Human activities link fruit bat presence to Ebola virus disease outbreaks

1. A significant link between forest loss and fragmentation and outbreaks of Ebola virus disease (EVD) in humans has been documented. Deforestation may alter the natural circulation of viruses and change the composition, abundance, behaviour and possibly viral exposure of reservoir species. This in turn might increase contact between infected animals and humans.
2. Fruit bats of the family Pteropodidae have been suspected as reservoirs of the Ebola virus. At present, the only evidence associating fruit bats with EVD is the presence of seropositive individuals in eight species and polymerase chain reaction-positive individuals in three of these.
3. Our study investigates whether human activities can increase African fruit bat geographical ranges and whether this influence overlaps geographically with EVD outbreaks that, in turn, are favoured by deforestation.
4. We use species observation records for the 20 fruit bat species found in favourable areas for the Ebola virus to determine factors affecting the bats' range inside the predicted Ebola virus area. We do this by employing a hypothetico-deductive approach based on favourability modelling.
5. We show that the range of some fruit bat species is linked to human activities within the favourable areas for the Ebola virus. More specifically, the areas where human activities favour the presence of five fruit bat species overlap with the areas where EVD outbreaks in humans were themselves favoured by deforestation. These five species are as follows: Eidolon helvum, Epomops franqueti, Megaloglossus woermanni, Micropteropus pusillus and Rousettus aegyptiacus. Of these five, all but Megaloglossus woermanni have recorded seropositive individuals. For the remaining 15 bat species, we found no biogeographical support for the hypothesis that positive human influence on fruit bats could be associated with EVD outbreaks in deforested areas within the tropical forest biome in West and Central Africa.
6. Our work is a useful first step allowing further investigation of the networks and pathways that may lead to an EVD outbreak. The modelling framework we employ here can be used for other emerging infectious diseases.

     

Phylogenetic Systematics of Peccaries (Tayassuidae: Artiodactyla) and a Classification of South American Tayassuids

Tayassuidae is a family of pig-like Artiodactyla restricted to the New World. Despite its rich fossil history, they have received less attention from a taxonomic and phylogenetic perspective when compared to the Old World pigs, Suidae. In this study, we performed a computer assisted phylogenetic analysis using morphological and molecular data including fossil and extant Tayassuidae, using parsimony and Bayesian approaches. We recovered the monophyly of the family Tayassuidae, confirming previous proposals, as well as the monophyly of the subfamilies Hesperhyinae and Tayassuinae, and the genus Platygonus, which we placed in a new taxon of tribe level. The three living peccaries and a number of fossil species belong to a new, tribe level, monophyletic group. The genus Catagonus comes out as paraphyletic, leading us to propose to restrict the generic name to the type species, C. metropolitanus, and a new taxonomic arrangement for the remaining species previously included in it, revalidating the genera Brasiliochoerus and Parachoerus, and describing a new genus, Protherohyus, gen. nov.     

Taxonomic notes on the genus Otoptera (Phaseoleae, Fabaceae) in southern Africa

A taxonomic study of the genus Otoptera (tribe Phaseoleae) is presented. This distinct genus consists of two species, O. burchellii in southern Africa (Namibia, Botswana, South Africa and Zimbabwe) and O. madagascariensis endemic to Madagascar. The two species differ in the shape and size of leaflets, size and orientation of the spur located at the base of the wing petal, and also by size of the pod. A key to the two species is provided. This study focuses mainly on the southern African O. burchellii DC., which is described and illustrated. The species name is lectotypified and the known geographical distribution is recorded for the first time.     

Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa

The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.     

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (～4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (～1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (～1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (～0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.     

Loss of forest cover and host functional diversity increases prevalence of avian malaria parasites in the Atlantic Forest

