Combined mitochondrial and nuclear data enhance resolution of a rapid radiation of Australian rainbow skinks (Scincidae: Carlia)

Molecular Phylogenetics and Evolution

Volumn 49, Issue 3, 2008, Pages 782-794

  Dolman, Gaynor ^a,b   Hugall, Andrew F ^c  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b CSIRO   (Australia)

^c UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Carlia; Comparative diversification rates; Gene tree conflict; Intron; Liburnascincus; Lygisaurus; Rapid radiation

Indexed keywords

BETA GLOBIN; FRUCTOSE BISPHOSPHATE ALDOLASE; MITOCHONDRIAL DNA; RNA 16S;

ANIMAL; ARTICLE; AUSTRALIA; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; GENETICS; LIZARD; MITOCHONDRIAL GENE; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; RNA GENE; SEQUENCE ALIGNMENT; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; AUSTRALIA; BAYES THEOREM; BETA-GLOBINS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FRUCTOSE-BISPHOSPHATE ALDOLASE; GENES, MITOCHONDRIAL; GENES, RRNA; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; LIZARDS; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CARLIA PARRHASIUS; LYGISAURUS; SCINCIDAE;

EID: 56549106900     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.09.021     Document Type: Article

References (66)

1. Arevalo E., Davis S.K., and Sites J.W. Mitochondrial-DNA sequence divergence and phylogenetic-relationships among eight chromosome races of the Sceloporus Grammicus Complex (Phrynosomatidae) in Central Mexico. Syst. Biol. 43 (1994) 387-418
2. Austin J.J., and Arnold E.N. Using ancient and recent DNA to explore relationships of extinct and endangered Leiolopisma skinks (Reptilia: Scincidae) in the Mascarene islands. Mol. Phylogenet. Evol. 39 (2006) 503-511
3. Baker R.H., and DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst. Biol. 46 (1997) 654-673
4. Benavides E., Baum R., McClellan D., and Jack W.J. Molecular phylogenetics of the lizard genus Microlophus (Squamata: Tropiduridae): Aligning and retrieving indel signal from nuclear Introns. Syst. Biol. 56 (2007) 776-797
5. Bowler J.M. Aridity in the late Tertiary and Quaternary of Australia. In: Barker W.R., and Greenslade P.J.M. (Eds). Evolution of the Flora and Fauna of Arid Australia (1982), Peacock Publishing, Adelaide, South Australia 35-45
6. Brandley C.M., Schmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54 (2005) 373-390
7. Carstens B.C., and Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56 (2007) 400-411
8. Chapple D.G., Keogh J.S., and Hutchinson M.N. Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group. Mol. Ecol. 14 (2005) 1279-1292
9. Cogger H.G. Reptiles and Amphibians of Australia (2000), Reed New Holland, Sydney
10. Couper P.J., Worthington Wilmer J., Roberts L., Amey A.P., and Zug G.R. Skinks currently assigned to Carlia aerata (Scincidae: Lygosominae) of north-eastern Queensland: a preliminary study of cryptic diversity and two new species. Aust. J. Zool. 53 (2005) 35-49
11. Crisp M., Cook L., and Steane D. Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359 (2004) 1551-1571
12. de Queiroz A., Donoghue M.J., and Kim J. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26 (1995) 657-681
13. De Rijk P., Robbrecht E., de Hoog S., Caers A., Van de Peer Y., and De Wachter R. Database on the structure of large subunit ribosomal RNA. Nucleic Acids Res. 27 (1999) 174-178
14. Degnan J.H., and Salter L.A. Gene tree distributions under the coalescent process. Evolution 59 (2005) 24-37
15. Dolman G., and Moritz C. A multi-locus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 60 (2006) 573-582
16. Dolman G., and Phillips B. Single copy nuclear DNA markers characterized for comparative phylogeography in Australian Wet Tropics rainforest skinks. Mol. Ecol. Notes 4 (2004) 185-187
17. Edwards S.V., and Beerli P. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54 (2000) 1839-1854
18. Fitch A.J., Goodman A.E., and Donnellan S.C. A molecular phylogeny of the Australian monitor lizards (Squamata: Varanidae) inferred from mitochondrial DNA sequences. Aust. J. Zool. 54 (2006) 253-269
19. 10Be. Geology 33 (2005) 993-996
20. Gatesy J., O'Grady P., and Baker R.H. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15 (1999) 271-313
21. Greer A.E. The generic relationships of the scincid lizard genus Leiolopisma and its relatives. Aust. J. Zool. Suppl. Ser. 22 (1974) 1-67
22. Greer A.E. A phylogenetic subdivision of Australian skinks. Rec. Aust. Mus. 32 (1979) 339-371
23. Greer A.E. The Biology and Evolution of Australian Skinks (1989), Surrey Beatty, Sydney
24. Greer A.E. Two new species of Menetia from northeastern Queensland with comments on the generic diagnoses of Lygisaurus and Menetia. J. Herpetol. 25 (1991) 268-272
25. Harmon L.J., Schulte J.A., Larson A., and Losos J.B. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301 (2003) 961-964
26. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
27. Hugall A.F., Foster R., Hutchinson M., and Lee M.S.Y. Phylogeny of Australasian agamid lizards based on nuclear and mitochondrial genes: implications for morphological evolution and biogeography. Biol. J. Linn. Soc. 93 (2008) 343-358
28. Hugall A.F., and Lee M.S.Y. Molecular claims of Gondwanan age for Australian agamid lizards are untenable. Mol. Biol. Evol. 21 (2004) 2102-2110
