoplocephalid tapeworms of the genus Bertiella Stiles and Hassall, 1902 and Anoplocephala Blanchard, 1848, found in the Asian, African and American non-human primates are presumed to sporadic ape-to-man transmissions. Variable nuclear (5.8S-ITS2; 28S rRNA) and mitochondrial genes (cox1; nad1) of isolates of anoplocephalids originating from different primates (Callicebus oenanthe, Gorilla beringei, Gorilla gorilla, Pan troglodytes and Pongo abelii) and humans from various regions (South America, Africa, South-East Asia) were sequenced. In most analyses, Bertiella formed a monophyletic group within the subfamily Anoplocephalinae, however, the 28S rRNA sequence-based analysis indicated paraphyletic relationship between Bertiella from primates and Australian marsupials and rodents, which should thus be regarded as different taxa. Moreover, isolate determined as Anoplocephala cf. gorillae from mountain gorilla clustered within the Bertiella clade from primates. This either indicates that A. gorillae deserves to be included into the genus Bertiella, or, that an unknown Bertiella species infects also mountain gorillas. The analyses allowed the genetic differentiation of the isolates, albeit with no obvious geographical or host-related patterns. The unexpected genetic diversity of the isolates studied suggests the existence of several Bertiella species in primates and human and calls for revision of the whole group, based both on molecular and morphological data.

The giant house bat Scotophilus nigrita, one of the largest vespertilioniform bat species in the world, is a poorly known taxon, especially with respect to its phylogenetic relationships to congeneric species. Its phylogenetic position was thus assessed by analysing DNA sequences of single mitochondrial and nuclear genes. Based on the mitochondrial cytochrome b, S. nigrita was found to be paraphyletic with respect to continental African species S. colias, S. dinganii, S. nigritellus and S. viridis. Analysis of sequences of the nuclear zinc finger protein gene on the Y chromosome corroborated the general pattern of the cytochrome b phylogeny, although phylogenetic relationships were poorly resolved. These results clearly contradict the published data on S. nigrita from Kenya for both markers, rendering the hypothesis of historical hybridization with S. colias implausible and questioning the taxonomic affiliation of the particular Kenyan sequence. A deep split in the cytochrome b phylogeny between S. nigrita from West and Southern Africa reached sequence divergence values of 7.6% to 8.1%, a finding that supports taxonomic elevation of the two currently recognized subspecies into separate species S. nigrita and S. alvenslebeni.

Nature Communications 3: Article number: 796 (2012); Published: 24 April 2012; Updated: 23 January 2014. The authors inadvertently omitted Veronika M. Cottontail and Mirjam Knornschild, who collected samples in Panama and Costa Rica, from the author list. This has now been corrected in both the PDF and HTML versions of the Article.

International audience; The rising incidence of emerging infectious diseases (EID) is mostly linked to biodiversity loss, changes in habitat use and increasing habitat fragmentation. Bats are linked to a growing number of EID but few studies have explored the factors of viral richness in bats. These may have implications for role of bats as potential reservoirs. We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. We performed the first comparative analysis testing the correlation of the fragmented geographical distribution (defined as the perimeter to area ratio) with viral richness in bats. Because of their potential effect, sampling effort, host body weight, ecological and behavioural traits such as roosting behaviour, migration and geographical range, were included into the analysis as variables. The results showed that the geographical distribution size, shape and host body weight have significant effects on viral richness in bats. Viral richness was higher in large-bodied bats which had larger and more fragmented distribution areas. Accumulation of viruses may be related to the historical expansion and contraction of bat species distribution range, with potentially strong effects of distribution edges on virus transmission. Two potential explanations may explain these results. A positive distribution edge effect on the abundance or distribution of some bat species could have facilitated host switches. Alternatively, parasitism could play a direct role in shaping the distribution range of hosts through host local extinction by virulent parasites. This study highlights the importance of considering the fragmentation of bat species geographical distribution in order to understand their role in the circulation of viruses in Africa.

