Antoinette Kotze

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross‐tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa

Poaching of wildlife animals for subsistence and commercial purposes has lead to population declines in Africa. In forensic cases, a need exists to identify the species of origin of carcasses, meat or blood. In the study presented here, the mitochondrial COI gene was sequenced to determine the species of unknown samples in three suspect South African forensic wildlife cases. In two cases the unknown samples were identified as originating from domestic cattle (Bos taurus) and in the third case the sample was identified as common reedbuck (Redunca arundinum). This is the first report of the COI sequence of common reedbuck. The study highlights the need for accurate wildlife reference material from each country in order to convict wildlife cases.

Mixed infections of Corynebacterium pseudotuberculosis and non-tuberculous mycobacteria in South African antelopes presenting with tuberculosis-like lesions.

Routine meat inspection of antelope carcasses from a South African game reserve revealed a high prevalence of tuberculosis-like lesions. This study aimed to identify the causative agent of this disease and to describe its pathological features. In total, 139 antelopes were randomly harvested from the game reserve and subjected to meat inspection. Of these animals, 46 (33%) showed gross visible, tuberculosis-like lesions. Histopathological examination revealed the presence of encapsulated necrogranulomas in organs and/or lymph nodes of 22 of 27 animals tested. Tissue samples from lesions were processed for both non-selective bacterial culture and mycobacterial culture following decontamination. In non-selective cultures of lesions from 25 of 31 animals tested, Corynebacterium pseudotuberculosis was detected. Isolation of C. pseudotuberculosis was closely associated with the presence of necrogranulomas. In mycobacterial cultures of lesions from 9 of 41 animals tested, different species of non-tuberculous mycobacteria (NTMs) were detected. In 5 instances, depending on the culture procedure that was applied, either C. pseudotuberculosis or NTMs were isolated from the same tissue sample. Our results suggest that the disease has been caused by infections with C. pseudotuberculosis. In sub-Saharan Africa, the role of pathogens other than Mycobacterium bovis may be underestimated in causing tuberculosis-like lesions. In cases where potentially pathogenic NTMs are isolated from mycobacterial cultures of tuberculosis-like lesions, the non-use of additional non-selective culture techniques could lead to misinterpretations of the diagnostic test results.

Management of hybridization in an endemic species: decision making in the face of imperfect information in the case of the black wildebeest—Connochaetes gnou

Hybridization between introduced and endemic ungulates, resulting from anthropogenic actions, has been reported for several species. Several studies of such events contain the common themes of extralimital movements, problematic phenotypic and genetic detection, and imperfect management. In southern Africa, the endemic black wildebeest (Connochaetes gnou) currently faces a serious threat of hybridization and introgression. This species survived near extinction and consequent genetic bottlenecks in the late 1800s and in the 1930s. Initiatives by private farmers followed by conservation authorities led to a dramatic recovery in numbers of this species. However, in an ironic twist, the very same advances in conservation and commercial utilisation which led to the recovery of numbers are now themselves threatening the species. Injudicious translocation has brought the species into contact with its congener, the blue wildebeest (Connochaetes taurinus), and in recent times, hybridization between the species has occurred at numerous localities in South Africa. Consequently, a significant proportion of the national black wildebeest population potentially carries a proportion of introgressed blue wildebeest genetic material. We discuss completed and ongoing attempts to find molecular markers to detect hybrids and highlight the difficulty of detecting advanced backcrosses. Additional avenues of research, such as work on morphology (cranial and postcranial elements), estimating of the probability of introgression and modelling of diffusion rates are also introduced. In addition to the difficulty in detecting hybrid animals or herds, the lack of consensus on the fate of hybrid herds is discussed. Finally, in an environment of imperfect information, we caution against implementation of management responses that will potentially induce a new genetic bottleneck in C. gnou.

The genetic status of an isolated black wildebeest (Connochaetes gnou) population from the Abe Bailey Nature Reserve, South Africa: Microsatellite data on a putative past hybridization with blue wildebeest (C. taurinus)

Summary The present study aimed at assessing genetic purity of black wildebeest ( Connochaetes gnou ) at Abe Bailey Nature Reserve, Gauteng Province, South Africa, using a multilocus microsatellite approach. Five loci were studied in black and blue ( C. taurinus ) wildebeest, the latter being a closely related species and known to produce hybrids with the morphologically very similar black wildebeest. In fact, the entire national black wildebeest population of South Africa potentially contains a significant proportion of introgressed blue wildebeest genes. In our case, eight out of 39 alleles were unique to black and 22 to blue wildebeest, with nine alleles shared between pure populations of the two species in line with their taxonomic proximity. A possible limited past introgression of blue wildebeest genes into the Abe Bailey population, corresponding to documents on population history, was only supported by the presence of a single allele otherwise exclusively found in samples of four pure blue but not in samples of two pure black wildebeest control populations. However, an assignment test and coefficients of population divergence did not support an extended introgression of C. taurinus alleles into the C .gnou population under study. Average heterozygosity at Abe Bailey proved to be intermediate between black and blue wildebeest, the latter species generally harbouring more genetic variation than the former owing to larger population sizes and the absence of population bottlenecks in historical times. The implications of our data are discussed with reference to the persistence of introgressed genes and the conservation of pure black wildebeest gene pools.

