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Evaluation of microsatellites for common ungulates in the South African wildlife industry

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Abstract

Wildlife is a multi-million dollar industry in South Africa ranging from intensively farmed animals on small properties to free-roaming animals in large functional ecosystems. Specific concerns surrounding the conservation value of the intensively managed wildlife have been raised. Increasingly it is recognised that genetics must be considered when developing conservation policy and management practices. Minimal genetic data are available to assist with decisions within the industry. Microsatellite markers have been developed for some species and are currently used for individual identification, parentage assessment and to inform translocation decisions. However, validation for standardized application in wildlife management has not been completed. Common species for which conservation management decisions have to be made include: Cape buffalo (Syncerus caffer), blue wildebeest (Connochaetes taurinus taurinus), common impala (Aepyceros melampus) and sable antelope (Hippotragus niger). Using existing microsatellite markers for domestic and wild species, we have developed multiplex panels for use in these species. We discriminated between 751 buffalo (four pairs were not distinguishable), 1307 blue wildebeest (three pairs were not distinguishable), 580 impala and 493 sable antelope. We determined parentage in four case studies using a combination of microsatellite and demographic data. We also tested microsatellite markers on roan antelope (Hippotragus equinus), gemsbok (Oryx gazella) and eland (Tragelaphus oryx) and report preliminary data. Further research to improve this validation includes: extensive sampling from more diverse areas, targeted or full genome sequencing to identify additional microsatellite loci, development of sampling kits and training of veterinarians, as well as expansion of the species tested.

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Acknowledgments

SMM was partially funded by a Post-doctoral Fellowship from the Faculty of Natural and Agricultural Sciences of the University of Pretoria. The authors thank an anonymous reviewer for constructive comments that improved the manuscript.

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Authors and Affiliations

  1. Molecular Ecology and Evolution Program, Department of Genetics, University of Pretoria, Pretoria, South Africa

    Susan M. Miller & Paulette Bloomer

  2. Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa

    Susan M. Miller, Amy B. Clarke & Cindy K. Harper

  3. Equine Research Centre, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa

    Alan J. Guthrie

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  1. Susan M. Miller
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  2. Amy B. Clarke
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  3. Paulette Bloomer
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  4. Alan J. Guthrie
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  5. Cindy K. Harper
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Correspondence to Susan M. Miller.

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Miller, S.M., Clarke, A.B., Bloomer, P. et al. Evaluation of microsatellites for common ungulates in the South African wildlife industry. Conservation Genet Resour 8, 329–341 (2016). https://doi.org/10.1007/s12686-016-0554-7

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