Botany & Zoology
Welcome to Stellenbosch University

Prof. Conrad Matthee

​​Evolutionary Genomics Group

My Research Focu​s

The conservation of biodiversity is very much dependent on explaining the evolutionary patterns and processes associated with living organisms.  The African continent, and particularly also southern Africa, is known for a rich terrestrial and marine biodiversity that is associated with a complex landscape. This environment lends itself to test various hypothesis associated with evolution and speciation. By studying the interplay between life history, biogeography and ecology we address systematic uncertainties at all taxonomic levels using a variety of different molecular techniques. To advance our knowledge in this field we currently focus our research on:

1) Parasite-host codivergence at the phylogeographic and species level

2) Stock assessment and conservation of marine resources

3) Comparative phylogeography of terrestrial vertebrates

4) Evolution and systematics of free-living and parasitic arthropods

Students & Post-Docs


Jessica KiplingRebecca AckermannSara Andreotti
Amore MalanDeon BakkesTess Gridley
Demi-Lee MartinBridget James 
 Jake Mulvaney 
 Hendre van Rensburg 


Graduated / Past Associates

J.C. BothmaSara AndreottiNina du Toit
Nidia CangiFenton CotterillGeeta Eick
Shelley EdwardsAndrew David
Romina Henriques
Keshni GopalSavel DanielsAnne Ropiquet
Jane MakokhaNina du ToitPascal Rousse
Nicole MartinsAdriaan EngelbreghtSamantha Stoffberg
Ann McLachlanGavin GouwsKrystal Tolley
Thomas MkareTanya KerrLuther van der Mescht
CM MullerTinashe MuteveriSophie Von Der Heyden
Terry ReynoldsTerry Reynolds 
James RhodesSamantha Stoffberg 
Francis SandsPeter Teske 
Belinda SwartLuther van der Mescht 
Sandy van NiekerkSandy Willows-Munro 
Hendre van Rensburg  
Lee Williams  
Sandi Willows-Munro  



119. Bothma J.C., Matthee S., Matthee C.A. (2020). Comparative phylogeography between parasitic sucking lice and their host the Namaqua rock mouse, Micaelamys namaquensis. Zoological Journal of the Linnaen Society (in press)

118. Simon C.A., Kara J., Naidoo C., Matthee C.A. (2020). Genetic structure of bloodworm, Arenicola loveni (Annelida; Arenicolidae) suggests risk of local extinction in the face of overexploitation is lower than expected. African Zoology (in press)

117. van der Mescht L., Matthee S., Matthee C.A. (2020). New taxonomic and evolutionary insights relevant to the cat flea, Ctenocephalides felis: a geographic perspective. Molecular Phylogenetics and Evolution (in press)

116. Davenport D., Butcher P.A., Andreotti S., Matthee C.A. , Jones A., Ovenden J.  (2020). Effective number of white shark (Carcharodon carcarias, Linneaus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand.  Ecology and Evolution (in press)

115. Durden L, Bothma J.C., Matthee S., Matthee C.A. (2020). Description of two new anoplurid lice on the South African endemic, Micaelamys granti. Journal of Parasitology, 106(4), 478–489

114. Elgetany A.H, van Rensburg H., Hektoen M., Matthee C.A., Budaeva N., Simon C.A., Struck T.H. (2020). Delimiting species in the grey zone of speciation – the problematic case of Diopatra aciculata (Annelida, Onuphidae). Zoologica Scripta, 49, 516–534

113. Bakkes D.K., Mans B.J., Chitimia-Dobler L., Mumcuoglu K.Y., Matthee C.A. (2020). Integrative taxonomy and species delimitation of Rhipicephalus turanicus (Acari: Ixodida: Ixodidae). International Journal for Parasitology, 50(8), 577-594

112. Malan A., Williams J.D., Abe H., Sato-Okoshi W., Matthee C.A., Simon, C.A. (2020). Clarifying the cryptogenic species Polydora neocaeca Williams & Radashevsky, 1999 (Annelida: Spionidae): a shell-boring invasive pest of molluscs from locations worldwide. Marine Biodiversity, 50(1), 1-19

