Conservation Genetics

, Volume 15, Issue 6, pp 1479–1489 | Cite as

Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa

  • Antoinette Kotzé
  • Desiré Lee Dalton
  • Raoul du Toit
  • Natasha Anderson
  • Yoshan Moodley
Research Article
First Online:
Received:
Accepted:

Abstract

Despite an on-going struggle to conserve the endangered black rhinoceros (Diceros bicornis) since the 1980s, huge capital investment and several genetic surveys, the level of genetic structure and connectivity among populations in southern Africa is not well understood. Here, we undertake a major population genetic study of black rhinoceros in the Zimbabwe Lowveld, an area inhabited by over half of that country’s original Zambezi descendants plus one large population sourced from the relict KwaZulu stock of South Africa. Using nuclear microsatellite and mitochondrial DNA data, we found much higher levels of genetic diversity in the indigenous Zimbabwean populations, where observed multilocus heterozygosity was 0.54 versus 0.40 in KwaZulu, and maternal haplotype diversity was 0.77 versus 0.03. We show, for the first time, that both gene pools can be differentiated from each other on the basis of nuclear markers. This, along with the discovery of recent gene flow between all Lowveld populations, suggests that Zimbabwean and South African gene pools were prehistorically connected.

Keywords

Diceros bicornis Black rhino Structure Connectivity Conservation 
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Notes

Acknowledgments

We thank the International Rhino Foundation and the US Fish and Wildlife Service for financial support. We thank Steve Smith for comments on an earlier version of the manuscript.

Conflict of interest

The authors of this article have no financial or non-financial competing interests.

Funding

This work was supported by the International Rhino Foundation and the United States Fish and Wildlife Service.

Supplementary material

10592_2014_632_MOESM1_ESM.doc (42 kb)
Supplementary material 1 (DOC 42 kb)

