Between a rock and a hard polytomy: Rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae)

Molecular Phylogenetics and Evolution

Volumn 58, Issue 1, 2011, Pages 53-70

  Stanley, Edward L ^a,b   Bauer, Aaron M ^a   Jackman, Todd R ^a   Branch, William R ^c,d   Mouton, P Le Fras N ^e  

^a VILLANOVA UNIVERSITY   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^c PORT ELIZABETH MUSEUM   (South Africa)

^d NELSON MANDELA METROPOLITAN UNIVERSITY   (South Africa)

^e STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

Likelihood branch support; New genera; Phycas; Rapid radiation; Southern Africa; Taxonomic revision

Indexed keywords

AFRICA SOUTH OF THE SAHARA; ANIMAL; ARTICLE; CLASSIFICATION; GENE; GENETICS; LIZARD; MITOCHONDRIAL GENE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

AFRICA SOUTH OF THE SAHARA; ANIMALS; GENES; GENES, MITOCHONDRIAL; LIZARDS; MOLECULAR SEQUENCE DATA; PHYLOGENY;

CHAMAESAURA; CORDYLIDAE; CORDYLUS; PLATYSAURUS; PSEUDOCORDYLUS; SQUAMATA;

EID: 78651062025     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.08.024     Document Type: Article

References (96)