111. Matthee C.A. (2020). The influence of host dispersal and specialization on parasite gene flow and genetic diversity. African Zoology, 55:2, 119-126

110. Bothma J.C., Matthee S., Matthee C.A. (2020). The evolutionary history of parasitic sucking lice and their rodent hosts: a case of evolutionary co-divergences. Zoologica Scripta, 49, 72-85

109. Wessels C., Matthee S., Espinaze M.P.A., Matthee C.A. (2019). Comparative mtDNA phylogeographic patterns reveal marked differences in population genetic structure between generalist and specialist ectoparasites of the African penguin. Parasitology Research, 118 (2), 667-672

108. O'Connell C.P., Andreotti S., Rutzen M., Meӱer M., Matthee C.A. (2019). The influence of kelp density on white shark presence within the Dyer Island Nature Reserve, South Africa. Ocean & Coastal Management 179, 104819

107. Matthee C.A., Engelbrecht A., Matthee S. (2018). Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH). BMC Evolutionary Biology 18 (1), 131.

106. Mkare T.K., Groeneveld J.C., Teske P.R , Matthee C.A. (2018). Departures from panmixia in two high-dispersal prawn species from the Southwest Indian Ocean. African Journal of Marine Science, 39 (4), pp 467-474.

105. Kerr T.J. , Matthee S., Govender D., Engelbrecht S., Matthee C.A. (2018). Viruses as indicators of contemporary host dispersal and phylogeography: an example of Feline Immunodeficiency Virus (FIVPle) in free-ranging African lion (Panthera leo). Journal of Evolutionary Biology, 31 (10), pp. 1529-1543

104. O'Connell C.P., Andreotti S., Rutzen M., Meӱer M., Matthee C.A. (2018). Testing the white shark (Carcharodon carcharias) exclusion capabilities and durability of the sharksafe barrier to determine its viability as an Eco-Friendly alternative to current shark culling methodologies. Marine and Freshwater Ecosystems 28 (1), 252-258.

103. Andreotti, S., Holtzhausen, P., Rutzen, M., Meÿer, M., van der Walt, S., Herbst, B., Matthee, C.A. (2018). Semi-automated software for dorsal fin photographic identification of marine species: application to Carcharodon carcharias. Marine Biodiversity, 48 (3), pp. 1655-1660

102. Andreotti S., von der Heyden S. , Henriques R., Rutzen M., Meÿer M., Matthee C.A. (2017). Erring on the side of caution: Reply to Irion et al. Marine Ecology Progress Series, 577, pp. 251-255.

101. Kerr T.J., Matthee C.A., Matthee S., Govender D., Engelbrecht S. (2017). Evaluating the diversity of the Feline Immunodeficiency Virus (FIV): a leopard perspective. African Journal of Wildlife Research, 47(2), pp. 92-105.

100. Sands A.F., Apanaskevich D.A., Matthee S., Horak I.G., Harrison A., Karim S., Mohammad M.K., Mumcuoglu K.Y., Rajakaruna R.S., Santos-Silva M.M. and Matthee C.A. (2017). Effects of tectonics and large scale climatic changes on the evolutionary history of Hyalomma ticks. Molecular Phylogenetics and Evolution, 114, pp. 153-165.

99. Sands, A.F., Apanaskevich, D.A., Matthee, S., Horak, I.G., Matthee, C.A. (2017). The effect of host vicariance and parasite life history on the dispersal of the multi-host ectoparasite, Hyalomma truncatum. Journal of Biogeography, 44 (5), pp. 1124-1136.

98. Williams, L., Matthee, C.A., Simon, C.A. (2016). Dispersal and genetic structure of Boccardia polybranchia and Polydora hoplura (Annelida: Spionidae) in South Africa and their implications for aquaculture. Aquaculture, 465, pp. 235-244.

97. Henriques, R., von der Heyden, S., Lipinski, M.R., du Toit, N., Kainge, P., Bloomer, P., Matthee, C.A. (2016). Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes. Molecular Ecology, 25 (23), pp. 5843-5861.