Host phylogenetic relatedness and ecological similarity are thought to contribute to parasite community assembly and infection rates. However, recent landscape level anthropogenic changes may disrupt host-parasite systems by impacting functional and phylogenetic diversity of host communities. We examined whether changes in host functional and phylogenetic diversity, forest cover, and minimum temperature influence the prevalence, diversity, and distributions of avian haemosporidian parasites (genera Haemoproteus and Plasmodium) across 18 avian communities in the Atlantic Forest. To explore spatial patterns in avian haemosporidian prevalence and taxonomic and phylogenetic diversity, we surveyed 2241 individuals belonging to 233 avian species across a deforestation gradient. Mean prevalence and parasite diversity varied considerably across avian communities and parasites responded differently to host attributes and anthropogenic changes. Avian malaria prevalence (termed herein as an infection caused by Plasmodium parasites) was higher in deforested sites, and both Plasmodium prevalence and taxonomic diversity were negatively related to host functional diversity. Increased diversity of avian hosts increased local taxonomic diversity of Plasmodium lineages but decreased phylogenetic diversity of this parasite genus. Temperature and host phylogenetic diversity did not influence prevalence and diversity of haemosporidian parasites. Variation in the diversity of avian host traits that promote parasite encounter and vector exposure (host functional diversity) partially explained the variation in avian malaria prevalence and diversity. Recent anthropogenic landscape transformation (reduced proportion of native forest cover) had a major influence on avian malaria occurrence across the Atlantic Forest. This suggests that, for Plasmodium, host phylogenetic diversity was not a biotic filter to parasite transmission as prevalence was largely explained by host ecological attributes and recent anthropogenic factors. Our results demonstrate that, similar to human malaria and other vector-transmitted pathogens, prevalence of avian malaria parasites will likely increase with deforestation.     

Dental and phylogeographic patterns of variation in gorillas

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure.Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation.Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.     

Taxonomy of the African giant pouched rats (Nesomyidae: Cricetomys): molecular and craniometric evidence support an unexpected high species diversity

Our study combined a mitochondrial cytochrome b phylogeny with cranial measurements from giant pouched rats collected across sub‐Saharan Africa. The mitochondrial phylogeny resolves two West African clades and a clade with east and central Africa representatives. This last clade can be further divided into four subclades. Altogether they represent six species (Cricetomys gambianus, Cricetomys ansorgei, Cricetomys emini, and three undescribed taxa) that can be distinguished on the basis of their mitochondrial DNA sequences and craniometry. In the absence of adequate craniometric data the existence of Cricetomys kivuensis cannot be confirmed by our data. Our combined molecular and craniometric data allowed us to broadly delineate the distribution ranges of the detected species. Cricetomys gambianus occurs in the savannah and forest clearings of West Africa. Cricetomys ansorgei is distributed in the savannah of East and southern Africa. Cricetomys emini, as currently recognized across the Guineo‐Congolian forest of Africa, is shown to be diphyletic. Cricetomys sp. 1, a separate operational taxonomic unit closely resembling C. emini, occurs in the forest zone of West Africa. An undescribed sister‐species of C. ansorgei, Cricetomys sp. 2, occurs in the forest of Central Africa along the left bank of the Congo River. Cricetomys sp. 3 occurs on the right bank of the Congo River from Cameroon to the Republic of Congo, whereas the true C. emini also occurs on the right bank of the Congo River but appears to be restricted to the Democratic Republic of Congo. Cranial phenotype within the genus tends to conform to ecological zonation (either forest or savannah) rather than to phylogenetic affiliation of the species concerned, suggesting that diversifying selection across environmental gradients could be responsible for biological diversification within the genus.     

Systematics of the southern Patagonian-Fueguian endemic Abrothrix lanosus (Rodentia: Sigmodontinae): Phylogenetic position,karyotypic and morphological data

Abrothrix lanosus (Thomas, 1897) is morphologically redescribed on the basis of new specimens collected in Tierra del Fuego (Argentina). Cranial, mandibular, skeletal, penile, and chromosomal characteristics are described and compared with other species of Abrothrix, especially those of the Patagonian-Fueguian region. Its phylogenetic position within Abrotrichini is explored using DNA sequences of the mitochondrial cytochrome b (cyt b) and the nuclear Interphotoreceptor Retinoid Binding Protein (IRBP) genes. Phylogenetically, cyt b places A. lanosus as sister of A. jelskii, whereas IRBP groups A. lanosus and A. longipilis. The latter topology is most consistent with morphological data and taxonomic history. Several cranial and mandibular characters distinguish A. lanosus from the other species of the genus, including A. longipilis, which is its most similar species. A. lanosus shares with other congeners a 2n=52 karyotype and differs from other species of Abrothrix by at least 10% (p-distances) sequence divergence in cyt b. In conclusion, A. lanosus is a valid species, readily distinguishable from other Abrothrix in the southern Patagonian-Fueguian region. Although many data, including penile and skull morphology, suggest that A. longipilis is its closest living relative, A. jelskii is retained as a viable alternative until additional data are obtained.     