The hepatitis B virus (HBV), family Hepadnaviridae, is one of most relevant human pathogens. HBV origins are enigmatic, and no zoonotic reservoirs are known. Here, we screened 3,080 specimens from 54 bat species representing 11 bat families for hepadnaviral DNA. Ten specimens (0.3%) from Panama and Gabon yielded unique hepadnaviruses in coancestral relation to HBV. Full genome sequencing allowed classification as three putative orthohepadnavirus species based on genome lengths (3,149–3,377 nt), presence of middle HBV surface and X-protein genes, and sequence distance criteria. Hepatic tropism in bats was shown by quantitative PCR and in situ hybridization. Infected livers showed histopathologic changes compatible with hepatitis. Human hepatocytes transfected with all three bat viruses cross-reacted with sera against the HBV core protein, concordant with the phylogenetic relatedness of these hepadnaviruses and HBV. One virus from Uroderma bilobatum, the tent-making bat, cross-reacted with monoclonal antibodies against the HBV antigenicity determining S domain. Up to 18.4% of bat sera contained antibodies against bat hepadnaviruses. Infectious clones were generated to study all three viruses in detail. Hepatitis D virus particles pseudotyped with surface proteins of U. bilobatum HBV, but neither of the other two viruses could infect primary human and Tupaia belangeri hepatocytes. Hepatocyte infection occurred through the human HBV receptor sodium taurocholate cotransporting polypeptide but could not be neutralized by sera from vaccinated humans. Antihepadnaviral treatment using an approved reverse transcriptase inhibitor blocked replication of all bat hepadnaviruses. Our data suggest that bats may have been ancestral sources of primate hepadnaviruses. The observed zoonotic potential might affect concepts aimed at eradicating HBV.

In sub-Saharan Africa, anthropogenic activities such as cocoa (Theobroma cacao) farming have replaced the natural forest vegetation, making agricultural environments more readily available to some ...

The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data., The large virus family, Paramyxoviridae, includes several human and livestock viruses. This study, testing 119 bat and rodent species distributed globally, identifies novel putative paramyxovirus species, providing data with potential uses in predictions of the emergence of novel paramyxoviruses in humans and livestock.

Bats may host emerging viruses, including coronaviruses (CoV). We conducted an evaluation of CoV in rhinolophid and vespertilionid bat species common in Europe. Rhinolophids carried severe acute respiratory syndrome (SARS)-related CoV at high frequencies and concentrations (26% of animals are positive; up to 2.4 × 10 8 copies per gram of feces), as well as two Alphacoronavirus clades, one novel and one related to the HKU2 clade. All three clades present in Miniopterus bats in China (HKU7, HKU8, and 1A related) were also present in European Miniopterus bats. An additional novel Alphacoronavirus clade (bat CoV [BtCoV]/BNM98-30) was detected in Nyctalus leisleri . A CoV grouping criterion was developed by comparing amino acid identities across an 816-bp fragment of the RNA-dependent RNA polymerases (RdRp) of all accepted mammalian CoV species (RdRp-based grouping units [RGU]). Criteria for defining separate RGU in mammalian CoV were a >4.8% amino acid distance for alphacoronaviruses and a >6.3% distance for betacoronaviruses. All the above-mentioned novel clades represented independent RGU. Strict associations between CoV RGU and host bat genera were confirmed for six independent RGU represented simultaneously in China and Europe. A SARS-related virus (BtCoV/BM48-31/Bulgaria/2008) from a Rhinolophus blasii (Rhi bla) bat was fully sequenced. It is predicted that proteins 3b and 6 were highly divergent from those proteins in all known SARS-related CoV. Open reading frame 8 (ORF8) was surprisingly absent. Surface expression of spike and staining with sera of SARS survivors suggested low antigenic overlap with SARS CoV. However, the receptor binding domain of SARS CoV showed higher similarity with that of BtCoV/BM48-31/Bulgaria/2008 than with that of any Chinese bat-borne CoV. Critical spike domains 472 and 487 were identical and similar, respectively. This study underlines the importance of assessments of the zoonotic potential of widely distributed bat-borne CoV.

Entodiniomorphid ciliates are often present in the colons of wild apes. In captive apes the infection tends to gradually disappear, with the exception of Troglodytella abrassarti. We used fecal examinations to screen the gorillas (Gorilla gorilla gorilla) in European (Czech Republic, UK) and Australian Zoos to explore the ape-to-ape transmission pattern of T. abrassarti. Gorillas from two out of three European Zoos were positive for T. abrassarti, while gorillas from the Australian Zoo were negative. We documented a horizontal transmission of T. abrassarti to a non-infected adult gorilla introduced into a Troglodytella-positive group in the Prague Zoo and traced the origin of the ciliate infection to the Paignton Zoo (UK) using serial fecal examinations. During this study, two infant gorillas born in the Prague Zoo (CZ) first became positive for T. abrassarti at the age of 9 mo. Ciliate morphology and the sequencing of the small subunit rRNA gene and the internal transcribed spacer rDNA spacer region revealed that T. abrassarti affects both captive gorillas and chimpanzees. We conclude that zoo transport plays a major role in the distribution of T. abrassarti among captive gorillas.