Pulmonary Infection due to Mycobacterium bovis in a Black Rhinoceros (Diceros bicornis minor) in South Africa

We report a case of tuberculosis due to infection with Mycobacterium bovis in an elderly male black rhinoceros (Diceros bicornis minor) from the Limpopo Province in South Africa. The animal was euthanized due to very poor condition, old age, and dental attrition. Necropsy examination revealed two small nonencapsulated granulomas (∼40-mm diameter) in the dorsocaudal lobe of the left lung. Sequencing of isolated crude lung tissue PCR product and boiled lung culture samples confirmed that the causative organism was M. bovis. Genotyping revealed limited similarities with M. bovis strains isolated thus far from South African cattle or wildlife. The source of the infection could not be determined. This case illustrates that M. bovis could impact conservation of free-ranging rare and endangered species. Effective diagnostics are urgently needed for different animal species, such as white or black rhinoceroses, to certify with a reasonable degree of certainty that these animals are free of tuberculosis in natural habitats.

The complete mitochondrial genome of Temminck's ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic position of the Pholidota (Weber, 1904)

Temminckis ground pangolin is primarily a nocturnal mammal belonging to the order Pholidota. The body is covered in hard overlapping scales and these animals find refuge in burrows, feeding only on termites and ants. In this study, the whole mtDNA of Temminckis ground pangolin was sequenced and the phylogenetic position of Pholidota determined within Eutheria, using whole mtDNA sequences from various representative species. The results indicate that the whole mtDNA of Temminckis ground pangolin is 16,559 bp long and shared some similarities with the whole mtDNA of the back-bellied tree pangolin and the Chinese pangolin. Phylogenetic analysis indicate that the order Pholidota is closely related and share a recent common ancestor with the order Carnivora rather than with the ant/insect eating order Xenarthra and the group Afrotheria. A time measured phylogeny of Pholidota estimated a split from Carnivora at around 87 mya, followed by a split of the African pangolins from their Asian counterparts such as the Chinese pangolin at around 47 mya. This suggests a Laurasian origin and convergent evolution of the Pholidota with respect to Xenarthra and Afrotheria.

Knowledge and Uses of African Pangolins as a Source of Traditional Medicine in Ghana

Traditional medicine has been practised in Ghana for centuries with the majority of Ghanaians still patronising the services of traditional healers. Throughout Africa a large number of people use pangolins as a source of traditional medicine, however, there is a dearth of information on the use of animals in folk medicine in Ghana, in particular the use of pangolins. The aim of this study was to determine the prevalent use of pangolins and the level of knowledge of pangolin use among traditional healers in Ghana for the treatment of human ailments. Data was gathered from 48 traditional healers using semi-structured interviews on the traditional medicinal use of pangolin body parts in the Kumasi metropolis of Ghana. The cultural importance index, relative frequency of citation, informant agreement ratio and use agreement values were calculated to ascertain the most culturally important pangolin body part as well as the level of knowledge dissemination among traditional healers with regards pangolin body parts. Our study revealed that 13 body parts of pangolins are used to treat various medicinal ailments. Pangolin scales and bones were the most prevalent prescribed body parts and indicated the highest cultural significance among traditional healing practices primarily for the treatment of spiritual protection, rheumatism, financial rituals and convulsions. Despite being classified under Schedule 1 of Ghana’s Wildlife Conservation Act of 1971 (LI 685), that prohibits anyone from hunting or being in possession of a pangolin, our results indicated that the use of pangolins for traditional medicinal purposes is widespread among traditional healers in Ghana. A study on the population status and ecology of the three species of African pangolins occurring in Ghana is urgently required in order to determine the impact this harvest for traditional medical purposes has on their respective populations as current levels appear to be unmonitored and unsustainable.

PANSTEATITIS OF UNKNOWN ETIOLOGY ASSOCIATED WITH LARGE-SCALE NILE CROCODILE (CROCODYLUS NILOTICUS) MORTALITY IN KRUGER NATIONAL PARK, SOUTH AFRICA: PATHOLOGIC FINDINGS

Annual mortality events in Nile crocodiles (Crocodylus niloticus) in the Olifants River Gorge in Kruger National Park, South Africa, were experienced between 2008 and 2012, during which at least 216 crocodiles died. Live crocodiles were lethargic. Necropsy examination of 56 affected crocodiles showed dark yellow-brown firm nodules in both somatic fat and the abdominal fat body. In all of the 11 crocodiles submitted for histology, degenerative, necrotic, and inflammatory changes supported a diagnosis of steatitis in both fat types. Crocodiles are apex predators in this anthropogenically changed aquatic ecosystem that is used by humans upstream and downstream from the park for domestic, agricultural, fishing, and recreational purposes. This pathologic review of pansteatitis in crocodiles in the Olifants River system was part of a broad multidisciplinary research program. To date, no definitive causative agent has been identified. Epidemiologic evidence suggests that this event may have been a one-time event with long-standing repercussions on the health of the crocodiles. Pathologic findings are rarely documented in wild crocodilians. This study also reports on other conditions, including the presence of coccidian oocysts, capillarid and filaroid nematodes, digenetic trematodes, and pentastomes.

Extinctions, genetic erosion and conservation options for the black rhinoceros ( Diceros bicornis )

The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species’ mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.