Canine parvovirus detected from a serval (Leptailurus serval) in South Africa

Canine parvovirus first emerged in domestic dogs (Canis familiaris), most likely as a variant of the feline panleucopaenia virus. Relatively recently, canine parvovirus-2a and canine parvovirus-2b infections have been identified in both symptomatic and asymptomatic domestic cats, while canine parvovirus infections have also been demonstrated in wild felids. This report documents the first known case of canine parvovirus-2b detected in unvaccinated serval (Leptailurus serval) from South Africa. The serval presented with clinical signs of vomiting, anorexia and diarrhoea that responded to symptomatic treatment. Two weeks later, severe leucopaenia, thrombocytopenia and death occurred. Typical enteric histological lesions of parvovirus infection were not observed on histopathological examination of the small intestine; however, histological lesions consistent with septicaemia were present. Canine parvovirus was detected in formalin-fixed paraffin-embedded small intestine using polymerase chain reaction. Phylogenetic analysis of the sequence of the canine parvovirus viral capsid protein gene showed similarities between the sample from the serval and canine parvovirus-2b isolates from domestic dogs in Argentina and South Africa. A case of canine parvovirus-2b in a domestic dog from South Africa in 2012 that fell within the same clade as the serval sample appears distantly related because of the long branch length. The significance of these findings is explored. More extensive surveys of canine parvovirus in domestic and wild felids and canids are needed to understand the epidemiology of canine parvovirus in non-domestic felids in South Africa

An annotated checklist of the mammals of the Chimanimani National Park, Mozambique

The Chimanimani Mountains of Mozambique and Zimbabwe harbour a diverse and unique flora and fauna. Because of its unique flora this region has received considerable attention by botanists. In contrast, the vertebrates occurring here have received little attention. The aim of this paper was to synthesise data collected on multiple recent surveys into the first annotated checklist of the mammals the Chimanimani Mountains on the Mozambique side. We combined morphological and molecular methods to identify small mammals, and we report on echolocation calls of some of the poorly known bat species. In total, we recorded 69 species including 23 species of bats (Chiroptera), 15 species of rodents (Rodentia), 11 species of carnivores (Carnivora), nine species of ungulates (Cetartiodactyla), and the rest comprising Primates, Eulipotyphla, Lagomorpha, Proboscidea, and Pholidota. Of these, five species were threatened species, demonstrating the importance of the Chimanimani Mountains for biodiversity conservation

Biomes, geology and past climate drive speciation of laminate-toothed rats on South African mountains (Murinae: Otomys)

Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment)

Gene flow and population structure of a solitary top carnivore in a human-dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free-roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human-carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human-caused extinctions.Carnegie Corporation of New York to the Global Change and Sustainability Research Institute at the University of the Witwatersrand. ABAX Foundation, Henry and Iris Englund Foundation, National Lotteries Distribution Trust Fund, Mones Michaels Trust, Arne Hanson, and Deutsche Bank South Africa Foundation.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2045-7758hb201

A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species

Vespertilionidae (class Mammalia) constitutes the largest family of bats, with ~500 described species. Nonetheless, the systematic relationships within this family are poorly known, especially among the pipistrelle-like bats of the tribes Vespertilionini and Pipistrellini. Perhaps as a result of their drab pelage and lack of obvious morphological characters, the genus and species limits of pipistrelle-like bats remain poorly resolved, particularly in Africa, where more than one-fifth of all vesper bat species occur. Further exacerbating the problem is the accelerating description of new species within these groups. In this study, we attempt to resolve the systematic relationships among the pipistrelle-like bats of sub-Saharan Africa and Madagascar and provide a more stable framework for future systematic efforts. Our systematic inferences are based on extensive genetic and morphological sampling of > 400 individuals covering all named genera and the majority of described African pipistrelle-like bat species, focusing on previously unstudied samples of East African bats. Our study corroborates previous work by identifying three African genera in Pipistrellini (Pipistrellus, Scotoecus and Vansonia), none of which is endemic to Africa. However, the situation is more complex in Vespertilionini. With broad taxonomic sampling, we confirm that the genus Neoromicia is paraphyletic, a situation that we resolve by assigning the species of Neoromicia to four genera. Neoromicia is here restricted to Neoromicia zuluensis and allied taxa. Some erstwhile Neoromicia species are transferred into an expanded Laephotis, which now includes both long-eared and short-eared forms. We also erect two new genera, one comprising a group of mostly forest-associated species (many of which have white wings) and the other for the genetically and morphologically unique banana bat. All four of these genera, as recognized here, are genetically distinct, have distinctive bacular morphologies and can be grouped by cranial morphometrics. We also demonstrate that the genus Nycticeinops, until now considered monospecific, includes both Afropipistrellus and the recently named Parahypsugo, thus representing the fifth African genus in Vespertilionini. A sixth genus, Hypsugo, is mostly extra-limital to sub-Saharan Africa. Finally, we describe three new species of pipistrelle-like bats from Kenya and Uganda, uncovered during the course of systematic bat surveys in the region. Such surveys are greatly needed across tropical Africa to uncover further bat diversity.https://academic.oup.com/zoolinneanhj2022Mammal Research InstituteZoology and Entomolog

