The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: A molecular phylogenetic perspective

Molecular Phylogenetics and Evolution

Volumn 49, Issue 1, 2008, Pages 92-101

  Geurgas, Silvia Rodrigues ^a   Rodrigues, Miguel Trefaut ^a   Moritz, Craig ^b  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

16S; c mos; Coleodactylus; Phylogeny; Pleistocene refuges; RAG 1; Sphaerodactylinae

Indexed keywords

MITOCHONDRIAL DNA; RNA 16S;

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

ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENES, MOS; GENES, RAG-1; GENES, RRNA; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; LIZARDS; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

BRACHYSTOMA; COLEODACTYLUS; COLEODACTYLUS AMAZONICUS; GEKKOTA; MYA; SPHAERODACTYLINAE;

EID: 52449091851     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.05.043     Document Type: Article

References (78)

1. Avila L.J., Morando M., and Sites Jr. J.W. Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini). Biol. J. Linn. Soc. 89 (2006) 241-275
2. Ávila-Pires T.C. Lizards of Brazilian Amazonia (Reptilia Squamata) (1995), Zoologishe Verch., Leiden 299, 1-706
3. Barbour T. Sphaerodactylus. Mem. Mus. Comp. Zool. (Harvard) 47 (1921) 215-282
4. Barker F.K., and Lutzoni F.M. The utility of the incongruence length difference test. Syst. Biol. 51 (2002) 625-637
5. Böhme W. Erstfund eines fossilen Kugelfingergeckos (Sauria: Gekkonidae: Sphaerodactylinae) aus Dominikanischen Bernstein (Oligozän von Hispaniola, Antillen). Salamandra 20 (1984) 212-220
6. Burk A., Douzery E.J.P., and Springer M.S. The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach. J. Mammalian Evol. 9 (2002) 225-252
7. Colli G., Bastos R., and Araujo A. The character and dynamics of the Cerrado herpetofauna. In: Oliveira P., and Marquis R. (Eds). The Cerrados of Brazil: Ecology and Natural History of a Neotropical Savanna (2002), Columbia University, New York 223-241
8. da Silva M.N.F., and Patton J.L. Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha). Mol. Phylogenet. Evol. 2 (1993) 243-255
9. de Jong W.W., van Dijk M.A.M., Poux C., Kappe G., van Rheede T., and Madsena O. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol. Phylogenet. Evol. 28 (2003) 328-340
10. de Pinna M.C.C. Concepts and tests of homology in the cladistic paradigm. Cladistics 7 (1991) 367-394
11. Darlu P., and Lecointre G. When does the incongruence length difference test fail?. Mol. Biol. Evol. 19 (2002) 432-437
12. Delsuc F., Vizcaíno S.F., and Douzery E.J.P. Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans. BMC Evol. Biol. 4 (2004) 11
13. Dolphin K., Belshaw R., Orme C.D., and Quicke D.L.J. Noise and incongruence: interpreting results of the incongruence length difference test. Mol. Phyl. Evol. 17 (2000) 401-406
14. Dowton M., and Austin A.D. Increased congruence does not necessarily indicate increased phylogenetic accuracy - The behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51 (2002) 19-31
15. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
18. Fessler J.L., and Westneat M.W. Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family. Mol. Phylogenet. Evol. 45 (2007) 50-68
19. Freire E.M.X. Espécie nova de Coleodactylus Parker, 1926, das dunas de Natal, Rio Grande do Norte, Brasil, com notas sobre as relações de dicromatismo sexual no gênero (Squamata, Gekkonidae). Bol. Mus. Nac., N. S., Rio de Janeiro 399 (1999) 1-14
20. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34 (2003) 397-423
21. Funk W.C., Caldwell J.P., Peden C.E., Padial J.M., de la Riva I., and Cannatella D.C. Tests of biogeographic hypotheses for diversification in the Amazonian forest frog, Physalaemus petersi. Mol. Phylogenet. Evol. 44 (2007) 825-837
22. Flynn J.J., and Wyss A.R. Recent advances in South American mammalian paleontology. Trends Ecol. Evol. 13 (1998) 449-454
23. Gamble T., Bauer A.M., Greenbaum E., and Jackman T.R. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. J. Biogeogr. 35 (2008) 88-104
