Lessons for conservation management: Monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra)

The Cape mountain zebra (Equus zebra zebra) is a subspecies of mountain zebra endemic to South Africa. The Cape mountain zebra experienced near extinction in the early 1900's and their numbers have since recovered to more than 4,800 individuals. However, there are still threats to their long-term persistence. A previous study reported that Cape mountain zebra had low genetic diversity in three relict populations and that urgent conservation management actions were needed to mitigate the risk of further loss. As these suggestions went largely unheeded, we undertook the present study, fifteen years later to determine the impact of management on genetic diversity in three key populations. Our results show a substantial loss of heterozygosity across the Cape mountain zebra populations studied. The most severe losses occurred at De Hoop Nature Reserve where expected heterozygosity reduced by 22.85% from 0.385 to 0.297. This is alarming, as the De Hoop Nature Reserve was previously identified as the most genetically diverse population owing to its founders originating from two of the three remaining relict stocks. Furthermore, we observed a complete loss of multiple private alleles from all populations, and a related reduction in genetic structure across the subspecies. These losses could lead to inbreeding depression and reduce the evolutionary potential of the Cape mountain zebra. We recommend immediate implementation of evidence-based genetic management and monitoring to prevent further losses, which could jeopardise the long term survival of Cape mountain zebra, especially in the face of habitat and climate change and emerging diseases

Identification of low levels of neutral and functional genetic diversity in South African bontebok (Damaliscus pygargus pygargus)

Bontebok (Damaliscus pygargus pygargus) and blesbok (D. p. phillipsi) are classified as separated sub-species. The blesbok has a widespread distribution throughout South Africa and is listed as least concern by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Bontebok on the other hand is endemic within the Cape Floristic Region of the Western Cape in South Africa and has been listed as near-threatened species on the IUCN Red List of Threatened Species. Bontebok populations experienced a severe bottleneck and were brought back from the brink of extinction in the 1830’s. Currently, the subspecies is threatened by hybridization with blesbok resulting in fertile offspring. To date, molecular investigations using neutral markers have determined that genetic diversity in pure South African bontebok was significantly lower than pure blesbok. Here, we investigated genetic diversity in bontebok, blesbok, and hybrid individuals using microsatellites and an adaptive marker (toll-like receptor two (TLR2)). The study of SNPs revealed five mutations in TLR2 in different individuals and subspecies of D. pygargus. This included three synonymous and two non-synonymous mutations. The two amino acid substitution mutations were predicted to have no effect on protein function. Two of the five mutations, one of which resulted in an amino acid substitution, were not present in bontebok. The other three mutations were present to varying frequencies in the three groups. We confirm low adaptive and neutral diversity in bontebok. These mutations provide insights into the genetic diversity and relationships among the two sub-species of D. pygargus and may have implications for their conservation and management

Identification of low levels of neutral and functional genetic diversity in South African bontebok (Damaliscus pygargus pygargus)

Bontebok (Damaliscus pygargus pygargus) and blesbok (D. p. phillipsi) are classified as separated sub-species. The blesbok has a widespread distribution throughout South Africa and is listed as least concern by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Bontebok on the other hand is endemic within the Cape Floristic Region of the Western Cape in South Africa and has been listed as near-threatened species on the IUCN Red List of Threatened Species. Bontebok populations experienced a severe bottleneck and were brought back from the brink of extinction in the 1830’s. Currently, the subspecies is threatened by hybridization with blesbok resulting in fertile offspring. To date, molecular investigations using neutral markers have determined that genetic diversity in pure South African bontebok was significantly lower than pure blesbok. Here, we investigated genetic diversity in bontebok, blesbok, and hybrid individuals using microsatellites and an adaptive marker (toll-like receptor two (TLR2)). The study of SNPs revealed five mutations in TLR2 in different individuals and subspecies of D. pygargus. This included three synonymous and two non-synonymous mutations. The two amino acid substitution mutations were predicted to have no effect on protein function. Two of the five mutations, one of which resulted in an amino acid substitution, were not present in bontebok. The other three mutations were present to varying frequencies in the three groups. We confirm low adaptive and neutral diversity in bontebok. These mutations provide insights into the genetic diversity and relationships among the two sub-species of D. pygargus and may have implications for their conservation and management

