Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa

Journal of Biogeography

Volumn 36, Issue 1, 2009, Pages 78-87

  Swart, Belinda L ^a   Tolley, Krystal A ^b   Matthee, Conrad A ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b SOUTH AFRICAN NATIONAL BIODIVERSITY INSTITUTE   (South Africa)

Author keywords

Agamidae; Cape Fold Mountains; Coalescence; Control region; Landscape genetics; Lizard; mtDNA; ND2; Phylogeography; Southern Africa

Indexed keywords

CAPE FLORISTIC REGION; CLIMATE CHANGE; ENDEMISM; EVOLUTION; GENE FLOW; GENETIC STRUCTURE; LIZARD; MITOCHONDRIAL DNA; PHYLOGEOGRAPHY; SPECIATION (BIOLOGY); SPECIES DIVERSITY;

AFRICA; CAPE FOLD BELT; SOUTH AFRICA; SOUTHERN AFRICA; SUB-SAHARAN AFRICA;

AGAMA; AGAMA AGAMA; AGAMA ATRA; AGAMIDAE; ANIMALIA; REPTILIA; SQUAMATA;

EID: 57549104873     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2008.01988.x     Document Type: Article

References (60)

1. Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H.L., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Staden, R. Young, I.G. (1981) Sequence and organization of the human mitochondrial genome. Nature, 290, 457 465.
2. Baard, E.H.W., Branch, W.R., Channing, A.C., de Villiers, A.L., le Roux, A. Mouton, P. le F.N. (1999) A review of the amphibians and reptiles of the Cape Floristic Region as indicators of centres of biodiversity, sensitive habitats and sites of special interest. Western Cape Nature Conservation Board, Stellenbosch.
3. Bandelt, H.J., Forster, P. Röhl, A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37 48.
4. Barrable, A., Meadows, M.E. Hewitson, B.C. (2002) Environmental reconstruction and climate modelling of the Late Quaternary in the winter rainfall region of the Western Cape, South Africa. South African Journal of Science, 98, 611 616.
5. Bauer, A.M. (1999) Evolutionary scenarios in the Pachydactylus group geckos of Southern Africa: new hypotheses. African Journal of Herpetology, 48, 53 62.
6. Branch, W.R. (1988) Field guide to snakes and other reptiles of southern Africa. Struik Publishers, Cape Town.
7. Bromham, L. Penny, D. (2003) The modern molecular clock. Nature Reviews Genetics, 4, 216 224.
8. Burrage, B.R. (1974) Population structure in Agama atra and Cordylus cordylus in the vicinity of De Kelders, Cape Province. Annals of the South African Museum, 66, 1 23.
9. Carr, A.S., Thomas, D.S.A., Bateman, M.D., Meadows, M.E. Chase, B. (2006) Late Quaternary palaeoenvironments of the winter-rainfall zone of southern Africa: palynological and sedimentological evidence from the Agulhas Plain. Palaeogeography, Palaeoclimatology, Palaeoecology, 239, 147 165.
10. Channing, A., Hendricks, D. Dawood, A. (1994) Description of a new moss frog from the south-western Cape (Anura: Ranidae: Arthroleptella). South African Journal of Zoology, 29, 240 243.
11. Chase, B.M. Meadows, M.E. (2007) Late Quaternary dynamics of southern Africa's winter rainfall zone. Earth Science Reviews, 84, 103 138.
12. Cowling, R.M. Holmes, P.M. (1992) Flora and vegetation. The ecology of fynbos, nutrients, fire and diversity (ed. by R.M. Cowling pp. 23 61. Oxford University Press, Oxford.
13. Daniels, S.R., Stewart, B.A. Burmeister, L. (2001) Geographic patterns of genetic and morphological divergence amongst populations of a river crab (Decapoda, Potamonautidae) with the description of a new species from mountains streams in the Western Cape, South Africa. Zoologica Scripta, 30, 181 197.
14. deMenocal, P.B. (2004) African climate change and faunal evolution during the Pliocene-Pleistocene. Earth and Planetary Science Letters, 220, 3 24.
15. Dupanloup, I., Schneider, S. Excoffier, L. (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571 2581.