96. David, A.A., Matthee, C.A., Loveday, B.R., Simon, C.A. (2016). Predicting the dispersal potential of an invasive Polychaete pest along a complex coastal biome. Integrative and Comparative Biology, 56 (4), pp. 600-610.

95. van Der Mescht, L., Krasnov, B.R., Matthee, C.A., Matthee, S. (2016). Community structure of fleas within and among populations of three closely related rodent hosts: Nestedness and beta-diversity. Parasitology, 143 (10), pp. 1268-1278.

94. Rousse, P., Quicke, D.L.J., Matthee, C.A., Lefeuvre, P., van Noort, S. (2016). A molecular and morphological reassessment of the phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae). Zoological Journal of the Linnean Society, 178 (1), pp. 128-148.

93. Andreotti, S., Rutzen, M., Van Der Walt, S., Von Der Heyden, S., Henriques, R., Meer, M., Oosthuizen, H., Matthee, C.A. (2016) An integrated mark-recapture and genetic approach to estimate the population size of white sharks in South Africa. Marine Ecology Progress Series, 552, pp. 241-253.

92. Engelbrecht, A., Matthee, S., Du Toit, N., Matthee, C.A. (2016). Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with the rodent host, Rhabdomys. Molecular Ecology, 25 (4), pp. 1006-1021.

91. Andreotti, S., Von Der Heyden, S., Henriques, R., Rutzen, M., Meÿer, M., Oosthuizen, H., Matthee, C.A. (2016). New insights into the evolutionary history of white sharks, Carcharodon carcharias. Journal of Biogeography, 43 (2), pp. 328-339.

90. Matthee, C.A., Ropiquet, A. (2016) The importance of correctly identifying the process responsible for spatial genetic structure in Leopard: A response to McManus and Smuts (2016) Comptes Rendus - Biologies, 339 (11-12), pp. 439-441.

89. Henriques, R., Von Der Heyden, S., Matthee, C.A. (2016). When homoplasy mimics hybridization: A case study of Cape hakes (Merluccius capensis and M. paradoxus). PeerJ, 2016 (3), art. no. 1827

88. van Der Mescht, L., Le Roux, P.C., Matthee, C.A., Raath, M.J., Matthee, S. (2016) The influence of life history characteristics on flea (Siphonaptera) species distribution models. Parasites and Vectors, 9 (1), art. no. 178

87. van Der Mescht, L., Matthee, S., Matthee, C.A. (2015) Comparative phylogeography between two generalist flea species reveal a complex interaction between parasite life history and host vicariance: Parasite-host association matters. BMC Evolutionary Biology, 15 (1), art. no. 105

86. Ropiquet A., Knight A., Born C., Martins Q., Balme G., Kirkendall L., Hunter L., Senekal C., Matthee C.A. (2015). Implications of spatial genetic patterns for conserving African leopards. Comptes Rendus Biologies 338 (11), 728-737

85. van der Mescht, L., Matthee, S., Matthee, C.A. (2015) A genetic perspective on the taxonomy and evolution of the medically important flea, Dinopsyllus ellobius (Siphonaptera: Dinopsyllinae), and the resurrection of Dinopsyllus abaris. Biological Journal of the Linnean Society, 116 (3), pp. 541-557. 

84. Muteveri, T., Matthee, C.A., Bowie, R.C.K., von der Heyden, S. (2015) High population connectivity and Pleistocene range expansion in the direct-developing plough shell Bullia rhodostoma along the South African coast. African Journal of Marine Science, 37 (1), pp. 21-31.

83. Sands, A.F., Matthee, S., Mfune, J.K.E., Matthee, C.A. (2015) The influence of life history and climate driven diversification on the mtDNA phylogeographic structures of two southern African Mastomys species (Rodentia: Muridae: Murinae) (2015) Biological Journal of the Linnean Society, 114 (1), pp. 58-68.

