Re-assessed molecular phylogeny and evolutionary scenario within genets (Carnivora, Viverridae, Genettinae)

Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

The molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

A contextual review of the Carnivora of Kanapoi

The Early Pliocene is a crucial time period in carnivoran evolution. Holarctic carnivoran faunas suffered a turnover event at the Miocene-Pliocene boundary. This event is also observed in Africa but its onset is later and the process more drawn-out. Kanapoi is one of the earliest faunas in Africa to show evidence of a fauna that is more typical Pliocene than Miocene in character. The taxa recovered from Kanapoi are: Torolutra sp., Enhydriodon (2 species), Genetta sp., Helogale sp., Homotherium sp., Dinofelis petteri, Felis sp., and Parahyaena howelli. Analysis of the broader carnivoran context of which Kanapoi is an example shows that all these taxa are characteristic of Plio-Pleistocene African faunas, rather than Miocene ones. While some are still extant and some went extinct in the Early Pleistocene, P. howelli is unique in both originating and going extinct in the Early Pliocene.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.

Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria

Context Following recent socioeconomic transformations in western and central Africa, the volume of bushmeat hunting, a traditional source of proteins and revenue for rural populations, has reached unsustainable levels. The morphological identification of species sold on bushmeat market stalls may be challenging because of the presence of cryptic taxa and smoked or processed carcasses. Aims To assess the contribution of DNA-typing to traditional bushmeat surveys. We conducted a case study at a roadside bushmeat market in Asejire, south-western Nigeria, to characterise the mammalian diversity and sketch out the dynamics of the bushmeat trade. Methods We generated a 402-bp Cytochrome b fragment using a ‘universal’ mitochondrial primer pair that successfully amplified across five mammalian orders, and used assignment procedures to assess the taxonomic identification of the traded species. We combined DNA-typing with morphological-based market surveys and questionnaires to half (n = 20) of the market stakeholders. Key results Our combined morphological–DNA-based survey revealed a total of 17 species, representing seven mammalian orders (Rodentia, Lagomorpha, Primates, Hyracoidea, Carnivora, Pholidota and Artiodactyla). DNA-typing allowed identifying the Walter’s duiker, a cryptic, newly described species from the Dahomey Gap, and diagnosing an unidentified primate as the white-throated monkey, Cercopithecus erythrogaster, a species of high conservation concern in Nigeria. K2P pairwise genetic distances among all species exceeded the 11% threshold, indicative of species-level distinction. The most hunted species were the Walter’s duiker and, to a lesser extent, the greater cane rat, Thryonomys swinderianus. Questionnaires to traders revealed that the Asejire roadside market was a straightforward trader–hunter system centralising off-takes from distant hunting sites. Conclusions We showed how mitochondrial DNA-typing combined with assignment procedures improved the characterisation of the mammalian diversity sold on bushmeat markets. The hunted mammalian community consisted of versatile, small- to medium-sized secondary forest species characteristic of the Dahomey Gap assemblage; their sustainable management is in doubt because of the lack of conservation and health awareness within the traders’ community. Implications Given the utility of mitochondrial DNA-typing in identifying species sold in bushmeat markets, we argue in favour of multi-entry investigations to reach a comprehensive characterisation of the bushmeat trade. The building of a web-accessible mtDNA database covering the spectrum of the species hunted for bushmeat would appear to be a valuable diagnostic tool that may help Nigeria and neighbouring countries to set up a rigorous monitoring of wildlife extirpation.

