Skip to main content

Advertisement

SpringerLink
Log in

Population structuring in mountain zebras (Equus zebra): The molecular consequences of divergent demographic histories

  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

The endangered mountain zebra (Equus zebra) is endemic to the semi-arid inhospitable mountainous escarpments of southern Africa. The species is divided taxonomically into two geographically separated subspecies, each with differing recent population histories. In Namibia, Hartmann’s mountain zebra (E. z. hartmannae) is common and occurs in large free-ranging populations, whereas in South Africa, prolonged hunting and habitat destruction over the last 300 years has decimated populations of the Cape mountain zebra (E. z. zebra). In this study, we investigate the consequences of these divergent demographic histories for population genetic diversity and structure. We also examine the phylogeographic relationship between the two taxonomic groups. Genetic information was obtained at 15 microsatellite loci for 291 individuals from a total of 10 populations as well as 445 bp of the mitochondrial control region sequence data from 77 individuals. Both model-based and standard analytical approaches were used to examine the data. Both types of marker returned levels of diversity and structure that were consistent with population history. Low genetic variation within individual Cape mountain zebra populations, the characteristic indicator of population fragmentation and drift, was offset by moderate variation in the entire E. z. zebra sample. This implies that higher levels of diversity still exist within the Cape mountain zebra gene pool. A management strategy that entailed the mixing of aboriginal populations is therefore advocated in order to halt the further loss of Cape mountain zebra genetic diversity. Allele frequencies in Hartmann’s mountain zebra were relatively resilient to demographic fluctuations. Due to the high incidence of mitochondrial haplotype sharing between populations, the hypothesis that Cape and Hartmann’s mountain zebra mitochondrial lineages were reciprocally monophyletic was not supported. However, the presence of private alleles at nuclear loci rendered the two subspecies genetically distinct evolutionary significant units.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: l 37–148

    Google Scholar 

  • Belkhir K (2001) Genetix 4.01, Software for population genetics. Laboratoire Génome, Populations et Interactions, University of Montpelier, Montpelier, France

    Google Scholar 

  • Bigalke R (1952) Early history of the Cape mountain zebra (Equus zebra zebra. Linn). African Wildlife 6: 143–153

    Google Scholar 

  • Binns MM, Holmes NG, Holliman A, Scott AM (1995) The identification of polymorphic microsatellite loci in the horse and their use in thoroughbred parentage testing. Brit. Vet. J. 151: 9–15

    Article  CAS  Google Scholar 

  • Castley G, Lloyd PH, Moodley Y (2002) Cape mountain zebra, Equus zebra zebra taxon data sheet. IUCN Conservation Assessment Management Plan. Randburg, South Africa

    Google Scholar 

  • Ciofi C, Beaumont MA, Swingland IR, Bruford MW (1999) Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis. Proc. Roy. Soc. Lond. B 266: 2269–2274

    Article  Google Scholar 

  • Coogle L, Bailey E (1997) Equine dinucleotide repeat loci LEX049–LEX063. Anim. Genet. 28: 378

    PubMed  CAS  Google Scholar 

  • Coogle L, Reid R, Bailey E (1996) Equine dinucleotide repeat loci LEX015–LEX024. Anim. Genet. 27: 217–218

    Article  PubMed  CAS  Google Scholar 

  • Dawson KJ, Belkhir K (2001) A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet. Res. 78: 59–77

    Article  PubMed  CAS  Google Scholar 

  • Eggleston-Stott ML, DelValle A, Bautista M et al. (1997) Nine equine dinucleotide repeats at microsatellite loci UCDEQ136, UCDEQ405, UCDEQ412, UCDEQ425, UCDEQ437, UCDEQ467, UCDEQ487, UCDEQ502, UCDEQ505. Anim. Genet. 28: 370–371

    Article  PubMed  CAS  Google Scholar 

  • Ellegren H, Johansson M, Sandberg K, Andersson L (1992) Cloning of highly polymorphic microsatellites in the horse. Anim. Genet. 23: 133–142