Molecular genotyping and epidemiology of equine piroplasmids in South Africa

Recently reported substantial genetic diversity within Theileria equi 18S rRNA gene sequences has led to the identification of five genotypes A, B, C, D, and E, complicating molecular and serological diagnosis. In addition, T. haneyi has lately been reported as a species closely related to the T. equi 18S rRNA genotype C (Knowles et al., 2018). Theileria spp. of this group have a monophyletic origin and are therefore referred to as Equus group to distinguish them from the remaining Theileria lineages (Jalovecka et al., 2019). In this study, we report on the development of genotype-specific quantitative real-time PCR assays capable of detecting and distinguishing between each parasite genotype. Alignment of complete 18S rRNA sequences available on GenBank allowed for the design of a single primer pair and five TaqMan minor groove binder (MGB™) probes specific for each genotype (A–E). The assays, evaluated as qPCR simplex and two qPCR multiplex formats (Multiplex EP–ABC and Multiplex EP–DE), were shown to be both efficient and specific in the detection of T. equi genotypes. The developed qPCR assays were used to study (i) the intra-specific diversity of parasite genotypes within horse and zebra, (ii) the inter-specific differences in parasite genotype diversity in horses as compared to zebra, and (iii) the geographic distribution of T. equi 18S rRNA genotypes in South Africa. In addition, (iv) the presence of T. haneyi in South Africa was evaluated. An assessment of 342 equine field samples comprising 149 field horses, 55 racehorses, and 138 wild zebra confirmed the previously reported presence of T. equi 18S rRNA genotypes A, B, C, and D, and absence of genotype E in South African equids. Theileria equi genotypes A, B, C, and D, were detected in zebra, whereas only genotypes A, C and D, could be identified in field horses, and only genotypes A and C in racehorses. Genotypes B and D were the dominant genotypes identified in zebra in South Africa, while horses were predominantly infected with T. equi genotypes A and C. The greater diversity of T. equi genotypes in zebra suggests that it is an ancestral host for this piroplasmid lineage. Importantly, evidence is presented that each identified T. equi genotype segregates independently in each of the three studied equid populations reinforcing the notion that they represent individual separate entities corresponding to species. Preliminary investigations of the relationship between T. equi genotype C infections and Theileria haneyi, suggest that in addition to the five currently known T. equi genotypes, South African equids are also infected with T. haneyi.Fil: Bhoora, Raksha Vasantrai. University of Pretoria; Sudáfrica. Agricultural Research Council. Onderstepoort Veterinary Research; SudáfricaFil: Collins, Nicola Elaine. University of Pretoria; SudáfricaFil: Schnittger, Leonhard. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Patobiología Veterinaria - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Patobiología Veterinaria; ArgentinaFil: Troskie, Christo. Agricultural Research Council. Onderstepoort Veterinary Research; SudáfricaFil: Marumo, Ratselane. Agricultural Research Council. Onderstepoort Veterinary Research; SudáfricaFil: Labuschagne, Karien. Agricultural Research Council. Onderstepoort Veterinary Research; SudáfricaFil: Smith, Rae Marvin. South African National Biodiversity Institute; SudáfricaFil: Dalton, Desire Lee. South African National Biodiversity Institute; Sudáfrica. University of Venda; SudáfricaFil: Mbizeni, Sikhumbuzo. Agricultural Research Council. Onderstepoort Veterinary Research; Sudáfrica. University of South Africa; Sudáfric

Assessment of genetic and morphological differentiation among populations of the Diederik Cuckoo Chrysococcyx caprius

The Diederik Cuckoo Chrysococcyx caprius is an African species widely distributed south of the Sahara, which migrates seasonally between breeding and nonbreeding sites. It is currently unknown whether the species consists of a single panmictic population or if it is genetically structured. To investigate this, we analysed sequence variation in three mitochondrial and two nuclear gene regions in combination with morphological measurements in specimens from four localities. Phylogenetic relationships were estimated using maximum-likelihood methods and included samples of Klaas’s Cuckoo Chrysococcyx klaas, Red-chested Cuckoo Cuculus solitarius, and African Cuckoo Cuculus gularis. Haplotype networks and analysis of molecular variance were used to characterise the spatial distribution of genetic diversity. A principal component analysis was performed to investigate morphological variation among localities. Molecular analysis identified two divergent mitochondrial lineages, which were found to occur in sympatry in one South African locality (Limpopo Province). The magnitude of divergence between versus within these lineages was low (0.4–1%) yet significant (F ST: 0.84–0.88). Lack of apparent phylogeographic structure provides support for the absence of physical barriers to gene flow in this species. The divergent mitochondrial lineages did not differ in morphological measurements. The emergence and persistence of shallow mitochondrial divergence among sympatric lineages in the Diederik Cuckoo could be linked to maternal divergence in host selection of these brood parasites — a hypothesis requiring additional data to be tested.</p