Red drifters and dark residents: the phylogeny and ecology of a Plio-Pleistocene dragonfly radiation reflects Africa's changing environment (Odonata, Libellulidae, Trithemis)

In the last few million years, tropical Africa has experienced pronounced climatic shifts with progressive aridification. Such changes must have had a great impact on freshwater biota, such as Odonata. With about forty species, Trithemis dominates dragonfly communities across Africa, from rain-pools to streams, deserts to rainforests, and lowlands to highlands. Red-bodied species tend to favor exposed, standing and often temporary waters, have strong dispersal capacities, and some of the largest geographic ranges in the genus. Those in cooler habitats, like forest streams, are generally dark-bodied and more sedentary. We combined molecular analyses of ND1, 16S, and ITS (ITSI, 5.8S, and ITSII) with morphological, ecological, and geographical data for 81% of known Trithemis species, including three Asian and two Madagascan endemics. Using molecular clock analyses, the genus's origin was estimated 6-9Mya, with multiple lineages arising suddenly around 4Mya. Open stagnant habitats were inferred to be ancestral and the rise of Trithemis may have coincided with savannah-expansion in the late Miocene. The adaptation of red species to more ephemeral conditions leads to large ranges and limited radiation within those lineages. By contrast, three clades of dark species radiated in the Plio-Pleistocene, each within distinct ecological confines: (1) lowland streams, (2) highland streams, and (3) swampy habitats on alternating sides of the Congo-Zambezi watershed divide; together giving rise to the majority of species diversity in the genus. During Trithemis evolution, multiple shifts from open to more forested habitats and from standing to running waters occurred. Allopatry by habitat fragmentation may be the dominant force in speciation, but possibly genetic divergence across habitat gradients was also involved. The study demonstrates the importance of combining ecological and phylogenetic data to understand the origin of biological diversity under great environmental change.

Dogs, cats, and kin: a molecular species-level phylogeny of Carnivora

Phylogenies underpin comparative biology as high-utility tools to test evolutionary and biogeographic hypotheses, inform on conservation strategies, and reveal the age and evolutionary histories of traits and lineages. As tools, most powerful are those phylogenies that contain all, or nearly all, of the taxa of a given group. Despite their obvious utility, such phylogenies, other than summary 'supertrees', are currently lacking for most mammalian orders, including the order Carnivora. Carnivora consists of about 270 extant species including most of the world's large terrestrial predators (e.g., the big cats, wolves, bears), as well as many of man's favorite wild (panda, cheetah, tiger) and domesticated animals (dog, cat). Distributed globally, carnivores are highly diverse ecologically, having occupied all major habitat types on the planet and being diverse in traits such as sociality, communication, body/brain size, and foraging ecology. Thus, numerous studies continue to address comparative questions within the order, highlighting the need for a detailed species-level phylogeny. Here we present a phylogeny of Carnivora that increases taxon sampling density from 28% in the most detailed primary-data study to date, to 82% containing 243 taxa (222 extant species, 17 subspecies). In addition to extant species, we sampled four extinct species: American cheetah, saber-toothed cat, cave bear and the giant short-faced bear. Bayesian analysis of cytochrome b sequences data-mined from GenBank results in a phylogenetic hypothesis that is largely congruent with prior studies based on fewer taxa but more characters. We find support for the monophyly of Carnivora, its major division into Caniformia and Feliformia, and for all but one family within the order. The only exception is the placement of the kinkajou outside Procyonidae, however, prior studies have already cast doubt on its family placement. In contrast, at the subfamily and genus level, our results indicate numerous problems with current classification. Our results also propose new, controversial hypotheses, such as the possible placement of the red panda (Ailuridae) sister to canids (Canidae). Our results confirm previous findings suggesting that the dog was domesticated from the Eurasian wolf (Canis lupus lupus) and are congruent with the Near East domestication of the cat. In sum, this study presents the most detailed species-level phylogeny of Carnivora to date and a much needed tool for comparative studies of carnivoran species. To demonstrate one such use, we perform a phylogenetic analysis of evolutionary distinctiveness (EDGE), which can be used to help establish conservation priorities. According with those criteria, and under one of the many possible sets of parameters, the highest priority Carnivora species for conservation of evolutionary diversity include: monk seals, giant and red panda, giant otter, otter civet, Owston's palm civet, sea otter, Liberian mongoose, spectacled bear, walrus, binturong, and the fossa.