1. Alexander, G., Marais, J., 2007. A Guide to the Reptiles of Southern Africa, Struik, Cape Town.
2. Baker R.H., DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 1997, 46:654-673.
3. Bates M.F. Taxonomic history and geographical distribution of the Pseudocordylus melanotus (A. Smith, 1838) and P. microlepidotus (Cuvier, 1829) complexes (Sauria: Cordylidae). Navors. Nas. Mus. Bloemfontein 1829, 21:37-112.
4. Bates, M.F., 2007. An analysis of the Pseudocordylus melanotus complex (Sauria: Cordylidae). Unpublished Ph.D. Dissertation. Stellenbosch University, Stellenbosch.
5. Bauer A.M. Evolutionary scenarios in the Pachydactylus Group geckos of southern Africa: new hypotheses. Afr. J. Herpetol. 1999, 48:53-62.
6. Bauer A.M., Good D.A., Branch W.R. The taxonomy of the southern African leaf-toed geckos (Squamata: Gekkonidae), with a review of Old World " Phyllodactylus" and the description of five new genera. Proc. Calif. Acad. Sci. 4th Ser. 1997, 49:447-497.
7. Blackburn D.G. Evolutionary origins of viviparity in the Reptilia. 1. Sauria. Amphibia-Reptilia 1982, 3:185-205.
8. Bobe R. The evolution of arid ecosystems in eastern Africa. J. Arid Environ. 2006, 66:564-584.
9. Boulenger G. Synopsis of the families of existing Lacertilia. Ann. Mag. Nat. Hist. Ser. 5 1884, 14:117-122.
10. Boulenger, G., 1885. Catalogue of the Lizards in the British Museum (Natural History), second ed., vol. 2. Trustees of the British Museum, London.
11. Branch W.R. An annotated checklist of the lizards of the Cape Province, South Africa. Ann. Cape Prov. Mus. 1981, 13:141-167.
12. Branch W.R. Field Guide to Snakes and Other Reptiles of Southern Africa 1998, Ralph Curtis Books Publishing, Sanibel Island. third ed.
13. Bremer K. Branch support and tree stability. Cladistics 1994, 10:295-304.
14. Broadley D.G. A review of the crag lizards (Genus Pseudocordylus) of Natal. Ann. Natal. Mus. 1964, 16:99-100.
15. Broadley D.G. Some taxonomic and distributional problems presented by Central African reptiles. J. Herpetol. Assoc. Rhodesia 1965, 23(24):19-30.
16. Broadley D.G. A reassessment of the northern forms currently assigned to the Cordylus cordylus group. J. Herpetol. Assoc. Afr. 1971, 7:20-22.
17. Broadley D.G. The reptiles of Zambia. The Puku. Occ. Pap. Dept. Wildl., Fish. Natl, Parks, Zambia 1971, 6:1-143.
18. Broadley D.G. A revision of the genus Platysaurus A. Smith (Sauria: Cordylidae). Occ. Pap. Natl. Mus. Rhodesia Ser. B. (Nat. Sci.) 1978, 6(4):131-185.
19. Broadley, D.G., 2006. CITES Standard Reference for the Species of Cordylus (Cordylidae, Reptilia). CITES Nomenclature Committee for the 14th meeting of the Conference of the Parties. Available from: http://www.cites.org/common/docs/Res/12_11/Cordylus_CoP14_update.pdf.
20. Broadley D.G., Branch W.R. A review of the small east African Cordylus (Sauria: Cordylidae), with the description of a new species. Afr. J. Herpetol. 2002, 51:9-34.
21. Burgess N., Hales J.D.A., Underwood E., Dinerstein E. Terrestrial Ecoregions of Africa and Madagascar: A Conservation Assessment (World Wildlife Fund Ecoregion Assessments) 2004, Island Press, Washington, DC.
22. Cooper W.E. Duration of movement as a lizard foraging movement variable. Herpetologica 2005, 61:363-372.
23. Costandius E., Mouton P.LeF.N. Sexual size dimorphism in montane cordylid lizards: a case study of the dwarf crag lizard, Pseudocordylus nebulosus. Afr. Zool. 2006, 41:103-112.
24. Curtin A.J., Mouton P.LeF.N., Chinsamy A. Bone growth patterns in two cordylid lizards, Cordylus cataphractus and Pseudocordylus capensis. Afr. Zool. 2005, 40:1-7.
25. Daniels S.R., Mouton P.LeF.N., Du Toit D.A. Molecular data suggest that melanistic ectotherms at the south-western tip of Africa are the products of Miocene climatic events: evidence from cordylid lizards. J. Zool. Lond. 2004, 263:373-383.
26. De Waal S.W.P. The Squamata (Reptilia) of the Orange Free State. Mem. Nas. Mus. Bloemfontein 1978, 11:1-160.
27. Drummond, A.B., Ashton, B., Cheung, M., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Thierer, T., Wilson, A., 2009. Geneious v4.7. Available from: http://www.geneious.com/.
28. Du Toit A., Mouton P.LeF.N., Geertsema H., Flemming A.F. Foraging mode of serpentiform, grass-living cordylid lizards: a case study of Cordylus anguina. Afr. Zool. 2002, 37:141-149.
29. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32(5):1792-1797.
30. Eifler D.A., Eifler M.A., Eifler E.N. Habitat use and movement patterns in the graceful crag lizard, Pseudocordylus capensis. Afr. Zool. 2007, 42:152-157.
31. Fitzinger, L., 1843. Systema Reptilium, Fasciculus Primus, Amblyglossae, Braumüller et Seidel, Vindobonae.
32. FitzSimons, V., 1943. The lizards of South Africa. Mem. Transvaal Mus. No. 1, 1-528 pp., pls. i-xxiv+map.
33. Frost, D., Janies, D., Mouton, P.LeF.N., Titus, T., 2001. A molecular perspective on the phylogeny of the girdled lizards (Cordylidae, Squamata). Am. Mus. Novit. 3310, 1-10.