    Article  PubMed  CAS  Google Scholar 

  • Excoffier L, Smouse P (1994) Using allele frequencies and geographic subdivision to reconstruct gene genealogies within species. Molecular variance parsimony. Genetics 136: 343–359

    PubMed  CAS  Google Scholar 

  • Frankham R, Ballou JD, Briscoe DA (2002). Introduction to Conservation Genetics. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Fraser DJ, Bernatchez L (2001) Adaptive evolutionary conservation: Towards a unified concept for defining conservation units. Mol. Ecol. 10: 2741–2752

    PubMed  CAS  Google Scholar 

  • Groves CP, Bell CH (2004) New investigations on the taxonomy of zebras genus Equus, subgenus Hippotigris. Mammal. Biol. 69: 182–196

    Article  Google Scholar 

  • Groves CP, Ryder OA (2000) Systematics and phylogeny of the horse. In: The Genetics of the Horse (eds. Bowling AT, Ruvinsky A) CAB International

  • Hartl GB, Pucek Z (1994) Genetic depletion in the European Bison (Bison bonasus) and the significance of electrophoretic heterozygosity for conservation. Conserv. Biol. 8: 167–174

    Article  Google Scholar 

  • Hedrick PW (1999) Highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313–318

    Article  Google Scholar 

  • Hilton-Taylor C (2000) 2000 IUCN Red List of Threatened Species. IUCN, Gland, Switzerland and Cambridge, UK

    Google Scholar 

  • Hopman TJ, Han EB, Story, MR et al. (1999) Equine dinucleotide repeat loci COR001–COR020. Anim. Genet. 30: 225–226

    Article  PubMed  CAS  Google Scholar 

  • Karesh WB, Smith F, Frazier-Taylor H (1987) A remote method for obtaining skin biopsy samples. Conservation Biology 3: 261–262

    Article  Google Scholar 

  • Lazary S, Gerber H, Glatt PA, Straub R (1985) Equine leucocyte antigens in sarcoid-affected horses. Equine Vet. J. 17: 283–286

    Article  PubMed  CAS  Google Scholar 

  • Lloyd PH (1984) The Cape mountain zebra 1984. African Wildlife 38: 144–149

    Google Scholar 

  • Marklund S, Ellegren H, Eriksson S, Sandberg K, Andersson L (1994) Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites. Anim. Genet. 25: 19–23

    PubMed  CAS  Google Scholar 

  • Matschie P (1898) Sitzungsberichte der Gesellschaft naturforschender Freunde zu Berlin, 174 pp

  • Meredith D, Elser AH, Wolf B (1986) Equine leukocyte antigens: Relationships with sarcoid tumors and laminitis in two pure breeds. Immunogenetics 23: 221–225

    Article  PubMed  CAS  Google Scholar 

  • Millar JCG (1970a) Census of Cape mountain zebras: Part I. African Wildlife 24: 17–25

    Google Scholar 

  • Millar JCG (1970b) Census of Cape mountain zebras: Part II. African Wildlife 24: 105–114

    Google Scholar 

  • Moodley Y (2002) Population structuring in southern African zebras. University of Cape Town, South Africa, PhD thesis

    Google Scholar 

  • Moritz C (1994) Defining “Evolutionarily Significant Units” for conservation. Trends Ecol. Evol. 9: 373–375

    Article  Google Scholar 

  • Muwanika VB, Nyakaana S, Siegismund HR, Arctander P (2003) Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity 91: 361–372

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590

    PubMed  CAS  Google Scholar 

  • Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York

    Google Scholar 

  • Novellie P, Lindeque M, Lindeque P, Lloyd PH, Koen J (2002) Status and Action Plan for the Mountain Zebra (Equus zebra). In: Moehlman PD (eds) Equids: zebras, asses and horses: status survey and conservation action plan. IUCN/SSC, Gland, Switzerland