24. Gamble T., Simons A.M., Colli G.R., and Vitt L.J. Tertiary climate change and the diversification of the Amazonian gecko genus Gonatodes (Sphaerodactylidae, Squamata). Mol. Phylogenet. Evol. 46 (2008) 269-277
25. Giugliano L.G., Collevatti R.G., and Colli G.R. Molecular dating and phylogenetic relationships among Teiidae (Squamata) inferred by molecular and morphological data. Mol. Phylogenet. Evol. 45 (2007) 168-179
26. Glor R.E., Vitt L.J., and Larson A. A molecular phylogenetic analysis of diversification in Amazonian Anolis lizards. Mol. Ecol. 10 (2001) 2661-2668
27. Godinho R., Crespo E.G., Ferrand N., and Harris D.J. Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences. Amph. Rept. 26 (2005) 271-285
28. Grimaldi D. On the age of Dominican amber. In: Anderson K.B., and Crelling J.C. (Eds). Amber, Resinite, and Fossil Resins (1995), American Chemical Society, Washington DC, USA 203-217
29. Gruber K.F., Voss R.S., and Jansa S.A. Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Syst. Biol. 56 (2007) 83-96
30. Harris D.J. Codon bias variation in C-mos between squamate families might distort phylogenetic inferences. Mol. Phylogenet. Evol. 27 (2003) 540-544
31. Hipp A.L., Hall J.C., and Sytsma K.J. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst. Biol. 53 (2004) 81-89
32. Kluge A.G. Higher taxonomic categories of gekkonid lizards and their evolution. Bull. Amer. Mus. Natur. Hist. 135 (1967) 1-59
33. Kluge A.G. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173 (1987) 1-54
34. Kluge A.G. Cladistic relationships of sphaerodactyl lizards. Am. Mus. Novitates 3139 (1995) 1-23
35. Kronauer D.J.C., Bergmann P.J., Mercera J.M., and Russell A.P. A phylogeographically distinct and deep divergence in the widespread Neotropical turnip-tailed gecko, Thecadactylus rapicauda. Mol. Phylogenet. Evol. 34 (2005) 431-437
36. Maddison W. Reconstructing character evolution on polytomous cladograms. Cladistics 5 (1989) 365-377
37. Morando M., Avila L.J., and Sites Jr. J.W. Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America. Syst. Biol. 52 (2003) 159-185
38. Moritz C., Patton J.L., Schneider C.J., and Smith T.B. Diversification of rainforest faunas: an integrated molecular approach. Annu. Rev. Ecol. Syst. 31 (2000) 533-563
39. Nahum L.A., Pereira S.L., Fernandes F.M.C., Matioli S.R., and Wajntal A. Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences. Genet. Mol. Biol. 26 (2003) 411-418
40. Noble G.K. T. he bony structure and phyletic relations of Sphaerodactylus and allied lacertilian genera, with the description of a new genus. Am. Mus. Novitates 4 (1921) 1-16
41. Nylander, J.A.A., 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
42. Parker H.W. The Neotropical lizards of the genera Lepidoblepharis, Pseudogonatodes, Lathrogecko, and Sphaerodactylus, with the description of a new genus. Ann. Mag. Nat. Hist. 17 (1926) 291-301
43. Parker H.W. The frogs, lizards, and snakes of British Guiana. Proc. Zool. Soc. London 3 (1935) 505-530
44. Parrish J.T. Palaeoclimatic history of the opening South Atlantic. In: George W., and Lavocat R. (Eds). The Africa-South America Connection (1993), Clarendon Press, Oxford 28-43
45. Pellegrino K.C.M., Rodrigues M.T., Waite A.N., Morando M., Yonenaga-Yassuda Y., and Sites Jr. J.W. Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic Forest. Biol. J. Linn. Soc. 85 (2005) 13-26
46. Planet P.J. Tree disagreement: measuring and testing incongruence in phylogenies. J. Biomed. Inform. 39 (2006) 86-102
47. Poux C., Chevret P., Huchon D., de Jong W.W., and Douzery E.J.P. Arrival and Diversification of Caviomorph Rodents and Platyrrhine Primates in South America. Syst. Biol. 55 (2006) 228-244
48. Ramos A.R. Aspectos do nicho alimentar de Coleodactylus amazonicus (Sauria, Gekkonidae). Acta Amazon. 11 (1981) 511-526
49. Rokas A., and Holland W.H.P. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15 (2000) 454-459
