Molecular phylogeny and phylogeography of the Australian Diplodactylus stenodactylus (Gekkota; Reptilia) species-group based on mitochondrial and nuclear genes reveals an ancient split between Pilbara and non-Pilbara D. stenodactylus

Molecular Phylogenetics and Evolution

Volumn 41, Issue 3, 2006, Pages 539-555

  Pepper, Mitzy ^a   Doughty, Paul ^b   Keogh, J Scott ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b WESTERN AUSTRALIAN MUSEUM   (Australia)

Author keywords

16s; Australian arid zone; Biogeography; Diplodactylus stenodactylus; Gekkonidae; Gekkota; ND2; Phylogeography; Pilbara; RAG 1; Reptile

Indexed keywords

PRIMER DNA; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; RNA 16S; TRANSFER RNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; AUSTRALIA; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENE; GENETICS; GEOGRAPHY; LIZARD; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

ANIMALS; AUSTRALIA; DNA PRIMERS; GENES, RAG-1; GEOGRAPHY; LIZARDS; NADH DEHYDROGENASE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

DIPLODACTYLUS; DIPLODACTYLUS DAMAEUS; DIPLODACTYLUS PULCHER; DIPLODACTYLUS STENODACTYLUS; EREMAEA; GEKKONIDAE; GEKKOTA; REPTILIA; RHYNCHOEDURA ORNATA; SQUAMATA;

EID: 33750949386     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.05.028     Document Type: Article

References (66)

