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

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

Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera

The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.

Discovery of two new populations of the rare endemic freshwater crab Louisea yabassi Mvogo Ndongo, von Rintelen & Cumberlidge, 2019 (Brachyura: Potamonautidae) from the Ebo Forest near Yabassi in Cameroon, Central Africa, with recommendations for conservation action

The endemic freshwater crab, Louisea yabassi Mvogo Ndongo, von Rintelen & Cumberlidge, 2019, is currently only known from three populations in the biodiversity-rich rainforests of southwestern Cameroon.  The first record of L. yabassi dates back to 1908 from Yabassi, while the other two populations were discovered in December 2019 and March 2020 from the Ebo Forest near Yabassi.  These specimens were initially identified as L. edeaensis (Bott, 1969), but were subsequently assigned to L. yabassi.  The newly-discovered populations of L. yabassi provided important data on its habitat, population structure and geographical distribution, all critical knowledge for conservation measures.  Reported here are the anthropogenic threats to L. yabassi and its rainforest habitat, which include forest destruction, agricultural encroachment, water pollution and firewood collection.  This information is inherently useful in the assessment of the extinction risk of L. yabassi and highlights the importance of implementing strategies for preserving primary rainforest and its associated aquatic habitats in Central Africa.

Description of Heteracris lecoqi Yetchom-Fondjo amp; Kekeunou sp. nov. and Heteracris hannai Wandji amp; Kekeunou sp. nov. and redescription of Heteracris guineensis (Krauss, 1890) (Orthoptera: Acrididae) with comments on its ecology in the Southern part of Cameroon

The specimens studied were collected with sweep net and pitfall in the forests, agro-forests, herbaceous fallows, and crop fields of 14 localities in the southern part of Cameroon, from August 2015 to February 2018. The results show that Heteracris hannai sp. nov. and Heteracris lecoqi sp. nov. differ from previously known species of the same genus by the pattern of coloration and the details or shape of the phallic complex. H. lecoqi sp. nov. is characterized by light brownish body; male cercus with flattened, downcurved and obtuse apex; lophus strongly curved; interlophal space with V shape; apodeme of cingulum bow, convergent, with V-shape; valve of cingulum in lateral view longer than apical valve of penis; ramus in ventral view joined. H. hannai sp. nov. is distinct to other species by brown to grey body; male cercus with apex rounded, curved inside; lophus curved; interlophal space with U-shape; apodeme of cingulum thick, slightly parallel, with U shape; valve of cingulum in lateral view hardly longer than apical valve of penis; ramus in ventral view opened. The characteristics of H. guineensis are closer to H. hannai sp. nov. than to H. lecoqi sp. nov. H. lecoqi sp. nov. was collected only in the fallows while H. hannai sp. nov. was collected in the forests, agro-forests, fallows, and crop fields. Compared to H. guineensis, both new species are scarce in the natural vegetation and their distribution area is limited to two and four localities respectively for H. lecoqi sp. nov. and H. hannai sp. nov. All these three grasshopper's species were recorded as accidental species in all types of vegetation.

Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota)

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.

A Checklist of Short-horned Grasshopper Species (Orthoptera: Caelifera) from Littoral Region of Cameroon with description of a new species of the genus Hemierianthus Saussure, 1903 (Orthoptera: Chorotypidae)

The Littoral Region of Cameroon is one of the most highly disturbed regions in Cameroon that remain poorly studied and where no investigation regarding the grasshopper fauna has been conducted. Hence a survey was conducted from August 2015 to November 2018 in 11 localities of this region. In each locality, grasshoppers were sampled in three vegetation types (forests, fallows and cultivated farms) using sweep nets sampling method. We collected in total 51 short-horned grasshopper species belonging to the families Acrididae, Chorotypidae, Euschmidtiidae, Pyrgomorphidae and Thericleidae. Among these species, 43 belong to Acrididae, 5 to Pyrgomorphidae and only one belongs to the Chorotypidae, Euschmidtiidae and Thericleidae respectively. The Chorotypidae species Hemierianthus mbongueensis Yetchom Xu sp.nov. is also described in this study. Twelve grasshopper species were widely distributed as they occurred in all study sites and 11 were recorded exclusively from one study site. This study showed that there is high species richness of short-horned grasshoppers in the Littoral Region of Cameroon. However, more sampling effort in different ecosystems of this region and other regions of Cameroon will certainly improve our understanding on grasshopper taxonomy, ecology and biogeography.

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.

Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae)

The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.

Biodiversity conservation, ecosystem functioning, and economic incentives under cocoa agroforestry intensification

World chocolate demand is expected to more than double by 2050. Decisions about how to meet this challenge will have profound effects on tropical rainforests and wild species in cocoa-producing countries. Cocoa, "the chocolate tree," is traditionally produced under a diverse and dense canopy of shade trees that provide habitat for a high diversity of organisms. The current trend to reduce or eliminate shade cover raises concerns about the potential loss of biodiversity. Nevertheless, few studies have assessed the ecological consequences and economic trade-offs under different management options in cocoa plantations. Here we describe the relationships between ant ecology (species richness, community composition, and abundance) and vegetation structure, ecosystem functions, and economic profitability under different land-use management systems in 17 traditional cocoa forest gardens in southern Cameroon. We calculated an index of profitability, based on the net annual income per hectare. We found significant differences associated with the different land-use management systems for species richness and abundance of ants and species richness and density of trees. Ant species richness was significantly higher in floristically and structurally diverse, low-intensity, old cocoa systems than in intensive young systems. Ant species richness was significantly related to tree species richness and density. We found no clear relationship between profitability and biodiversity. Nevertheless, we suggest that improving the income and livelihood of smallholder cocoa farmers will require economic incentives to discourage further intensification and ecologically detrimental loss of shade cover. Certification programs for shade-grown cocoa may provide socioeconomic incentives to slow intensification.