Interspecific hybridization between greater kudu and nyala

Hybridization of wildlife species, even in the absence of introgression, is of concern due to wasted reproductive effort and a reduction in productivity. In this study we detail an accidental mating between a female nyala (Tragelaphus angasii) and a male greater kudu (T. strepsiceros). The hybrid was phenotypically nyala and was identified as such based on mitochondrial DNA. Further genetic analysis based on nine microsatellite markers, chromosome number and chromosome morphology however, confirmed its status as an F1 hybrid. Results obtained from a reproductive potential assessment indicated that this animal does not have the potential to breed successfully and can be considered as sterile.http://link.springer.com/journal/10709hb201

Broad-scale genetic assessment of southern ground-hornbills (Bucorvus leadbeateri) to inform population management

DATA AVAILABILITY : Bucorvus leadbeateri sequences are available on GenBank, accession numbers: OP046521-OP046574, and OP122231 - OP122407.The Southern Ground-hornbill (SGH) (Bucorvus leadbeateri) is considered an umbrella species for biodiversity conservation in savannah biomes since they require large territories and significant protection measures that help to conserve a wide range of biodiversity with similar savanna and grassland requirements. Declines of the species are attributed to low reproductive rates coupled with multiple anthropogenic threats, including secondary poisoning, and persecution. Little is known about connectivity and population structure of SGH populations in Africa, south of the equator. Knowledge of population differentiation is needed to ensure that targeted conservation management plans can be implemented to slow population declines and ensure survival of the species. To inform a long-term conservation strategy, we investigated the broad-scale population structure of Southern Ground-hornbill across their sub-equatorial range. Our study based on 16 microsatellite loci identified moderate variation (average of 5.889 alleles per locus and a mean observed heterozygosity of 0.546) similar to other long-lived avian species. In contrast, mitochondrial DNA sequences analysis identified low diversity (Hd = 0.3313, π = 0.0015). A Bayesian assignment approach, principal component analysis, analysis of molecular variance and phylogenetic analysis identified weak to moderate population structuring across long distances and mitochondrial data showed a shallow phylogeny. Restriction to long-distance dispersal was detected that could not be attributed to isolation by distance, suggesting that other factors, such as their dispersal biology, are shaping the observed genetic differentiation. Although our study does not support the designation of populations as independent conservation units, we advocate that population management should continue to follow the Precautionary Principle (mixing founders from the same range state, rather than allowing mixing of founders from the extremes of the range) until there is scientific certainty. Following further research, if no independent conservation units are detected, then the global captive population can contribute to reintroductions across the range. In the wild, populations at the edge of the species range may need additional management strategies and gene flow should be promoted between neighbouring populations.https://www.elsevier.com/locate/geccohj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results

Genetic diversity and origin of captive lion (Panthera leo) in South Africa : an assessment and comparison to wild populations

DATA AVAILABILITY : All data used in this manuscript are included in the supplementary materials. The supplementary materials are archived here: https://DOI.org/10.25375/uct.23174729.South Africa has a large captive lion (Panthera leo) sector, but detailed knowledge on the origin of individuals and any potential genetic value to conservation targets is lacking. In 2021, the South African government committed to closing the sector and have since appointed a Ministerial Lion Task Team (2022) to initiate this process. Some have suggested that captive lions could be integrated into wild populations as part of the process but information on the genetic origins and diversity of captive lions is critical if this is to be explored further. Both the Biodiversity Management Plan for lions in South Africa (2015) and a High-Level Ministerial report for the South African government (2021) have called for more information on the genetic composition of captive lions. To determine the probable origin of captive lions in South Africa we summarised existing survey responses from captive facilities (collected 2017–2018) and CITES permit data (issued 1991–2019). Survey data suggest that most lions were sourced from within the South African captive sector. However, many CITES permits were also issued for the import of lions from across Africa and beyond, indicating possible mixed origins within the sector. To evaluate genetic relationships between captive and wild lions in South Africa we standardised existing microsatellite marker data from three laboratories and analysed genotypes of captive lions from 31 properties. A comparison of captive and wild lion genotypes revealed that the genetic composition of captive lions is currently comparable to existing wild South African lions. Captive lions cluster with similar probabilities to three of four regional reference populations of wild lions included in the study and no major signatures of inbreeding were identified. However, captive lions are highly genetically interconnected across properties and represent a smaller effective population size compared to Kruger National Park, the largest population of wild lions in South Africa, suggesting some risk of future inbreeding. There were also signatures of genetic drift which should be investigated further as it will likely compromise any potential conservation genetic value of captive lions in the future. The findings of this study should be considered when planning the fate of individuals within South Africa’s captive lion sector and within the broader context of African lion conservation.Open access funding provided by University of Cape Town.http://link.springer.com/journal/10592am2024Microbiology and Plant PathologySDG-15:Life on lan