    Google Scholar 

  • Novellie P, Lloyd PH, Joubert E (1992) Mountain Zebras. In: Duncan P (ed) Zebras, Asses and Horses: An Action Plan for the Conservation of Wild Equids. IUCN, Gland, Switzerland

    Google Scholar 

  • Nyakaana S, Arctander P, Siegismund HR (2002) Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity 89: 90–98

    Article  PubMed  CAS  Google Scholar 

  • Oakenfull EA, Lim HN, Ryder OA (2000) A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus. Conserv. Genet. 1: 341–355

    Article  CAS  Google Scholar 

  • Pesole G, Gissi C, De Chirico A, Saccone C (1999) Nucleotide substitution rate of mammalian mitochondrial genomes. Journal of Molecular Evolution 48: 427–434

    Article  PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959

    PubMed  CAS  Google Scholar 

  • Rau RE (2002) Are the two mountain zebra subspecies distinguishable? Mainly About Anim. 54: 20–21

    Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86: 248–249

    Google Scholar 

  • Rice WR (1989) Analysing tables of statistical tests. Evolution 43: 223–225

    Article  Google Scholar 

  • Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pair-wise genetic differences. Mol. Biol. Evol. 9: 552–569

    PubMed  CAS  Google Scholar 

  • Rozas J, Rozas R (1999) DNAsp version 3: An integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174–175

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning - A Laboratory Manual 2nd edn. Cold Spring Harbour Laboratory Press, New York

    Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin version 2.000: Software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland

    Google Scholar 

  • Skinner JD, Smithers RHN (1990) The Mammals of the Southern African Subregion. University of Pretoria

  • Spencer CC, Neigel JE, Leberg PL (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol. Ecol. 9: 1517–1528

    Article  PubMed  CAS  Google Scholar 

  • Strimmer K, von Haeseler A (1996) Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964–969

    CAS  Google Scholar 

  • Swinburne JE, Marti E, Breen M, Binns MM (1997) Characterisation of twelve new horse microsatellite loci: AHT 12 – AHT 23. Anim. Genet. 28: 453

    PubMed  CAS  Google Scholar 

  • Tozaki T, Kakoi H, Mashima S (2000) The isolation and characterization of 18 equine microsatellite loci, TKY272-TKY289. Anim. Genet. 31: 149–150

    Article  PubMed  CAS  Google Scholar 

  • Uphyrkina O, Johnson WE, Quigley H, et al. (2001) Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus. Mol. Ecol. 10: 2617–2633

    Article  PubMed  CAS  Google Scholar 

  • van Haeringen WA, van de Goor LHP, van der Hout N, Lenstra A (1998) Characterization of 24 microsatellite loci. Anim. Genet. 29: 153–156

    PubMed  Google Scholar 

  • Woods DH (1960) Mountain zebras. Journal of the Mountain Club of South Africa 63: 4–9

    Google Scholar 

Download references

Acknowledgements

This study was funded by the National Research Foundation of the Republic of South Africa. The authors are indebted to Peter Lloyd, Banie Penzhorn, Peter Novellie, Pauline Lindeque, Holger Kolberg, Tom Barry, Gail Cleaver, Piet Morkel, Paul Meyer, numerous tanneries and taxidermists and the staff of the Western Cape Nature Conservation Board, South African National Parks and the Ministry of the Environment and Tourism of Namibia.

Author information

Authors and Affiliations

  1. Wildlife Genetics Unit, University of Cape Town, Observatory, Cape Town, 7925, Republic of South Africa

    Yoshan Moodley & Eric H. Harley

  2. School of Biosciences, Main Building, Cardiff University, Cathays Park, CF10 3TL, Cardiff, UK

    Yoshan Moodley

Authors
  1. Yoshan Moodley
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eric H. Harley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yoshan Moodley.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Moodley, Y., Harley, E. Population structuring in mountain zebras (Equus zebra): The molecular consequences of divergent demographic histories. Conserv Genet 6, 953–968 (2005). https://doi.org/10.1007/s10592-005-9083-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-005-9083-8

Keywords

Search

Navigation