The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae, Gekkota) revealed by molecular data

Molecular Phylogenetics and Evolution

Volumn 54, Issue 2, 2010, Pages 583-593

  Geurgas, Silvia Rodrigues ^a   Rodrigues, Miguel Trefaut ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

c mos; Coleodactylus; Cryptic species; Mitochondrial genes; RAG 1; Sphaerodactylinae

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; LIZARD; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENTIATION;

ANIMALS; BAYES THEOREM; CELL NUCLEUS; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETIC VARIATION; GENETICS, POPULATION; LIZARDS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

COLEODACTYLUS; COLEODACTYLUS AMAZONICUS; GEKKONIDAE; GEKKOTA; SPHAERODACTYLINAE;

EID: 73149087457     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.10.004     Document Type: Article

References (86)

1. Agapow P.M., Bininda-Edmonds O.R.P., Crandall K.A., Gittleman J.L., Mace G.M., Marshall J.C., and Purvis A. The impact of species concept on biodiversity. Q. Rev. Biol. 79 (2004) 161-179
2. Aleixo A. Historical diversification of a ''terra-firme" forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58 (2004) 1303-1317
3. Aleixo A., and Rossetti D.F. Avian gene trees, landscape evolution, and geology: towards a modern synthesis of Amazonian historical biogeography?. J. Ornithol. 148 (2007) 443-453
4. Arévalo E.S., Davis S.K., and Sites Jr. 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
5. Ávila-Pires T.C. Lizards of Brazilian Amazonia (Reptilia, Squamata). Zoologishe Verch., Leiden 299 (1995) 1-706
6. Avise J.C. Molecular Markers, Natural History and Evolution (1994), Chapman & Hall, New York
7. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard Univ. Press, Cambridge, MA
8. Avise J.C. Phylogeography: retrospect and prospect. J. Biogeogr. 36 (2009) 3-15
9. Avise J.C., and Ball R.M. Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surv. Evol. Biol. 7 (1990) 45-67
10. Avise J.C., Nelson W.S., and Sugita H. A speciational history of "living fossils": molecular evolutionary patterns in horseshoe crabs. Evolution 48 (1994) 1986-2001
11. Baker R.J., and Bradley R.D. Speciation in mammals and the genetic species concept. J. Mamm. 87 (2006) 643-662
12. Bandelt H.-J., Forster P., and Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16 (1999) 37-48
13. Baum D.A., and Shaw K.L. Genealogical perspectives on the species problem. In: Hoch P.C., and Stephenson A.G. (Eds). Experimental and Molecular Approaches to Plant Biosystematics (1995), St. Louis Mo., Botan. Gard. 289-303
14. Bickford D., Lohman D.J., Sodhi N.S., Ng P.K.L., Meier R., Winker K., Ingram K.K., and Das I. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22 (2007) 148-155
15. Bickham J.W., Wood C.C., and Patton J.C. Biogeographic implications of cytochrome b sequences and allozymes in sockeye (Oncorhynchus nerka). J. Hered. 86 (1995) 140-144
16. Brown J.M., and Lemmon A.R. The importance of data partitioning and the utility of bayes factors in bayesian phylogenetics. Syst. Biol. 56 (2007) 643-655
17. Brown R.P. Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages. J. Mol. Evol. 60 (2005) 45-56
18. Bruen T.C., Philippe H., and Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 172 (2006) 2665-2681
19. de Queiroz K. The general lineage concept of species, species criteria, and the process of speciation. In: Howard D.J., and Berlocher S.H. (Eds). Endless Forms: Species and Speciation (1998), Oxford Univ. Press, NewYork/Oxford 57-75
20. Dettman J.R., Jacobson D.J., and Taylor J.W. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57 (2003) 2703-2720
21. Edwards C.E., Lefkowitz D., Soltis D.E., and Soltis P.S. Phylogeny of Conradina and related southeastern scrub mints (Lamiaceae) based on GapC gene sequences. Int. J. Plant Sci. 169 (2008) 579-594
22. Elmer K.R., Dávila J.A., and Lougheed S.C. Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni. BMC Evol. Biol. 7 (2007) 247
23. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
24. Felsenstein J. Evolutionary trees from DNA-sequences - a maximum-likelihood approach. J. Mol. Evol. 17 (1981) 368-376
25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
26. Fouquet A., Vences M., Salducci M., Meyer A., Marty C., Blanc M., and Gilles A. Revealing cryptic diversity using molecular phylogenetics and phylogeography in frogs of the Scinax ruber and Rhinella margaritifera species groups. Mol. Phylogenet. Evol. 43 (2007) 567-582
27. 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
28. Fu J., and Zeng X. How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China. Mol. Ecol. 17 (2008) 1469-1488
29. 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
30. Gardner T.A., Ribeiro-Júnior M.A., Barlow J., Ávila-Pires T.C.S., Hoogmoed M.S., and Peres C.A. The value of primary, secondary, and plantation forests for a neotropical herpetofauna. Conserv. Biol. 21 (2007) 775-787