1. Ballard J.W.O., and Whitlock M.C. The incomplete natural history of mitochondria. Molecular Ecology 13 (2004) 729-744
2. Beard J.S. The natural regions of the deserts of Western Australia. Journal of Ecology 57 (1969) 677-711
3. Beard J.S. Plant Life of Western Australia (1990), Kangaroo Press, Kenthurst, NSW
4. Bunting, J.A., van de Graff, W.J.E., Jackson, M.J., 1974. Palaeodrainages and Cainozoic palaeogeography of the eastern goldfields, Gibson Desert and Great Victoria Desert. Geological Survey of Western Australia Annual Report for 1973, 45-50.
5. Chapple D.G., and Keogh J.S. Parallel adaptive radiations in arid and temperate Australia: molecular Phylogeography and systematics of Egernia whitii (Lacertilia: Scincidae) species group. Biological Journal of the Linnean Society 83 (2004) 157-173
6. Chapple D.G., Keogh J.S., and Hutchinson M.N. Molecular phylogeography and systematics of the arid-zone members of the Egernia whitii (Lacertilia: Scincidae) species group. Molecular Phylogenetics and Evolution 33 (2004) 549-561
7. Cogger H.G. Reptiles in the Australian arid zone. In: Cogger H.G., and Cameron E.E. (Eds). Arid Australia (1984), Surrey Beatty & Sons Pty. Ltd., Chipping Norton, NSW 235-253
8. Cogger H.G. Reptiles and Amphibians of Australia (2000), Reed New Holland, Sydney
9. Cogger H.G., and Heatwole H. The Australian reptiles: origins, biogeography, distribution patterns and island evolution. In: Keast A. (Ed). Ecological Biogeography of Australia (1981), Dr W Junk Publishers, The Hague 1393-1434
10. Cracraft J. Patterns of diversification within continental biotas: hierarchical congruence among the areas of endemism of Australian vertebrates. Australian Systematic Biology 4 (1991) 211-227
11. Crisp M.D., Linder H.P., and Weston P.H. Cladistic biogeography of plants in Australia and New Guinea: congruent pattern reveals two endemic tropical tracks. Systematic Biology 44 (1995) 457-473
12. Crisp M.D., Laffan S., Linder H.P., and Monro A. Endemism in the Australian flora. Journal of Biogeography 28 (2001) 183-198
13. Donnellan S.C., Hutchinson M.N., and Saint K.M. Molecular evidence for the phylogeny of Australian gekkonoid lizards. Biological Journal of the Linnean Society 67 (1999) 97-118
14. Edwards S.V. Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences. Proceedings of the Royal Society of London series B 252 (1993) 177-185
15. Finston T.L., and Johnson M.S. Geographic patterns of genetic diversity in subterranean amphipods of the Pilbara, Western Australia. Marine and Freshwater Research 55 (2004) 619-628
16. Finston T.L., Bradbury J.H., Johnson M.S., and Knott B. When morphology and molecular markers conflict: a case history of subterranean amphipods from the Pilbara, Western Australia. Animal Biodiversity and Conservation 27 (2004) 83-94
17. Fry D.B. On a collection of reptiles and batrachians from Western Australia. Records of Western Australian Museum 1 (1914) 175-177
18. Geological Survey of Western Australia, 1990. Geology and Mineral Resources of Western Australia, Memoir 3, East Perth: Geological Survey of Western Australia.
19. Geoscience Australia, 1997. Australia's River Basins. ANZLIC identifier number: ANZCW0703005427, .
20. Han D., Zhou K., and Bauer A.M. Phylogenetic relationships among the higher taxonomic categories of gekkotan lizards inferred from C-mos nuclear DNA sequences. Biological Journal of the Linnean Society 83 (2004) 353-368
21. Haq B.U., Hardenbol J., and Vail P.R. Chronology of fluctuating sea levels since the Triassic (250 million years ago to present). Science 235 (1987) 1156-1167
22. Hare M.P. Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution 16 (2001) 700-707
23. Hillis D.M., and Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogeographic analysis. Systematic Biology 42 (1993) 181-192
24. Hopper S.D., and Gioia P. The Southwest Australian Floristic region: evolution and conservation of a global hot spot of biodiversity. Annual Review of Ecology, Evolution and Systematics 35 (2004) 623-650
25. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
26. Hugall A., Moritz C., Moussalli A., and Stanisic J. Reconciling paleodistribution models and comparative Phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences of United States of America 99 (2002) 6112-6117
27. Jennings W.B., Pianka E.R., and Donnellan S. Systematics of the lizard Family Pygopodidae with implications for the diversification of the arid temperate biotas. Systematic Biology 52 (2003) 757-780
28. Joseph L., Moritz C., and Hugall A. Molecular data support vicariance as a source of diversity in rainforests. Proceedings of the Royal Society of London Series B 260 (1995) 177-182
29. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.N. (Ed). Mammalian Protein Metabolism (1969), Academic Press, New York 21-132
30. Kearney M., Moussalli A., Strasburg J., Lindenmayer D., and Moritz C. Geographic parthenogenesis in the Australian arid zone: 1. A climatic analysis of the Heteronodia binoei complex (Gekkonidae). Evolutionary Ecology Research 5 (2003) 953-976
31. Keogh J.S., Scott I.A.W., Fitzgerald M., and Shine R. Molecular phylogeny of the Australian venomous snake genus Hoplocephalus and conservation genetics of the threatened H. stephensi. Conservation Genetics 4 (2003) 57-65
32. Keogh J.S., Scott I.A.W., and Hayes C. Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes. Evolution 59 (2005) 226-233
33. King M. Chromosomal evolution in the Diplodactylinae (Gekkonidae: Reptilia). 1. Evolutionary relationships and patterns of change. Australian Journal of Zoology 35 (1987) 507-531