A morphological re-evaluation of the taxonomic status of the genus Pellegriniodendron (Harms) J. Léonard (Leguminosae–Caesalpinioideae–Detarieae) and its inclusion in Gilbertiodendron J. Léonard

The taxonomic status of the genus Pellegriniodendron J. Léonard (Leguminosae, Caesalpinioideae), which consists in one tree species endemic to West Central tropical Africa, is re-evaluated. Based on our morphological comparison and on published phylogenetic studies, we conclude that P. diphyllum should be included within the genus Gilbertiodendron J. Léonard, and the new combination Gilbertiodendron diphyllum (Harms) Estrella & Devesa is proposed. A lectotype for Macrolobium reticulatum, synonym of G. diphyllum, is also designated. The species is fully described and illustrated, and a distribution map is also presented.     

Der Langzungen-FlughundMegaloglossus Woermanni,ein Blütenbesucher

Zusammenfassung Auf Grund von Pollenfunden im Magen mu? der einzige in Afrika heimische Vertreter der Langzungen-Flughunde,Megaloglossus woermanni, als Blütenbesucher angesehen werden. Es werden kurz die morphologisch-anatomischen Merkmale, die eine Anpassung an den Blütenbesuch erkennen lassen, beschrieben.     

Parallel occurrence of asynaptic sex chromosomes in gray voles (Microtus Schrank, 1798)

In many eutherian species, pairing and recombination of X and Y chromosomes are indispensable for normal meiotic progression and correct segregation of sex chromosomes. The rodent subfamily Arvicolinae provides an interesting exception. The majority of arvicoline species with asynaptic sex chromosomes belong to the genus Microtus sensu lato. However, some vole species of the genus Microtus and other genera display normal X-Y pairing in meiosis. These observations indicate that synaptic condition was typical for the common ancestor of all voles, but the gaps in taxonomic sampling makes impossible to identify a lineage or lineages, in which the asynapsis occurred. The methods of electron and fluorescent microscopy were used to study the synapsis of sex chromosomes in males of some additional species of the subfamily Arvicolinae. This extended taxonomic list allowed us to identify asynaptic species in every large lineage of the tribe Microtini. Apparently, the ability of sex chromosomes to pair and recombine in male meiosis was lost in arvicoline evolution for at least three times independently. Our results indirectly suggest the unnecessity of sex chromosome pairing in male meiosis of arvicoline rodents, and presence of alternate molecular mechanism of sex chromosome segregation in this large mammalian tribe.     

Early Carboniferous spiriferoid brachiopods from the Qaidam Basin,Northwest China: Taxonomy,biostratigraphy and biogeography

Six Early Carboniferous brachiopod species in four genera of the Superfamily Spiriferoidea are described from the Qaidam Basin, northwestern China, including a new genus, Qaidamospirifer, and two new species: Grandispirifer qaidamensis and Qaidamospirifer elongatus. Additionally, a new genus, Triangulospirifer, is also proposed to replace Triangularia Poletaev, 2001 that was preoccupied by a Devonian molluscan genus.On the basis of the new material as well as published information, we have reviewed the taxonomic composition and the stratigraphic and palaeobiogeographic distributions of the three previously established genera from the viewpoint of palaeobiogeography. The study reveals that Grandispirifer has a relatively long stratigraphic range from the late Tournaisian to Serpukhovian. During this interval, the genus attained a wide geographical distribution, reaching Northwest China, western Yunnan of West China, Japan, as well as Iran and North Africa. Angiospirifer first occurred in western Europe in the Viséan, and later migrated to North Africa during the late Viséan. In the Serpukhovian, it migrated eastward, reaching the Donets Basin of Ukraine and the Qaidam Basin in Northwest China. Anthracothyrina evolved from Brachythyrina in North Africa in late Viséan, then dispersed north-westward to western and eastern Europe and, further eastward to the Qaidam Basin during the Serpukhovian.     

