Monitoring the impact of translocation on the genetic diversity and fitness of the cape mountain zebra (Equus zebra zebra)
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Date
2019
Authors
Smith, Rae Marvin
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
Historic efforts to restore the Cape Mountain zebra (Equus zebra zebra, CMZ) population from near extinction was implemented through initiatives by government conservation agencies. While the animals have recovered in number, concerns over the genetic diversity of this sub-species have been raised. Efforts to preserve genetic diversity and mitigate risks to population decline have been outlined in a Biodiversity Management Plan (BMP) gazetted in 2018. This study addressed various objectives of the BMP. Specifically, the aim of this study was to monitor the impact that translocations have on the genetic diversity, fitness and long-term survival of the Cape mountain zebra. The study was carried out in four parts: First, the temporal change in genetic diversity was investigated over the last decade using 14 microsatellite markers. This was done to determine how past translocations conservation management has affected the genetic diversity of key populations. Second, single nucleotide polymorphism (SNP) variation in Toll-like receptor 9 was investigated to evaluate genetic diversity at adaptive sites and how they relate to protein function. Thirdly, the prevalence of two protozoa attributed to equine piroplasmosis was surveyed using real-time PCR to determine the risks associated with translocation. Lastly, the Cation Sperm Associated (CATSPER) gene 1-3 was screened to identify SNPs that may be associated with reproductive fitness in CMZ. Temporal declines in measures of genetic diversity such as allelic richness, observed heterozygosity and well as a low estimated effective population size (Ne) were identified in MZNP. Notable shifts in genetic structure of DHNR were also observed. Loss of genetic variation in the TLR 9 gene was observed in DHNR and a private reserve in Grahamstown when compared to the source population, MZNP. When investigating the structural implications caused by the genetic mutations in the gene, mutations were determined to not affect active binding regions of the protein structure. All animals tested in three reserves were infected with the equine piroplasm, Theileria equi. Translocations and founding new populations pose a risk to domestic animals in adjacent farms and could potentially introduce new genotypes in these areas. Four SNPs were identified at intronic regions of CATSPER 1 while no SNPs were found in exons screened in CATSPER genes 2 and 3 for the CMZ. This study played a key role in informing conservation actions to be implemented through the BMP. The aim of future analyses will be to incrementally sample each generation for better estimations of effective population size as a measure of genetic health. Collaborative efforts with conservation agencies will enable monitoring and controlled mixing of relict populations to assess which populations would best enable the preservation of the maximum number of alleles.
Description
Thesis (Ph.D.(Genetics))--University of the Free State, 2019
Keywords
Cape mountain zebra, Genetic diversity, Translocation, Equine piroplasms, Conservation, Microsatellites, Single nucleotide polymorphisms