82. Wright, D., Bishop, J., Matthee C.A., von der Heyden S. (2015) Isolation by distance reveals highly restricted dispersal: implications for biodiversity planning across a highly variable marine environment. Diversity and Distributions 21 (6), 698-710

81. O'Connell C. Andreotti, S., Rutzen, M., Meӱer, M., Matthee, C.A., He, P. (2014) Effects of the Sharksafe Barrier on Great White Shark (Carcharodon carcharias) Behavior and its Implications for Future Conservation Technologies. Journal of Experimental Marine Biology and Ecology 460, 37-46.

80. Reynolds T.V., Matthee, C.A. and von der Heyden S. (2014) The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia). PloS One e102115

79. Engelbrecht A., Matthee C.A., Ueckermann E.A., Matthee S. (2014) Evidence for cryptic speciation in Mesostigmatid mites from South Africa. Parasitology 141 (10), 1322-1332

78. Andreotti, S, Rutzen, M., Wesche, P., Meÿer, M., Oosthuizen, H., O'Connell, Matthee, C.A. (2014). A novel categorization system to organize large photo identification databases for great white sharks, Carcharodon carcharias. African Journal of Marine Science 36 (1), 59-67

77. Robinson, T.J., Cernohorska, H., Diedericks, G., Cabelova, K., Duran, A., Matthee C.A. (2014) Phylogeny and vicariant speciation of the Grey Rhebok, Pelea capreolus. Heredity 112 (3), 325-332

76. Mkare, T., von der Heyden, S., Groeneveld, J.C., Matthee, C.A. (2014) Genetic population structure and recruitment patterns of three sympatric shallow-water penaeid prawns in Ungwana Bay, Kenya, with implication for fisheries management. Marine and Freshwater Research 65 (3), 255-266

75. David, A.A., Matthee, C.A., Simon C.A. (2014) Poecilogony in Polydora hoplura (Polychaeta: Spionidae) from commercially important molluscs in South Africa. Marine Biology 161(4), 887-898

74. Rius, M., Clusella-Trullas, S., McQuaid , CD, Navarro, R., Griffiths, CL, Matthee, CA, von der Heyden, S. and Turon, X. (2014) Range expansions across ecoregions: interactions of climate change, physiology and genetic diversity. Global Ecology and Biogeography 23 (1), 76-88

73. Cangi, N. , Horak, I.G. , Apanaskevich, D.A. , Matthee, S. , das Neves, L.C.B., Estrada- Peña, A. , Matthee, C.A. (2013) The influence of interspecific competition and host preference on the phylogeography of two African ixodid tick species. PloS one 8 (10), e76930

72. du Toit, N., Jansen van Vuuren, B., Matthee S., Matthee C.A. (2013) Biogeography and host-related factors trump parasite life-history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts. Molecular Ecology 22, 5185-5204

71. Nyangiwe, N., Matthee, C.A., Horak, I., Matthee S. (2013) First record of the pantropical blue tick Rhipicephalus microplus in Namibia. Experimental and Applied Acarology 61, 503-505

70. du Toit, N., Matthee, S., Matthee, C.A. (2013) The sympatric occurrence of two genetically divergent lineages of sucking louse, Polyplax arvicanthis (Phthiraptera: Anoplura), on the four-striped mouse genus, Rhabdomys (Rodentia: Muridae). Parasitology 140, 604–616.

69. Muller, C.M., von der Heyden, S., Bowie, R.C.K., Matthee, C.A. (2012) Oceanic circulation, local upwelling and palaeoclimatic changes linked to the phylogeography of the Cape sea urchin Parechinus angulosus Marine Ecology Progress Series 468, 203

68. Groeneveld, J.C., von der Heyden, S., Matthee, C.A. (2012) High connectivity and lack of mtDNA differentiation among two previously recognized spiny lobster species in the southern Atlantic and Indian Oceans Marine Biology Research, 8 (8), pp. 764-770.

67. du Toit, N., Jansen van Vuuren, B., Matthee, S., Matthee, C.A. (2012) Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy Molecular Phylogenetics and Evolution, 65 (1), 75-86.

66. Montgelard, C., Matthee, C.A. (2012) Tempo of genetic diversification in southern African rodents: The role of Plio-Pleistocene climatic oscillations as drivers for speciation Acta Oecologica, 42, pp. 50-57.