34. Fuchs J., Fjeldsa J., Pasquet E. An ancient African radiation of corvoid birds (Aves: Passeriformes) detected by mitochondrial and nuclear sequence data. Zool. Scr. 2006, 35:375-385.
35. Gray J.E. Catalogue of the Specimens of Lizards in the Collection of the British Museum 1845, Trustees of the British Museum, London.
36. Greenbaum E., Bauer A.M., Jackman T.R., Vences M., Glaw F. A phylogeny of the enigmatic Madagascan geckos of the genus Uroplatus (Squamata: Gekkonidae). Zootaxa 2007, 1493:41-51.
37. Günther A. Notice of reptiles and batrachians collected in the eastern half of Tropical Africa. Ann. Mag. Nat. Hist. Ser. 6 1895, 15:523-529. pl. xxi.
38. Haagner G.V., Branch W.R., Haagner A.J.F. Notes on a collection of reptiles from Zambia and adjacent areas of the Democratic Republic of the Congo. Ann. East. Cape Mus. 2000, 1:1-25.
39. Heath T.A., Hedtke S.M., Hillis D.M. Taxon sampling and the accuracy of phylogenetic analyses. J. Syst. Evol. 2008, 46:239-257.
40. Herselman Y.M., Mouton P.LeF.N., Van Wyk J.H. Paraphyletic genera in the family Cordylidae. J. Herpetol. Assoc. Afr. 1992, 40:27.
41. Herselman Y.M., Mouton P.LeF.N., Van Wyk J.H. The status of the races of the graceful crag lizard Pseudocordylus capensis from South Africa. Amphibia-Reptilia 1992, 13:109-119.
42. Herselman, Y.M., 1991. A revision of the taxonomic status of Pseudocordylus capensis (Reptilia: Cordylidae). Unpublished M.Sc. Thesis, University of Stellenbosch, Stellenbosch, South Africa.
43. Hipsley C.A., Himmelmann L., Metzler D., Mueller J. Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals Early Cenozoic origin of African lacertid lizards. BMC Evol. Biol. 2009, 9:1-13.
44. Huelsenbeck J., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
45. Jacobsen, J.H.G., 1989. A Herpetological Survey of the Transvaal. Unpublished Ph.D. Dissertation. University of Natal, Durban.
46. Janse van Rensburg, D.A., 2009. Morphological and behavioural correlates of melanism in cordylid lizards: conservation implictions for melanistic lizards in the Greater Cederberg Biodiversity Corridor. Unpublished M.Sc. Thesis, University of Stellenbosch, Stellenbosch.
47. Janse van Rensburg D.A., Mouton P.leF.N., van Niekerk A. Why cordylid lizards are black at the south-western tip of Africa. J. Zool. Lond. 2009, 278:333-341.
48. Kappelman J., Rasmussen D.T., Sanders W.J., Feseha M., Bown T., Copeland P., Crabaugh J., Fleagle J., Glantz M., Gordon A., Jacobs B., Maga M., Muldoon K., Pan A., Pyne L., Richmond B., Ryan T., Seiffert E.R., Sen S., Todd L., Wiemann M.C., Winkler A. Oligocene mammals from Ethiopia and faunal exchange between Afro-Arabia and Eurasia. Nature 2003, 426:549-552.
49. Kodandaramaiah U., Peña C., Braby M.F., Grund R., Müller C.J., Nylin S., Wahlberg N. Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations. Mol. Phylogenet. Evol. 2010, 54:386-394.
50. Lang M. Generic relationships within Cordyliformes (Reptilia: Squamata). Bull. Inst. R. Sci. Nat. Belg., Biol. 1991, 61:121-188.
51. Lee M.S.Y. Hidden support from unpromising data sets strongly unites snakes with anguimorph 'lizards'. J. Evol. Biol. 2009, 22:1308-1316.
52. Lee M.S.Y., Hugall A.F. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 2003, 52:15-22.
53. Lewis, P., Holder, M., Swofford, D. 2009. Phycas. Version 1.1.1. http://www.phycas.org.
54. Lewis P.O., Holder M.T., Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 2005, 54:241-253.
55. Loveridge A. Revision of the African lizards of the family Cordylidae. Bull. Mus. Comp. Zool. 1944, 95:1-118. pls. 1-12.
56. Losos J.B., Mahler D.L. Adaptive radiation: the interaction of ecological opportunity, adaptation, and speciation. Evolution Since Darwin: The First 150 Years 2010, 381-420. Sinauer Assoc., Sunderland, MA. M.A. Bell, D.J. Futuyma, W.F. Eanes, J.S. Levinton (Eds.).
57. Lynch V.J., Wagner G.P. Did egg-laying boas break Dollo's Law? Phylogenetic evidence for reversal to oviparity in Sand Boas (Eryx: Boidae). Evolution 2009, 64:207-216.
58. Macey J.R., Larson A., Ananjeva N.B., Fang Z., Papenfuss T.J. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 1997, 14:91-104.
59. Maddison W.P., Maddison D.R. MacClade: Analysis of Phylogeny and Character Evolution 2000, Sinauer, Sunderland, Mass.
60. McConnachie S., Whiting M.J. Costs associated with tail autotomy in an ambush foraging lizard, Cordylus melanotus melanotus. Afr. Zool. 2003, 38:57-65.
61. McDowell S., Bogert C. The systematic position of Lanthanotus and the affinities of the anguinolnorphan lizards. Bull. Am. Mus. Nat. Hist. 1954, 105:1-142.
62. Menegon M., Salvidio S., Moyer D. Reptiles and amphibians from a montane grassland: Gendawaki Valley, Udzungwa Mountains, Tanzania. Afr. Herp. News 2006, 40:8-14.