16. ESRI (1999) ArcView 3.2. Environmental Science Research Institute, Redlands, CA, USA.
17. Excoffier, L., Smouse, P.E. Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479 491.
18. Excoffier, L., Laval, G. Schneider, S. (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics (Online), 1, 47 50.
19. Flemming, A.F. (1996) An analysis of the Agama atra complex (Reptilia: Agamidae) in Namaqualand and Southern Namibia. PhD Thesis, University of Stellenbosch, Stellenbosch.
20. Flemming, A.F. Mouton, P. le F.N. (2000) Geographic variation in sexual size dimorphism in the rock agama, Agama atra (Sauria: Agamidae). African Zoology, 35, 233 249.
21. Forest, F., Grenyer, R., Rouget, M., Davies, T.J., Cowling, R.M., Faith, D.P., Balmford, A., Manning, J.C., Procheş, S., van der Bank, M., Reeves, G., Hedderson, T.A.J. Savolainen, V. (2007) Preserving the evolutionary potential of floras in biodiversity hotspots. Nature, 445, 757 760.
22. Gouws, G., Stewart, B.A. Daniels, S.R. (2003) Cryptic species within the freshwater isopod Mesamphisopus capensis (Phreatoicidea: Amphisopodidae) in the Western Cape, South Africa: allozyme and 12S rRNA sequence data and morphometric evidence. Biological Journal of the Linnean Society, 81, 235 253.
23. Hendey, Q.B. (1983a) Cenozoic geology and palaeogeography of the fynbos region. Fynbos palaeoecology: a preliminary synthesis (ed. by H.J. Deacon, Q.B. Hendey N.N.J. Lambrechts pp. 35 60. Council for Scientific and Industrial Research, Pretoria.
24. Hendey, Q.B. (1983b) Palaeontology and palaeoecology of the fynbos region: an introduction. Fynbos palaeoecology: a preliminary synthesis (ed. by H.J. Deacon, Q.B. Hendey N.N.J. Lambrechts pp. 87 99. Council for Scientific and Industrial Research, Pretoria.
25. Huelsenbeck, J.P. Ronquist, F. (2001) MrBayes: a program for the Bayesian inference of phylogeny. Available at: http://mrbayes.csit.fsu.edu/index.php ; last accessed 8 August 2008.
26. Kumar, S. (2005) Molecular clocks: four decades of evolution. Nature Reviews Genetics, 6, 654 662.
27. Kumar, S., Tamura, K., Jakobsen, I.B. Nei, M. (2001) MEGA ver. 2.1. Molecular Evolutionary Genetics Analysis software, Arizona State University, Tempe, AZ, USA.
28. Lamb, T. Bauer, A.M. (2000) Relationship of the Pachydactylus rugosus group of geckos (Reptilia: Squamata: Gekkodidae). African Zoology, 35, 55 67.
29. Linder, H.P. (2003) The radiation of the Cape flora, Southern Africa. Biological Reviews, 78, 597 638.
30. Linder, H.P. (2005) Evolution of diversity: the Cape flora. Trends in Plant Science, 11, 536 541.
31. Linder, H.P. Mann, D.M. (1998) The phylogeny and biogeography of Thamnochortus (Restionaceae). Botanical Journal of the Linnean Society, 128, 319 357.
32. Linder, H.P., Meadows, M.E. Cowling, R.M. (1992) History of the Cape flora. The ecology of fynbos, nutrients, fire and diversity (ed. by R.M. Cowling pp. 113 134. Oxford University Press, Oxford.
33. Macey, J.R., Larson, A., Ananjeva, N.B. Papenfuss, T.J. (1997a) Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. Journal of Molecular Evolution, 44, 660 674.
34. Macey, J.R., Larson, A., Ananjeva, N.B., Fang, Z.L. Papenfuss, T.J. (1997b) Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution, 14, 91 104.
35. Macey, J.R., Schulte, J.A., Ananjeva, N.B., Larson, A., Rastegar-Pouyani, N., Shammakov, S.M. Papenfuss, T.J. (1998) Phylogenetic relationships among agamid lizards of the Laudakia caucasia species group: testing hypotheses of biographic fragmentation and an area cladogram for the Iranian Plateau. Molecular Phylogenetics and Evolution, 10, 118 131.
36. Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209 220.