65. Montgelard, C., Matthee, C.A. (2012) The GDRI 191 (2007-2010): Biodiversity and global change in southern Africa Acta Oecologica, 42, pp. 1-2.

64. Horak, I.G., Lutermann, H., Medger, K., Apanaskevich, D.A., Matthee, C.A. (2012)  Natural hosts of the larvae of Nuttalliella sp. (N. namaqua?) (Acari: Nuttalliellidae) Onderstepoort Journal of Veterinary Research, 79 (1), pp. 176-182.

63. Stoffberg, S., Schoeman, M.C., Matthee, C.A. (2012) Correlated genetic and ecological diversification in a widespread southern African horseshoe bat PLoS ONE, 7 (2), art. no. e31946, .

62. Hassanin, A., Delsuc, F., Ropiquet, A., Hammer, C., Jansen Van Vuuren, B., Matthee, C., Ruiz-Garcia, M., Catzeflis, F., Areskoug, V., Nguyen, T.T., Couloux, A. (2012) Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes Comptes Rendus - Biologies, 335 (1), pp. 32-50.

61. Willows-Munro, S., Matthee, C.A. (2011) Exploring the diversity and molecular evolution of shrews (family Soricidae) using mtDNA cytochrome b data African Zoology 46 (2), pp. 246-262

60. Willows-Munro, S., Matthee, C.A. (2011) Linking lineage diversification to climate and habitat heterogeneity: Phylogeography of the southern African shrew Myosorex varius Journal of Biogeography, 38 (10), pp. 1976-1991.

59. Tolley, K.A., Tilbury, C.R., Measey, G.J., Menegon, M., Branch, W.R., Matthee, C.A. (2011) Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot Journal of Biogeography, 38 (9), pp.1748-1760.

58. Apanaskevich, D.A., Horak, I.G., Matthee, C.A., Matthee, S. (2011) A new species of Ixodes (Acari: Ixodidae) from South African mammals Journal of Parasitology, 97 (3), pp. 389-398.

57. Stoffberg, S., Jacobs, D.S., Matthee, C.A. (2011) The Divergence of Echolocation Frequency in Horseshoe Bats: Moth Hearing, Body Size or Habitat? Journal of Mammalian Evolution, 18 (2), pp. 117-129.

56. Miller, J.M., Hallager, S., Monfort, S.L., Newby, J., Bishop, K., Tidmus, S.A., Black, P., Houston, B., Matthee, C.A., Fleischer, R.C. (2011) Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus) Conservation Genetics, 12 (2), pp. 423-431.

55. Edwards, S., Claude, J., Van Vuuren, B.J., Matthee, C.A. (2011) Evolutionary history of the Karoo bush rat, Myotomys unisulcatus (Rodentia: Muridae): Disconcordance between morphology and genetics Biological Journal of the Linnean Society, 102 (3), pp. 510-526.

54. Abrantes, J., Carmo, C.R., Matthee, C.A., Yamada, F., van der Loo, W., Esteves, P.J. (2011) A shared unusual genetic change at the chemokine receptor type 5 between Oryctolagus, Bunolagus and Pentalagus Conservation Genetics, 12 (1), pp. 325-330.

53. Palero, F., Abelló, P., MacPherson, E., Matthee, C.A., Pascual, M. (2010) Genetic diversity levels in fishery-exploited spiny lobsters of the genus Palinurus (Decapoda: Achelata) Journal of Crustacean Biology, 30 (4), pp. 658-663.

52. von der Heyden, S., Lipinski, M.R., Matthee, C.A. (2010) Remarkably low mtDNA control region diversity in an abundant demersal fish Molecular Phylogenetics and Evolution, 55 (3), pp. 1183-1188.

51. Gouws, G., Matthee, C.A., Stewart, B.A. (2010) A multiple data set phylogeny for the endemic South African freshwater phreatoicidean isopod genus Mesamphisopus: Taxonomic and biogeographic implications Molecular Phylogenetics and Evolution, 55 (2), pp. 541-551.

