Monitoring compliance of CITES lion bone exports from South Africa

From 2008 to 2018, South Africa permitted the export of captive-bred African lion (Panthera leo) skeletons to Southeast Asia under CITES Appendix II. Legal exports rose from approximately 50 individuals in 2008 to a maximum of 1,771 skeletons in 2016, and has led to ongoing concerns over possible laundering of non-lion, multiple-source and wild-sourced bones. South Africa is required under its obligations to CITES to employ mechanisms for monitoring and reporting trade, and to limit the potential for illegal trade and laundering of lion and other large felid bones. Monitoring tools for legal trade are critical to compliance with CITES. Here we evaluate the CITES-compliance procedure implemented by South Africa for export of lion bones and identify six essential general points for consideration in the implementation of animal export quota compliance protocols. We provide specific insight into the South African lion bone export monitoring system through: i) outlining the protocols followed; ii) assessing the utility of cranial morphology to identify species; iii) evaluating skeleton consignment weight as a monitoring tool; and iv) presenting molecular (DNA) species assignment and pairwise-comparative sample matching of individuals. We describe irregularities and illicit behaviour detected in the 2017 and 2018 lion bone quotas. Notably, we report that the compliance procedure successfully identified and prevented the attempted laundering of a tiger (P. tigris) skeleton in 2018. We emphasise the utility of mixed-method protocols for the monitoring of compliance in CITES Appendix II export quota systems

Differentiation of two South African otter species (Aonyx capensis and Lutra maculicollis) from spraint based on partial CytB primer sets

AbstractAccurate species identification based on visual cues can be challenging due to morphological similarities and the cryptic nature of certain species. Thus a more conclusive method of identification is required, namely DNA barcoding. This is the case regarding two South African otter species, Cape Clawless otter (Aonyx capensis) and the spotted necked otter (Lutra maculicollis). Due to the cryptic nature of these animals faecal samples, known as spraints, are the easiest way of confirming the presence of the animal in an area. In this study, we compared results obtained for universal and partial CytB primer sets on collected spraint and tissue control samples. Universal CytB primers revealed a low percentage of amplified otter species from faecal samples (species specific amplification success of 10.9%) whereas, the partial CytB primer set resulted in successful amplification of 45 out of 55 (82%) samples. We were thus able to positively differentiate between the two otter species using the partial CytB primer set developed in this study. The ability to accurately identify species using partial DNA will be beneficial in understanding numerous aspects of the behaviour and ecological importance of animals in their environment

Ethnomedicinal use of African pangolins by traditional medical practitioners in Sierra Leone

Abstract Background: Pangolins (Manidae) have long been used for traditional medicinal purposes in most parts of sub-Saharan Africa. However, very little is known about the extent of this use, the body parts that are used and the ailments these practices are attempting to cure or alleviate. Pangolin body parts are used extensively and frequently by traditional medical practitioners in Sierra Leone. Methods: A total of 63 traditional medical practitioners consented and were interviewed using semi-structured questionnaires on the traditional medicinal use of pangolin body parts. The use value, informant agreement ratio and use agreement value for each pangolin part was calculated to ascertain the most sought after body part, the level of knowledge dissemination among traditional medical practitioners about body parts and the most culturally significant body part. Results: It was found that 22 pangolin parts are used to treat various ailments and conditions under 17 international categories of diseases. The highest use value was recorded for scales while eyes had the highest level of consensus among the traditional medical practitioners. The highest use value and informant agreement ratio for scales were recorded for spiritual ailments. Scales were the most culturally significant body part according to the use agreement value

Broad-scale genetic assessment of Southern Ground-Hornbills (Bucorvus leadbeateri) to inform population management.

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

Absence of 2899C<T mutation in the WNK4 gene in a free-ranging lion (Panthera leo) with polymyopathy

Polyphasic skeletal muscle degeneration, necrosis and mineralization of skeletal muscle was diagnosed in eight juvenile free-ranging lions (Panthera leo), from five different litters in the Greater Kruger National Park area that were unable to walk properly. A detailed investigation was not possible in free-ranging lions, so the cause could not be determined. The cases resembled hypokalemic polymyopathy in domestic cats with muscle weakness. A candidate-gene approach previously identified a nonsense mutation in the gene coding for the enzyme lysine-deficient 4 protein kinase (WNK4) associated with the disease in Burmese and Tonkinese cats. In this study, we sequenced all 19 exons of the gene in one case, and two control samples, to identify possible mutations that may be associated with polymyopathy in free-ranging lions. Here, no mutations were detected in any of the exons sequenced. Our findings indicate that the WNK4 gene is not a major contributor to the condition in these lions. Further studies into the pathogenesis of this condition are needed to inform conservation policies for this vulnerable, iconic African specieshttp://www.mdpi.com/journal/animalsCentre for Veterinary Wildlife StudiesParaclinical Science

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

Data from: Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation

Once widely distributed throughout Africa, cheetahs (Acinonyx jubatus) occur today within fragmented populations and are listed as vulnerable by the IUCN. Botswana currently hosts the second largest cheetah population throughout the species’ range. This study initiated a molecular genetic survey of wild Botswana cheetah populations. It focused on the relatedness within presumed social groups using 14 microsatellite markers and revealed a higher proportion of unrelated male coalitions than was expected. Based on the unrelated cheetahs only, the estimation of the genetic variation corresponded with results from recent studies on different African populations. The analysis of unrelated individuals indicated limited genetic differentiation between cheetahs from different regions of Botswana. This suggests that the Botswana cheetah population might represent a unique panmictic population as long as sufficient levels of gene flow are maintained within the distribution range. This baseline information will now be incorporated to develop management strategies and set priorities for cheetah conservation in Botswana

SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment

Abstract The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros. We found that a combined dataset of SNPs and microsatellites was most informative with the highest confidence level. This study thus provided us with a useful set of SNP and MS markers for parentage and relatedness testing. Further assessment of the utility of these markers over multiple (> three) generations and the incorporation of a larger variety of relationships among individuals (e.g. half-siblings or cousins) is strongly suggested

A targeted gene approach to SNP discovery in the White Rhino (Ceratotherium simum)

Abstract We report the characterization of 10 single nucleotide polymorphism (SNP) markers for the White Rhino (Ceratotherium simum), based on a targeted gene approach. The polymorphisms of these SNP loci were assessed using a captive population comprising 30 individuals. The minor allele frequency ranged from 0.256 to 0.413 and the observed and expected heterozygosity ranged from 0.05 to 0.37 and from 0.05 to 0.49, respectively. An understanding of genetic population structure is required to effectively formulate strategies for conservation and/or management. These SNP markers could be employed to provide estimates of parameters such as population structure, relatedness and current and historical gene flow