29. Ingram G., and Covacevich J. Comments on the proposed suppression for nomenclature of three works by R.W. Wells and C.R. Wellington (1). Bull. Zool. Nomencl. 45 (1988) 52
30. Ingram G., and Covacevich J.A. Revision of the genus Lygisaurus de Vis (Scincidae: Reptilia) in Australia. Mem. Queensland Mus. 25 (1988) 335-354
31. Ingram G., and Covacevich J.A. Revision of the genus Carlia (Reptilia, Scincidae) in Australia and comments on Carlia bicarinata of New Guinea. Mem. Queensland Mus. 27 (1989) 443-490
32. Jackman T.R., Larson A., de Queiroz K., and Losos J.B. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst. Biol. 48 (1999) 254-285
33. Kershaw A.P., Moss P.T., and Wild R. Patterns and causes of vegetation change in the Australian Wet Tropics region over the last 10 million years. In: Bermingham E., Dick C.W., and Moritz C. (Eds). Tropical Rainforests: Past, Present and Future (2005), University of Chicago Press, Chicago, IL 374-400
34. Kikkawa J., Monteith G.M., and Ingram G.J. Cape York Peninsula: major region of faunal interchange. In: Keast A. (Ed). Ecological Biogeography of Australia (1981), D.W. Junk, The Hague 1695-1742
35. Kraus F. Taxonomic partitioning within Papuan members of the Carlia novaeguineae complex (Squamata: Scincidae). J. Herpetology 41 (2007) 410-423
36. Kubatko L.S., and Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56 (2007) 17-24
37. Kumazawa Y., and Nishida M. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: Statistical evidence for Archosaurian affinity of turtles. Mol. Biol. Evol. 16 (1999) 784-792
38. Lee M.S.Y., and Hugall A.F. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 52 (2003) 15-22
39. Liu L., and Pearl D.K. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56 (2007) 504-514
40. Loader S.P., Pisani D., Cotton J.A., Gower D.J., Day J.J., and Wilkinson M. Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biol. Lett. 3 (2007) 505-508
41. Magallon S., and Sanderson M.J. Absolute diversification rates in angiosperm clades. Evolution 55 (2001) 1762-1780
42. McGowran B., Holdgate G.R., Li Q., and Gallagher S.J. Cenozoic stratigraphic succession in southeastern Australia. Aust. J. Earth Sci. 51 (2004) 459-496
43. Moussalli A., Hugall A.F., and Moritz C. A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984). Mol. Phylogenet. Evol. 34 (2005) 190-202
44. Nee S. Inferring speciation rates from phylogenies. Evolution 55 (2001) 661-668
45. Nee S., Holmes E.C., May R.M., and Harvey P.H. Extinction Rates Can Be Estimated from Molecular Phylogenies. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344 (1994) 77-82
46. Nicholls J.A., Double M.C., Rowell D.M., and Magrath R.D. The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). J. Avian Biol. 31 (2000) 165-176
47. 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, Sunderland, Mass 205-247
48. Poe S., and Chubb A.L. Birds in a bush: Five genes indicate explosive evolution of avian orders. Evolution 58 (2004) 404-415
49. Posada D., and Crandall K.A. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50 (2001) 580-601
50. Pybus O.G., and Harvey P.H. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Biol. Sci. Ser. B 267 (2000) 2267-2272
51. Rabosky D.L. LASER: a maximum likelihood toolkit for inferring temporal shifts in diversification rates. Evol. Bioinform. Online 2 (2006) 257-260
52. Rabosky D.L. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60 (2006) 1152-1164
53. Rabosky D.L., Donnellan S.C., Talaba A.L., and Lovette I.J. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proc. R. Soc. Biol. Sci. Ser. B 274 (2007) 2915-2923
54. Rambaut, A., 2002. PhyloGen: phylogenetic tree simulator package version 1.1. Department of Zoology, University of Oxford, Oxford, UK.
55. Rawlings L.H., Rabosky D.L., Donnellan S.C., and Hutchinson M.N. Python phylogenetics: inference from morphology and mitochondrial DNA. Biol. J. Linn. Soc. 93 (2008) 603-619
56. Ricklefs R.E. History and diversity: explorations at the intersection of ecology and evolution. Am. Nat. 170 (2007) S56-S70
57. Sanderson M. r8s. Section of Ecology and Evolution (2004), University of California, Davis, CA
58. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
59. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
60. Smith S.A., Sadlier R.A., Bauer A.M., Austin C.C., and Jackman T. Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: evidence for a single origin of the endemic skinks of Tasmantis. Mol. Phylogenet. Evol. 43 (2007) 1151-1166
61. Storr G.M. The genus Carlia (Lacertilia, Scincidae) in Western Australia and the Northern Territory. Rec. Western Aust. Mus. 3 (1974) 151-165
62. Stuart-Fox D.M., Hugall A.F., and Moritz C. A molecular phylogeny of rainbow skinks (Scincidae: Carlia): taxonomic and biogeographic implications. Aust. J. Zool. 50 (2002) 39-51
63. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony and Other Methods (2000), Natural History Survey, Champaign, IL
64. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface. flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
65. Wells R.W., and Wellington C.R. A synopsis of the class Reptilia in Australia. Aust. J. Herpetol. 1 (1984) 73-129
66. Zug G.R. Systematics of the Carlia "fusca" lizards (Squamata: Scincidae) of New Guinea and nearby islands (2004), Bishop Museum Press, Honolulu