50. Linder, H.P., Johnson, S.D., Kuhlmann, M., Matthee, C.A., Nyffeler, R., Swartz, E.R. (2010) Biotic diversity in the Southern African winter-rainfall region Current Opinion in Environmental Sustainability, 2 (1-2), pp. 109-116.

49. Van Vuuren, B.J.V., Robinson, T.J., Vazpinto, P., Estes, R., Matthee, C.A. (2010) Western Zambian sable: Are they a geographic extension of the giant sable antelope? South African Journal of Wildlife Research, 40 (1), pp. 35-42.

48. Sibeko, K.P., Geysen, D., Oosthuizen, M.C., Matthee, C.A., Troskie, M., Potgieter, F.T., Coetzer, J.A.W., Collins, N.E. (2010) Four p67 alleles identified in South African Theileria parva field samples Veterinary Parasitology, 167 (2-4), pp. 244-254.

47. Stoffberg, S., Jacobs, D.S., Mackie, I.J., Matthee, C.A. (2010) Molecular phylogenetics and historical biogeography of Rhinolophus bats Molecular Phylogenetics and Evolution, 54 (1), pp. 1-9.

46. Von Der Heyden, S., Barendse, J., Seebregts, A.J., Matthee, C.A. (2010) Misleading the masses: Detection of mislabelled and substituted frozen fish products in South Africa ICES Journal of Marine Science, 67 (1), pp. 176-185.

45. Willows-Munro, S., Matthee, C.A. (2009) The evolution of the southern African members of the shrew genus Myosorex: Understanding the origin and diversification of a morphologically cryptic group Molecular Phylogenetics and Evolution, 51 (2), pp. 394-398.

44. Tolley, K.A., Makokha, J.S., Houniet, D.T., Swart, B.L., Matthee, C.A. (2009) The potential for predicted climate shifts to impact genetic landscapes of lizards in the South African Cape Floristic Region Molecular Phylogenetics and Evolution, 51 (1), pp. 120-130.

43. Swart, B.L., Tolley, K.A., Matthee, C.A. (2009) Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa Journal of Biogeography, 36 (1), pp. 78-87.

42. Montgelard, C., Forty, E., Arnal, V., Matthee, C.A. (2008) Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments BMC Evolutionary Biology, 8 (1), art. no. 321, .

41. Neethling, M., Matthee, C.A., Bowie, R.C.K., Von Der Heyden, S. (2008) Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae) BMC Evolutionary Biology, 8 (1), art. no. 325, .

40. von der Heyden, S., Matthee, C.A. (2008) Towards resolving familial relationships within the Gadiformes, and the resurrection of the Lyconidae Molecular Phylogenetics and Evolution, 48 (2), pp. 764-769.

39. Matthee, C.A., Cockcroft, A.C., Gopal, K., Von Der Heyden, S. (2007) Mitochondrial DNA variation of the west-coast rock lobster, Jasus lalandii: Marked genetic diversity differences among sampling sites Marine and Freshwater Research, 58 (12), pp. 1130-1135.

38. Von Der Heyden, S., Groeneveld, J.C., Matthee, C.A. (2007) Long current to nowhere? - Genetic connectivity of Jasus tristani populations in the southern Atlantic Ocean African Journal of Marine Science, 29 (3), pp. 491-497.

37. Groeneveld, J.C., Gopal, K., George, R.W., Matthee, C.A. (2007) Molecular phylogeny of the spiny lobster genus Palinurus (Decapoda: Palinuridae) with hypotheses on speciation in the NE Atlantic/Mediterranean and SW Indian Ocean Molecular Phylogenetics and Evolution, 45 (1), pp. 102-110.

36. Teske, P.R., Hamilton, H., Matthee, C.A., Barker, N.P. (2007) Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage BMC Evolutionary Biology, 7, art. no. 138, .

35. Makokha, J.S., Bauer, A.M., Mayer, W., Matthee, C.A. (2007) Nuclear and mtDNA-based phylogeny of southern African sand lizards, Pedioplanis (Sauria: Lacertidae) Molecular Phylogenetics and Evolution, 44 (2), pp. 622-633.