Diversity and Distribution of Hantaviruses in South America

Hantaviruses are important contributors to disease burden in the New World, yet many aspects of their distribution and dynamics remain uncharacterized. To examine the patterns and processes that influence the diversity and geographic distribution of hantaviruses in South America, we performed genetic and phylogeographic analyses of all available South American hantavirus sequences. We sequenced multiple novel and previously described viruses (Anajatuba, Laguna Negra-like, two genotypes of Castelo dos Sonhos, and two genotypes of Rio Mamore) from Brazilian Oligoryzomys rodents and hantavirus pulmonary syndrome cases and identified a previously uncharacterized species of Oligoryzomys associated with a new genotype of Rio Mamore virus. Our analysis indicates that the majority of South American hantaviruses fall into three phylogenetic clades, corresponding to Andes and Andes-like viruses, Laguna Negra and Laguna Negra-like viruses, and Rio Mamore and Rio Mamore-like viruses. In addition, the dynamics and distribution of these viruses appear to be shaped by both the geographic proximity and phylogenetic relatedness of their rodent hosts. The current system of nomenclature used in the hantavirus community is a significant impediment to understanding the ecology and evolutionary history of hantaviruses; here, we suggest strict adherence to a modified taxonomic system, with species and strain designations resembling the numerical system of the enterovirus genus.     

A revision of the genus Dolichos (Fabaceae,Papilionoideae, Phaseoleae), including Lesotho and Swaziland

A revision of the genus Dolichos in South Africa (Lesotho and Swaziland included) is presented. This legume genus, belonging to the bean tribe Phaseoleae, mainly has an African distribution, extending into Asia. In South Africa it is represented by nine species, two (D. sericeus and D. trilobus) of which extend into Tropical Africa. Dolichos is closely related to the genus Macrotyloma from which it can be distinguished by the short standard appendages, reticulate pollen and the generally purple flowers (standard appendages long, pollen tuberculate or spinulose and flowers yellow or orange in Macrotyloma). It also has affinities with the genera Dipogon and Lablab. The correct nomenclature, as well as complete synonymy, typification and distribution maps of all the species are provided.     

The phylogeographic history of Megistostegium (Malvaceae) in the dry,spiny thickets of southwestern Madagascar using RAD‐seq data and ecological niche modeling

The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here, we investigate three species in the endemic genus Megistostegium (Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil, and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modeling provide evidence that past climatic change could be responsible for the current distribution, population structure, and maintenance of species in Megistostegium.     

Taxonomic status and evolutionary history of the Saxicola torquata complex

We explored variation in mitochondrial ND2 gene sequences from 171 stonechats (Saxicola torquata complex) collected from 27 Eurasian and 3 African localities. We found that two widespread neighboring Eurasian subspecies of Siberian stonechat, Saxicola maura maura and S. m. stejnegeri, although very similar in appearance, are not each other’s closest relatives. Eastern Asian S. m. stejnegeri appears to have split from other Palearctic, African, and island stonechats well before differentiation occurred among the latter taxa. Our data indicate that European (S. t. rubicola), central Palearctic (S. m. maura) and eastern Palearctic (S. m. stejnegeri) are independently evolving, and could each warrant separate species status, as assumed earlier for S. rubicola, S. maura and S. torquata. However, we found three localities at which individuals from different major groups occurred. Thus, although these are likely phylogenetic species it is unclear whether they are biological species. There was little phylogeographic structure within the three major Palearctic clades, although samples from Spain might be showing incipient divergence. We maintain that the topology of a mtDNA gene tree is a valid means to discern taxonomic limits.     

世界蓑藓属（Macromitrium,Bryophyta）植物分类修订与系统发育研究：历史、现状和问题

蓑藓属(Macromitrium Brid.)是藓类植物中分类最困难的类群之一。先后该属记录946个种,现接受351个种。目前中美洲、亚洲、澳大利亚、新西兰等地区的蓑藓属植物基本完成了分类修订,而南美洲、非洲中部、马达加斯加等地区的蓑藓属植物尚未进行系统的分类修订。蓑藓属的属下分类系统问题众多,先后在该属下建立了10个亚属、20个组和2个亚组,目前接受的有4个亚属和8个组,但是这些类群之间的分类地位和关系仍然不清。鉴于蓑藓属种数多,种间分类问题多,分布广泛,需要开展国际间的合作才能够解决世界蓑藓属的分类修订和系统学研究。     

Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5–7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.