37. 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.
38. Matthee, C.A. Robinson, T.J. (1996) Mitochondrial DNA differentiation among geographical populations of Pronolagus rupestris, Smith's red rock rabbit (Mammalia: Lagomorpha). Heredity, 76, 514 523.
39. Matthee, C.A., Tilbury, C.R. Townsend, T.A. (2004) 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, 1967 1975.
40. Midgley, G.F., Hannah, L., Roberts, R., MacDonald, D.J. Allsopp, J. (2001) Have Pleistocene climatic cycles influenced species richness patterns in the greater Cape Mediterranean Region? Journal of Mediterranean Ecology, 2, 137 144.
41. Miller-Butterworth, C.M., Jacobs, D.S. Harley, E.H. (2003) Strong population substructure is correlated with morphology and ecology in a migratory bat. Nature, 424, 187 191.
42. Mouton, P. le F.N. Herselman, Y.M. (1994) Paradoxical reproduction and body size in the rock lizard, Agama atra atra, Namaqualand, South Africa. South African Journal of Zoology, 29, 199 203.
43. Mucina, L. Rutherford, M.C. (2006) The vegetation of South Africa, Lesotho and Swaziland. Strelitzia 19, South African National Biodiversity Institute, Pretoria.
44. Myers, N., Mittermeier, C.G., da Fonseca, G.A.B. Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853 858.
45. Nielsen, R. (2002) MDIV software. Available at: http://cbsuapps.tc. cornell.edu/mdiv.aspx ; last accessed 8 August 2008.
46. Palumbi, S.R. (1996) Nucleic acids II: the polymerase chain reaction. Molecular systematics (ed. by D.M. Hillis, C. Moritz B.K. Mable pp. 205 221. Sinauer Associates, Sunderland, MA, USA.
47. Palumbi, S.R. Kessing, B.D. (1991) Population biology of the trans-arctic exchange: mtDNA sequence similarity between Pacific and Atlantic sea urchins. Evolution, 45, 1790 1805.
48. Picker, M.D. Samways, M.J. (1996) Faunal diversity and endemicity of the Cape Peninsula, South Africa - a first assessment. Biodiversity and Conservation, 5, 591 606.
49. Posada, D. Crandall, K.A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
50. Price, B.W., Barker, N.P. Villet, M.H. (2007) Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa. Molecular Ecology, 16, 2574 2588.
51. Rozen, S. Skaletsky, H.J. (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics methods and protocols: methods in molecular biology (ed. by S. Krawetz S. Misener pp. 365 386. Humana Press, Totowa, NJ, USA.
52. Sambrook, J., Fritsch, E.F. Maniatis, T. (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
53. Smit, H.A., Robinson, T.J. Van Vuuren, B.J. (2007) Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea). Molecular Ecology, 16, 2680 2692.
54. Swart, B.L. (2006) The phylogeography of the southern rock agama (Agama atra) in the Cape Fold Mountains. MSc Thesis, University of Stellenbosch, Stellenbosch.
55. Swofford, D.L. (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA, USA.
56. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. Higgins, D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876 4882.
57. Tolley, K.A., Tilbury, C.R., Branch, W.R. Matthee, C.A. (2004) Evolutionary history and phylogenetics of the southern African dwarf chameleons, Bradypodion. Molecular Phylogenetics and Evolution, 30, 354 365.
58. 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, 781 793.
59. Tolley, K.A., Chase, B.M. Forest, F. (2008) Speciation and radiations track climate transitions since the Miocene Climatic Optimum: a case study of southern Africa chameleons. Journal of Biogeography, 35, 1402 1414.
60. Trinder-Smith, T.H., Cowling, R.M. Linder, H.P. (1996) Profiling a besieged flora: endemic and threatened plants of the Cape Peninsula, South Africa. Biodiversity and Conservation, 5, 649 669.