34. Teske, P.R., Lourie, S.A., Matthee, C.A., Green, D.M. (2007) Hippocampus queenslandicus Horne, 2001 - A new seahorse species or yet another synonym? Australian Journal of Zoology, 55 (3), pp. 139-145.

33. Von Der Heyden, S., Lipinski, M.R., Matthee, C.A. (2007) Species-specific genetic markers for identification of early life-history stages of Cape hakes, Merluccius capensis and Merluccius paradoxus in the southern Benguela Current Journal of Fish Biology, 70 (SUPPL. B), pp. 262-268.

32. Matthee, C.A., Eick, G., Willows-Munro, S., Montgelard, C., Pardini, A.T., Robinson, T.J. (2007) Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics Molecular Phylogenetics and Evolution, 42 (3), pp. 827-837.

31. von der Heyden, S., Lipinski, M.R., Matthee, C.A. (2007) Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus Molecular Phylogenetics and Evolution, 42 (2), pp. 517-527.

30. Gopal, K., Tolley, K.A., Groeneveld, J.C., Matthee, C.A. (2006) Mitochondrial DNA variation in spiny lobster Palinurus delagoae suggests genetically structured populations in the southwestern Indian Ocean Marine Ecology Progress Series, 319, pp. 191-198.

29. Tolley, K.A., Burger, M., Turner, A.A., Matthee, C.A. (2006) Biogeographic patterns and phylogeography of dwarf chameleons (Bradypodion) in an African biodiversity hotspot Molecular Ecology, 15 (3), pp. 781-793.

28. Jacobs, D.S., Eick, G.N., Schoeman, M.C., Matthee, C.A. (2006) Cryptic species in an insectivorous bat, Scotophilus dinganii Journal of Mammalogy, 87 (1), pp. 161-170.

27. Matthee, C.A., Fourie, F., Oosthuizen, W.H., Meyër, M.A., Tolley, K.A. (2006) Mitochondrial DNA sequence data of the Cape fur seal (Arctocephalus pusillus pusillus) suggest that population numbers may be affected by climatic shifts Marine Biology, 148 (4), pp. 899-905.

26. Robinson, T.J., Matthee, C.A. (2005) Phylogeny and evolutionary origins of the Leporidae: A review of cytogenetics, molecular analyses and a supermatrix analysis Mammal Review, 35 (3-4), pp. 231-247.

25. Gouws, G., Stewart, B.A., Matthee, C.A. (2005) Lack of taxonomic differentiation in an apparently widespread freshwater isopod morphotype (Phreatoicidea: Mesamphisopidae: Mesamphisopus) from South Africa Molecular Phylogenetics and Evolution, 37 (1), pp. 289-305.

24. Eick, G.N., Jacobs, D.S., Matthee, C.A. (2005) A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (Chiroptera) Molecular Biology and Evolution, 22 (9), pp. 1869-1886.

23. Tolley, K.A., Groeneveld, J.C., Gopal, K., Matthee, C.A. (2005) Mitochondrial DNA panmixia in spiny lobster Palinurus gilchristi suggests a population expansion Marine Ecology Progress Series, 297, pp. 225-231.

22. Willows-Munro, S., Robinson, T.J., Matthee, C.A. (2005) Utility of nuclear DNA intron markers at lower taxonomic levels: Phylogenetic resolution among nine Tragelaphus spp. Molecular Phylogenetics and Evolution, 35 (3), pp. 624-636.

21. Teske, P.R., Hamilton, H., Palsbøll, P.J., Choo, C.K., Gabr, H., Lourie, S.A., Santos, M., Sreepada, A., Cherry, M.I., Matthee, C.A. (2005) Molecular evidence for long-distance colonization in an Indo-Pacific seahorse lineage Marine Ecology Progress Series, 286, pp. 249-260.

20. Verwey, R., Begg, C., Begg, K., Matthee, C.A. (2004) A microsatellite perspective on the reproductive success of subordinate male honey badgers, Mellivora capensis African Zoology, 39 (2), pp. 305-308.