63. Mertens R. Reptilien und Amphibien aus dem südlichen Inner-Afrika. Abhandlungen der Senckenbergischen Naturforschenden Gesellschaft (Frankfurt) 1937, 435:1-23.
64. Methuen P., Hewitt J. Records and descriptions of the reptiles and batrachians of the collection. Ann. Transvaal Mus. 1914, 4(3):118-145.
65. Moon S. Pseudocordylus melanotus melanotus (Drakensberg crag lizard). Copulation and aggression. Herpetol. Rev. 2001, 32:258-259.
66. Mott T., Vieites D.R. Molecular phylogenetics reveals extreme morphological homoplasy in Brazilian worm lizards challenging current taxonomy. Mol. Phylogenet. Evol. 2009, 51:190-200.
67. Mouton P.LeF.N., van Wyk J.H. Taxonomic status of geographical isolates in the Cordylus minor complex (Reptilia: Cordylidae): a description of three new species. J. Herpetol. Assoc. Afr. 1994, 43:6-18.
68. Mouton P.LeF.N., Van Wyk J.H. Adaptive radiation in cordyliform lizards: an overview. Afr. J. Herpetol. 1997, 46:78-88.
69. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
70. Odierna G., Canapa A., Andreone F., Aprea G., Barucca M., Capriglione T., Olmo E. A phylogenetic analysis of cordyliformes (Reptilia: Squamata): comparison of molecular and karyological data. Mol. Phylogenet. Evol. 2002, 23:37-42.
71. Olmo E., Odierna G. Chromosomal evolution and DNA of cordylid lizards. Herpetologica 1980, 36:311-316.
72. Overton L.C., Rhoads D.D. Molecular phylogenetic relationships based on mitochondrial and nuclear gene sequences for the Todies (Todus, Todidae) of the Caribbean. Mol. Phylogenet. Evol. 2004, 32:524-538.
73. Peters W. Übersicht einiger von dem, durch seine africanischen Sprachforschungen rühmlichst bekannten, Hrn. Missionär C. H. Hahn bei Neu-Barmen, im Hererolande, an der Westküste von Africa, im 21° südl Br. gesammelten Amphibien, nebst Beschreibungen der neuen Arten. Mber. königl. Preuß. Akad. Wiss. Berlin 1862, 1862:15-26.
74. Portik, D., Bauer, A. M., Jackman, T.R, in press. The phylogenetic affinities of Trachylepis sulcata nigra and the intraspecifc evolution of coastal melanism in the Western rock skink. Afr. Zool.
75. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
76. Romer A.S. Osteology of the Reptiles 1956, University of Chicago Press, Chicago.
77. Ronquist F., Huelsenbeck J. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
78. Scott I.A.W., Keogh J.S., Whiting M.J. Shifting sands and shifty lizards: molecular phylogeny and biogeography of African flat lizards (Platysaurus). Mol. Phylogenet. Evol. 2004, 31:618-629.
79. Shine R. Reconstructing an adaptationist scenario: what selective forces favor the evolution of viviparity in montane reptiles?. Am. Nat. 2002, 160:582-593.
80. Simon C., Frati F., Beckenbach A., Crespi B., Liu H., Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 1994, 87:651-701.
81. Sorenson M.D., Franzosa E.A. TreeRot 2007, Boston University, Boston.
82. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
83. Stanley, E.L., 2009. Evolutionary relationships within the family Cordylidae (Squamata). Unpublished M.Sc. Thesis, Villanova University, Villanova, USA.
84. Stejneger L. Types of the amphibian and reptilian genera proposed by Laurenti in 1768. Copeia 1936, 1936:133-141.
85. Swofford D.L. Paup* Phylogenetic Analysis Using Parsimony (and Other Methods) Version 4.0 2002, Sinauer Associates, Sunderland, Mass.
86. Swofford D.L., Olsen G.J., Waddell P.J., Hillis D.M. Phylogenetic Inference 1996, Sinauer Associates, Inc., Sunderland, Mass.
87. Thermudo G.E., Wielstra B., Arntzen J.W. Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae). Mol. Phylogenet. Evol. 2009, 52:321-328.
88. Tolley K.A., Tilbury C.R., Branch W.R., Matthee C.A. Evolutionary history and phylogenetics of the southern African dwarf chameleons, Bradypodion. Mol. Phylogenet. Evol. 2004, 30:354-365.
89. Townsend T.M., Alegre R.E., Kelley S.T., Wiens J.J., Reeder T.W. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol. Phylogenet. Evol. 2008, 47:129-142.
90. Townsend T.M.A., Larson A., Louis E., Macey J.R. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 2004, 53:735-757.
91. van Dam G.P.F. Descriptions of new species of Zonurus, and notes on the species of Zonurus occurring in the Transvaal. Ann. Transvaal. Mus. 1921, 7:239-243. pls. i-iv.
92. Visser J. Cordylus cordylus and its races in the Cape Province - a general discussion. J. Herpetol. Assoc. Afr. 1971, 7:18-20.
93. Vitt L.J., Caldwell J.P. Herpetology: An Introductory Biology of Amphibians and Reptiles 2008, Academic Press, London. third ed.
94. Whiting A.S., Sites J.W., Pellegrino K.C.M., Rodrigues M.T. Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae). Mol. Phylogenet. Evol. 2006, 38:719-730.
95. Zachos J., Pagani M., Sloan L., Thomas E., Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 2001, 292:686-693.
96. Zwickl D.J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion 2006, The University of Texas at Austin, Austin.