References

  1. Anderson-Lederer RM, Linklater WL, Ritchie PA (2012) Limited mitochondrial DNA variation within South Africa’s black rhino (Diceros bicornis minor) population and implications for management. Afr J Ecol 50:404–413CrossRefGoogle Scholar
  2. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedCrossRefGoogle Scholar
  3. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004). GENETIX 4.02, logiciel sous Windows TM pour la génétique des populations, Laboratoire Génome, Populations, Interactions; CNRS UMR 5000; Université Montpellier II, MontpellierGoogle Scholar
  4. Brown SM, Houlden BA (1999) Isolation and characterization of microsatellite markers in the black rhinos (D. bicornis). Mol Ecol 8:1559–1561PubMedCrossRefGoogle Scholar
  5. Brown SM, Houlden BA (2000) Conservation genetics of the black rhinoceros (D. bicornis). Conserv Genet 1:365–370CrossRefGoogle Scholar
  6. Campbell NJH, Harriss FC, Elphinstone MS, Baverstock PR (1995) Outgroup heteroduplex analysis using temperature gradient gel electrophoresis–high resolution large scale screening of DNA variation in the mitochondrial control region. Mol Ecol 4:407–418PubMedCrossRefGoogle Scholar
  7. Child GFT, Riney T (1987) Tsetse control hunting. I. Zimbabwe, 1919–1958. Zambezia 14:11–71Google Scholar
  8. Cumming D, Du Toit R, Stuart SN (1990) African elephants and rhinos: Status survey and conservation action plan. IUCN, GlandGoogle Scholar
  9. Cunningham J, Harley EH, O’Ryan C (1999) Isolation and characterization of microsatellite loci in black rhinoceros (Diceros bicornis). Electrophoresis 20:1778–1780PubMedCrossRefGoogle Scholar
  10. Drummond WH (1876) On the African rhinoceroses. Proc Zool Soc Lond 1876:109–114Google Scholar
  11. Emslie R (2013) African Rhinoceroses–Latest trends in rhino numbers and poaching. An update to Doc 54-2-Annexe 2 from the IUCN Species Survival Commission’s (IUCN/SSC)Google Scholar
  12. Emslie R, Brooks M (1999) African Rhino: Status survey and action plan. IUCN/SSC African rhino specialist group, GlandGoogle Scholar
  13. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  14. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567PubMedCrossRefGoogle Scholar
  15. Fernando P, Polet G, Foead N, Ng LS, Pastorini J, Melnick DJ (2006) Genetic diverisity, phylogeny and conservation of the Javan rhinoceros (Rhinoceros sondaicus). Conserv Genet 7:439–448CrossRefGoogle Scholar
  16. Florescu A, Davila JA, Scott C, Fernando P, Kellners K, Morales JC, Melnick D, Boag PT, van Coeverden de Groot P (2003) Polymorphic microsatellites in white rhinoceros. Mol Ecol Notes 3:344–345CrossRefGoogle Scholar
  17. Fraser AD (1958) On the present status of ungulates in Southern Rhodesia. Mammalia 22:469–475Google Scholar
  18. Groves CP (1967) Geographic variation in the black rhinoceros (Diceros bicornis Linnaeus, 1758). Zeitschrift fur Säugetierkunde 32:267–276Google Scholar
  19. Groves CP, Grubb P (2011) Ungulate Taxonomy. Johns Hopkins University Press, BaltimoreGoogle Scholar
  20. Hall-Martin A (1979) Black rhinoceros in Southern Africa. Oryx 15(1):26–32CrossRefGoogle Scholar
  21. Harley EH (2002) AGARST, version 2.8, a program for calculating allele frequencies, GST and RST from microsatellite data. Wildlife Genetics Unit, University of Cape Town, Cape TownGoogle Scholar
  22. Harley EH, Baumgarten I, Cunningham J, O’Ryan P (2005) Genetic variation and population structure in remnant populations of Black Rhinoceros, Diceros bicornis, in Africa. Mol Ecol 14:2981–2990PubMedCrossRefGoogle Scholar
  23. Karsten M, Jansen van Vuuren B, Goodman P, Barnaud A (2011) The history and management of black rhino in KwaZulu-Natal: a population genetic approach to assess the past and guide the future. Anim Conserv 14:363–370CrossRefGoogle Scholar
  24. Leader-Williams N (1992) The world trade in Rhinoceros horn: a review. TRAFFIC International, CambridgeGoogle Scholar
  25. Leader-Williams N (2002) Regulation and protection: successes and failures in rhinoceros conservation. In: Oldfield S (ed) The Trade in Wildlife: Regulation for Conservation. Earthscan, London, pp 89–99Google Scholar
  26. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452PubMedCrossRefGoogle Scholar
  27. Milliken TKN, Thomsen JB (1993) The decline of the black rhino in Zimbabwe: implications for future rhino conservation. TRAFFIC International, CambridgeGoogle Scholar
  28. Milliken, T, Emslie RH, Talukdar B (2009) African and Asian Rhinoceroses –Status, Conservation and Trade. In a report from the IUCN Species Survival Commission (IUCN/SSC), GlandGoogle Scholar
  29. Moro D, Campbell NJH, Elphinstone MS, Baverstock PR (1998) The Thevenard Island mouse: historic and conservation implications from mitochondrial DNA sequence-variation. Pac Conserv Biol 4:282–288Google Scholar
  30. Muya SM, Bruford MW, Muigai AW-T, Osiemo ZB, Mwachiro E, Okita-Ouma B, Goossens B (2011) Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation. Conserv Genet 12:1575–1588CrossRefGoogle Scholar
  31. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedCentralPubMedGoogle Scholar
  32. Nielsen L, Meehan-Meola D, Kilbourn A, Alcivar-Warren A (2008) Characterization of microsatellite loci in the black rhinoceros (Diceros bicornis) and white rhinoceros (Ceratotherium simum): their use for cross-species amplification and differentiation between the two species. Conserv Genet 9:239–242CrossRefGoogle Scholar
  33. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13:55–65PubMedCrossRefGoogle Scholar
  34. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  35. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Nat Acad Sci USA 94:9197–9201PubMedCentralPubMedCrossRefGoogle Scholar
  36. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  37. Rohrer GA, Alexander LJ, Keele JW, Smith TP, Beattie CW (1994) A microsatellite linkage map of the porcine genome. Genetics 136:231–244PubMedCentralPubMedGoogle Scholar
  38. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138CrossRefGoogle Scholar
  39. Roth HH (1967) White and black rhinoceros in Rhodesia. Oryx 9:217–231CrossRefGoogle Scholar
  40. Scott CA (2008) Microsatellite variability in four contemporary rhinoceros species: implications for conservation. Queen’s University Kingston, KingstonGoogle Scholar
  41. Swart MKJ, Ferguson JWH (1997) Conservation implications of genetic differentiation in Southern African populations of black rhinoceros (Diceros bicornis). Conserv Biol 11:79–83CrossRefGoogle Scholar
  42. Van Coeverden de Groot PJ, Putnam AS, Erb P, Scott C, Melnick D, O’Ryan C, Boag PT (2011) Conservation genetics of the black rhinoceros, Diceros bicornis bicornis, in Namibia. Conserv Genet 12:783–792CrossRefGoogle Scholar
  43. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Antoinette Kotzé
    • 1
    • 2
  • Desiré Lee Dalton
    • 1
    • 2
  • Raoul du Toit
    • 3
    • 4
  • Natasha Anderson
    • 3
    • 4
  • Yoshan Moodley
    • 5
  1. 1.Centre for Conservation ScienceNational Zoological Gardens of South AfricaPretoriaSouth Africa
  2. 2.Genetics DepartmentUniversity of the Free StateBloemfonteinSouth Africa
  3. 3.Lowveld Rhino TrustHarareZimbabwe
  4. 4.International Rhino FoundationFort worthUSA
  5. 5.Department of Integrative Biology and Evolution, Konrad Lorenz Institute for EthologyUniversity of Veterinary MedicineViennaAustria

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