Annotated checklist of moths of Zambia (Insecta: Lepidoptera)

An annotated checklist of moths was compiled for Zambia based on intensive and extensive reviews of the literature on insects of the country and on field surveys undertaken by the study for a period of five years from March 2013 to October 2017 to confirm some of the literature review records documented. The checklist contains 1,816 species of moths, arranged into 907 genera and 35 subspecies. One hundred and fifty of these moth species are endemic in Zambia. During our biodiversity field surveys, we verified the existence in Zambia of 3.07% of moth taxa reported in the literature. Some species of moths recorded to occur in Zambia are of traditional/nutritional value to some local ethnic groupings in the country. In addition to their use in traditional medicinal concoctions with plants to treat human maladies, some moth larvae or caterpillars serve as extra sources of animal protein and are consumed as snacks and/or relish by the local people. About one percent (0.9%) of all moth species recorded to occur in Zambia and 7.59% of species of the family Saturniidae serve as extra sources of animal protein for some tribes in the country. To date, no moth species in the country has been assessed for the IUCN Red List of Threatened Species. This present checklist will serve as a basis for future governmental decisions on the policy of environmental protection, Red List preparation, and management of natural food security issues in Zambia.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.

Integrative taxonomy and phylogeography of Colomys and Nilopegamys (Rodentia: Murinae), semi-aquatic mice of Africa, with descriptions of two new species

The semi-aquatic African murine genera Colomys and Nilopegamys are considered monotypic and thought to be closely related to one another. Colomys occurs across forested regions of equatorial Africa, whereas Nilopegamys is known only from the Ethiopian holotype, making it among the rarest mammalian genera in the world – and possibly extinct. Using morphological and genetic data, we reassess the taxonomy of Colomys and Nilopegamys. A multilocus phylogeny with outgroups demonstrates that Nilopegamys is sister to Colomys. In addition, we recognize at least four morphologically diagnosable and genetically distinct species within Colomys: C. eisentrauti (elevated from subspecies and restricted to north-west Cameroon), C. goslingi (with a more restricted range than previously reported) and two new species (one from Liberia and Guinea and one from central and southern Democratic Republic of the Congo and Angola). We also review the status of four other taxa currently recognized within Colomys goslingi (bicolor, denti, goslingi and ruandensis) and demonstrate that these names lack phylogenetic and/or morphological support. Finally, we discuss potential biogeographic barriers that may have played a role in the evolution of Colomys and Nilopegamys, emphasizing the importance of rivers in both facilitating and, possibly, limiting dispersal within these genera.

The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity

Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.

Taxonomic anarchy or an inconvenient truth for conservation? Accelerated species discovery reveals evolutionary patterns and heightened extinction threat in Afro-Malagasy small mammals

We respond to recent criticisms of supposed “taxonomic anarchy” which is said to hamper conservation efforts. Using examples from African small mammals, we document recent increases of 13% (rodents) and 18% (bats) over the past three decades in the number of recognized species of Afro-Malagasy rodents and bats. By reference to a number of case studies involving Afro-Malagasy taxa (predominantly from montane habitats), and a suggested four-criterion approach to delimiting species accurately, we show that these increases are a genuine reflection of speciation in cryptic species complexes. Moreover, we show that some of these cryptic species are subject to increased extinction risks due to small population size and anthropogenic changes (habitat degradation and climate change). These changes were captured accurately in a recent Mammal Red List of South Africa, Lesotho and Swaziland, indicating that taxonomists and conservationists can work together to assess the Red List status of cryptic species based on robust taxonomic revisions.

When Viruses Don't Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses

Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon’s range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa.

Reservoirs of zoonotic viruses are usually equated with a particular wildlife species. It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir, though this would have major implications on estimations of the zoonosis’ spatial distribution. Here we investigate whether geographically and genetically distinct subtaxa of the widespread African rodent Mastomys natalensis carry distinct arenaviruses, by sampling in detail across a contact zone of two of these subtaxa. Ongoing hybridization shows that individuals of the subtaxa are in direct physical contact, in principle allowing viral exchange, yet neither of the two arenaviruses -Gairo and Morogoro virus- were found to have crossed the zone. Such intraspecific genetic barriers to arenavirus spatial spread have important implications for our understanding of the related Lassa arenavirus, a pathogen potentially lethal to humans of which Mastomys natalensis is also the main reservoir. Although Lassa virus appears to infect several secondary hosts, its distribution is restricted to West Africa and matches that of another M. natalensis subtaxon. Our data thus indicates that it is because of M. natalensis intraspecific distinctions that the human Lassa fever endemic area has not expanded to the rest of sub-Saharan Africa.