50. Romero E.J. South American paleofloras. In: Goldblatt P. (Ed). Biological Relationships between Africa and South America (1993), Yale University Press, New Haven and London 62-85
51. Ron S.R. Biogeographic area relationships of lowland neotropical rainforest based on raw distributions of vertebrate groups. Biol. J. Linn. Soc. 71 (2000) 379-402
52. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
53. Sambrook, J., Fritsch, E.F., Maniatis, T., 1989. Molecular Cloning. A Laboratory Manual. Cold Spring Harbour: Cold Spring Harbour Laboratory Press.
54. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
55. Sanderson M.J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19 (2003) 301-302
56. Sanderson M.J., and Doyle J.A. Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Am. J. Bot. 88 (2001) 1499-1516
57. Santos R.M.L., Bertolotto C.E.V., Pellegrino K.C.M., Rodrigues M.T., and Yonenaga-Yassuda Y. Chromosomal studies on sphaerodactyl lizards of genera Gonatodes and Coleodactylus (Squamata, Gekkonidae) using differential staining and fragile sites analyses. Cyt. Gen. Res. 103 (2003) 128-134
58. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
59. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
60. *and other methods). Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts.
61. Symula R., Schulte R., and Summers K. Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates. Mol. Phylogenet. Evol. 26 (2003) 452-475
62. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
63. Townsend T., Larson A., Louis E., and Macey J. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 53 (2004) 735-757
64. Underwood G. On the classification and evolution of geckos. Proc. Zool. Soc. London 124 (1954) 469-492
65. van Rheede T., Bastiaans T., Boone D.N., Hedges S.B., de Jong W.W., and Madsen O. The Platypus is in its place: nuclear genes and indels confirm the sister group relation of Monotremes and Therians. Mol. Biol. Evol. 23 (2006) 587-597
66. Vanzolini P.E. O gênero Coleodactylus (Sauria, Gekkonidae). Pap. Avulsos Dep. Zool. (São Paulo) 13 (1957) 1-17
67. Vanzolini P.E. Lagartos brasileiros da família Gekkonidae (Sauria). Pap. Avulsos Dep. Zool. (São Paulo) 17 (1968) 1-84
68. Vanzolini P.E. Geography of the South American Gekkonidae (Sauria). Arq. Zool. (São Paulo) 17 (1968) 85-112
69. Vanzolini, P.E., 1970. Zoologia Sistemática, geografia e a origem das espécies. Inst. Geog. S. Paulo Teses e Monog. 3, pp. 1-56.
70. Vanzolini P.E. Coleodactylus septentrionalis, sp. n., with notes on distribution of the genus (Sauria, Gekkonidae). Pap. Avulsos Zool. (São Paulo) 34 (1980) 1-9
71. Vanzolini P.E., and Williams E.E. South American anoles: the geographic differentiation and evolution of the Anolis chrysolepis species group (Sauria, Iguanidae). Arq. Zool. (São Paulo) 19 (1970) 1-298
72. Venkatesh B., Erdmann M.V., and Brenner S. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc. Natl. Acad. Sci. USA 98 (2001) 11382-11387
73. Vidal N., and Hedges S.B. Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes. Comptes rendus. Biologies 325 (2002) 977-985
74. Vitt L.J., Sartorius S.S., Ávila-Pires T.C.S., Zani P.A., and Espósito M.C. Small in a big world: ecology of leaf-litter geckos in New World tropical forests. Herpetol. Monogr. 19 (2005) 137-152
75. Weisrock D.W., Harmon L.J., and Larson A. Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Syst. Biol. 54 (2005) 758-777
76. Wettstein O. Coleodactylus zernyi nov. spec., ein neuer Gecko aus Brasilien. Zool. Anz. 76 (1928) 110-112
77. Whiting A.S., Bauer A.M., and Sites Jr. J.W. Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae). Mol. Phylogenet. Evol. 29 (2003) 582-598
78. Zaldivar-Riverón A., Belokobylskij S.A., León-Regagnon V., Martínez J.J., Briceño R., and Quicke D.L.J. A single origin of gall association in a group of parasitic wasps with disparate morphologies. Mol. Phylogenet. Evol. 44 (2007) 981-992