34. King M., and Horner P. Faunas of Australia, 2A, Amphibia and Reptilia (1993), Australian Government Publishing Service pp. 221-233
35. Kluge A.G. Systematics, phylogeny, and zoogeography of the lizard Genus Diplodactylus Gray (Gekkonidae). Australian Journal of Zoology 15 (1967) 1007-1080
36. Macey J.R., Schulte J.A., Larson A., Fang Z., Wang Y., Tuniyev B.S., and Papenfuss T.J. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: a case of vicarience and dispersal. Molecular Phylogenetics and Evolution 9 (1998) 80-87
37. Macey J.R., Schulte J.A., Ananjeva N.B., Larson A., Rastegar-Pouyani N., Shammakov S.M., and Papenfuss T.J. Phylogenetic relationships among agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau. Molecular Phylogenetics and Evolution 10 (1998) 118-131
38. Macey J.R., Schulte J.A., Larson A., Ananjeva N.B., Wang Y., Pethiyagoda R., Rastegar-Pouyani N., and Papenfuss T.J. Evaluating trans-Tethys migration: an example using acrodont lizard phylogenetics. Systematic Biology 49 (2000) 233-256
39. Melville J., Schulte J.A., and Larson A. A molecular study of phylogenetic relationships and evolution of antipredator strategies in Australian Diplodactylus geckos, subgenus Strophurus. Biological Journal of the Linnean Society 82 (2004) 123-138
40. Moritz C., and Heideman A. The origin and evolution of parthenogenesis in Heteronodia binoei (Gekkonidae): reciprocal origins and diverse mitochondrial DNA in western populations. Systematic Biology 42 (1993) 293-306
41. Moussalli A., Hugall A.F., and Moritz C. A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984). Molecular Phylogenetics and Evolution 34 (2005) 190-202
42. Nichols R. Gene trees and species trees are not the same. Trends in Ecology and Evolution 16 (2001) 358-364
43. Palumbi S.R. Nucleic acids II: the polymerase chain reaction. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates Inc., Sunderland, Mass 205-247
44. Pianka E.R. Habitat specificity, speciation, and species density in Australian desert lizards. Ecology 50 (1969) 498-502
45. Pianka E.R. Sympatry of desert lizards (Ctenotus) in Western Australia. Ecology 50 (1969) 1012-1030
46. Pianka E.R. Diversity and adaptive radiations of Australian desert lizards. In: Keast A. (Ed). Ecological Biogeography of Australia (1981), Dr W. Junk, The Hague 1377-1392
47. Pianka E.R. Desert lizard diversity: additional comments and some data. The American Naturalist 134 (1989) 344-364
48. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
49. Read K., Keogh J.S., Scott I.A.W., Roberts J.D., and Doughty P. Molecular phylogeny of the Australian frog genera Crinia, Geocrinia and allied taxa (Anura: Myobatrachidae). Molecular Phylogenetics and Evolution 21 (2001) 294-308
50. Schauble C.S., and Moritz C. Comparative phylogeography of two open forest frogs from eastern Australia. Biological Journal of the Linnean Society 74 (2001) 157-170
51. Scott I.A., and Keogh J.S. Conservation genetics of the endangered grassland earless dragon Typmpanocryptis pinquicolla (Reptilia: Agamidae) in Southeastern Australia. Conservation Genetics 1 (2000) 357-363
52. Smith, L., Adams, M., (in press). Revision of the Lerista muelleri species group in Western Australia with a redescription of Lerista muelleri (Fischer) and the description of nine new species. Records of the Westerns Australian Museum.
53. Storr G.M. Three new Diplodactylus (Lacertilia: Gekkonidae) from the arid zone of Australia. Records of the Western Australian Museum 14 (1988) 217-223
54. Storr G.M., Smith L.A., and Johnstone R.E. Lizards of Western Australia 3, Geckos and Pygopods (1990), Western Australian Museum, Perth
55. Strasburg J.L., and Kearney M. Phylogeography of sexual Heteronodia binoei (Gekkonidae) in the Australian arid-zone: climatic cycling and repetitive hybridisation. Molecular Ecology 14 (2005) 2755-2772
56. Stuart-Fox D.M., Schneider C.J., Moritz C., and Couper P.J. Comparative phylogeography of three rainforest-restricted lizards from mid-east Queensland. Australian Journal of Zoology 49 (2001) 119-127
57. * and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25 (1997) 4876-4882
59. Townsend T.M., Larson A., Louis E., and Macey J.R. Molecular phylogenetics of Squamata: The position of Snakes, Amphisbaenians, and Dibamids, and the root of the Squamate tree. Systematic Biology 53 (2004) 735-757
60. van Vreeswyk, A.M.E., Payne, A.L., Leighton, K.A., Hennig, P., 2004. An Inventory and Condition Survey of the Pilbara Region, Western Australia, Technical Bulletin No. 92, Department of Agriculture, South Perth, WA.
61. Weisrock D.W., Harmon L.J., and Larson A. Resolving deep phylogenetic relationships in salamanders: Analysis of mitochondrial and nuclear genomic data. Systematic Biology 54 (2005) 758-777
62. Wilcox T.P., Zwickl D.J., Heath T.A., and Hillis D.M. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25 (2002) 361-371
63. Wilson S., and Swan G. A Complete Guide to Reptiles of Australia (2003), New Holland Publishers Pty. Ltd., Australia
64. Wilson A.C., Cann R.L., Carr S.M., George M., Gyllensten U.B., Helm-Brychowski K., Higuchi R.C., Palumbi S.R., Prager E.M., Sage R.D., and Stoneking M. Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society 26 (1985) 375-400
65. Wong B.M.B., Keogh J.S., and McGlashan D.J. Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae). Molecular Ecology 13 (2004) 391-401
66. Zamudio K.R., and Greene H.W. Phylogeography of the bushmaster (Lachesis muta: Viperidae): implications for neo-tropical biogeography, systematics and conservation. Biological Journal of the Linnean Society 62 (1997) 421-442