19. Matthee, C.A., Tilbury, C.R., Townsend, T. (2004) A phylogenetic review of the African leaf chameleons: Genus Rhampholeon (Chamaeleonidae): The role of vicariance and climate change in speciation Proceedings of the Royal Society B: Biological Sciences, 271 (1551), pp. 1967-1975.

18. Matthee, C.A., Jansen Van Vuuren, B., Bell, D., Robinson, T.J. (2004) A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene Systematic Biology, 53 (3), pp. 433-447.

17. Tolley, K.A., Tilbury, C.R., Branch, W.R., Matthee, C.A. (2004) Phylogenetics of the southern African dwarf chameleons, Bradypodion (Squamata: Chamaeleonidae) Molecular Phylogenetics and Evolution, 30 (2), pp. 354-365.

16. Teske, P.R., Cherry, M.I., Matthee, C.A. (2004) The evolutionary history of seahorses (Syngnathidae: Hippocampus): Molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean Molecular Phylogenetics and Evolution, 30 (2), pp. 273-286.

15. Stewart, B.A., Gouws, G., Daniels, S.R., Matthee, C.A. (2004) Delimitation of morphologically similar sponge crab species of the genus Pseudodromia (Crustacea, Decapoda, Dromiidae) from South Africa Zoologica Scripta, 33 (1), pp. 45-55.

14. Bronner, G.N., Hoffmann, M., Taylor, P.J., Chimimba, C.T., Best, P.B., Matthee, C.A. & Robinson, T.J. (2003). A revised systematic checklist of the extant mammals of the southern African subregion. Durban Museum Novitas 28: 56-106.

13. Teske P.R., Cherry M.I. & Matthee C.A. (2003) Population genetics of the endangered Knysna Seahorse, Hippocampus capensis. Molecular Ecology 12:1703-1715.

12. Montgelard C, Matthee C.A. & Robinson T.J. (2003) Molecular systematics of dormice (Gliridae, Rodentia) and the African colonization by Graphiurus. Proceedings of the Royal Society London, Series B 270:1947-1955.

11. Daniels S.R., Stewart B.A., Gouws G., Cunningham M. & Matthee C.A. (2002) Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning. Molecular Phylogenetics and Evolution 25: 511-523.

10. Gatesy J., Matthee C., DeSalle R & Hayashi C. (2002) Resolution of a Supertree/Supermatrix paradox. Systematic Biology 51: 652-664.

9. Matthee C.A. & Flemming A.F. (2002) Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in Southern Africa. Molecular Ecology 11:465-471

8. Matthee C.A. & Davis S.K. (2001) Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective. Molecular Biology and Evolution 18: 1220-1230

7. Matthee C.A., Burzlaff J.D., Taylor J.F. & Davis S.K. (2001) Mining the mammalian genome for artiodactyl systematics. Systematic Biology 50: 367-390.

6. Robinson T.J. & Matthee C.A. (1999) Molecular genetic relationships of the extinct ostrich, Struthio camelus syriacus: consequences for ostrich introductions into Saudi Arabia. Animal Conservation 2: 165-171.

5. Matthee C.A. & Robinson T.J. (1999) Mitochondrial DNA genetic structure of sable and roan: conservation and translocation of rare African antelope. Molecular Ecology 8:227-238.

4. Matthee C.A. & Robinson T.J. (1999) Cytochrome b phylogeny of the family Bovidae with emphasis on the evolution of the Alcelaphini, Antilopini, Neotragini and Tragelaphini. Molecular Phylogenetics and Evolution 12:31-46.

3. Matthee C.A. & Robinson T.J. (1997). Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences. Molecular Biology and Evolution 14:20-29.

2. Matthee C.A. & Robinson T.J. (1997). Mitochondrial DNA phylogeography and comparative cytogenetics of the springhare, Pedetes capensis (Mammalia: Rodentia). Journal of Mammalian Evolution 4:53-73.

​1. Matthee C.A. & Robinson T.J. (1996). Mitochondrial DNA differentiation among geographic populations of Smith's red rock rabbit, Pronolagus rupestris (Mammalia: Lagomorpha). Heredity 76:514-523.