31. Geurgas S.R., Rodrigues M.T., and Moritz C. The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: a molecular phylogenetic perspective. Mol. Phylogenet. Evol. 49 (2008) 92-101
32. 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
33. Godinho R., Domingues V., Crespo E.G., and Ferrand N. Extensive intraspecific polymorphism detected by SSCP at the nuclear Cmos gene in the endemic Iberian lizard Lacerta schreiberi. Mol. Ecol. 15 (2006) 731-738
34. Good D.A., and Wake D.B. Geographic variation and speciation in the torrent salamanders of the genus Rhyacotriton (Caudata: Rhyacotritonidae). Univ. Calif. Pub. Zool. 126 (1992) 1-91
35. Gübitz T., Thorpe R.S., and Malhotra A. Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii: testing historical and adaptive hypotheses. Mol. Ecol. 9 (2000) 1213-1221
36. Hare M.P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16 (2001) 700-706
37. Harris D.J. Reassessment of comparative genetic distance in reptiles from the mitochondrial cytochrome b gene. Herpetol. J. 12 (2002) 85-87
38. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2 (2004) e312
39. Hendry A.P., Vamosi S.M., Latham S.J., Heilbuth J.C., and Day T. Questioning species realities. Cons. Genet. 1 (2000) 67
40. Hoorn C., Guerrero J., Sarmiento G.A., and Lorente M.A. Andean tectonics as a cause for changing drainage patterns in Miocene northern South America. Geology 23 (1995) 237-240
41. Huson, D.H., Bryant, D., 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267. Available from .
42. Irwin D.E. Phylogeographic breaks without geographic barries to gene flow. Evolution 56 (2002) 2383-2394
43. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
44. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., and Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196-6200
45. 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
46. Kuo C.-H., and Avise J.C. Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124 (2005) 179-186
47. Leaché D.A., Koo M.S., Spencer C.L., Papenfuss T.J., Fisher R.N., and McGuire J.A. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma). Proc. Natl. Acad. Sci. USA 106 (2009) 12418-12423
48. Losos J.B., and Glor R.E. Phylogenetic comparative methods and the geography of speciation. Trends Ecol. Evol. 18 (2003) 220-227
49. Lovejoy N.R., Bermingham E., and Martin A.P. Marine incursion into South America. Nature 396 (1998) 421-422
50. Lundberg J.G., Marshall L.G., Guerrero J., Horton B., Malabarba M.C.S.L., and Wesselingh F. The stage for Neotropical fish diversification: a history of tropical South American rivers. In: Malabarba L.R., Reis R.E., Vari R.P., Lucena Z.M.S., and Lucena C.A.S. (Eds). Phylogeny and Classification of Neotropical Fishes (1998), EDIPUCRS, Porto Alegre 13-48
51. 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
52. Moritz C., Patton J.L., Schneider C.J., and Smith T.B. Diversification of rainforest faunas: an integrated molecular approach. Ann. Rev. Ecol. Syst. 31 (2000) 533-563
53. Moritz C., and Cicero C. DNA barcoding: promise and pitfalls. PLoS Biol. 2 (2004) e279
54. Nei M., and Kumar S. Molecular Evolution and Phylogenetics (2000), Oxford Univ. Press, New York
55. Neigel J.E., and Avise J.C. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In: Nevo E., and Karlin S. (Eds). Evolutionary Processes and Theory (1986), Academic, New York 515-534
56. Newton M.A., and Raftery A.E. Approximate bayesian inference by the weighted likelihood bootstrap (with discussion). J. R. Stat. Soc. B Met. 56 (1994) 3-48
57. Nylander, J.A.A., 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
58. Palumbi S.R., Martin A., Romano S., McMillan W.O., Stice L., and Grabowski G. The simple fool's guide to PCR (1991), University of Hawaii Press, Honolulu, HI
59. Pfenninger M., and Schwenk K. Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol. Biol. 7 (2007) 121
60. Posada D., Crandall K.A., and Holmes E.C. Recombination in evolutionary genomics. Annu. Rev. Genet. 36 (2002) 75-97
61. Raxworthy C.J., Ingram C.M., Rabibisoa N., and Pearson R.G. Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Syst. Biol. 56 (2007) 907-923
62. Rissler L.J., and Apodaca J.J. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst. Biol. 56 (2007) 924-942
63. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
64. Rull V. Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence. Mol. Ecol. 17 (2008) 2722-2729
65. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning (1989), Cold Spring Harbour Laboratory Press, A Laboratory Manual. Cold Spring Harbour
66. Santos J.C., Coloma L.A., Summers K., Caldwell J.P., Ree R., and Cannatella D.C. Amazonian amphibian diversity is primarily derived from Late Miocene Andean lineages. PLoS Biol. 7 3 (2009) e1000056
67. Schierup M.H., and Hein J. Consequences of recombination on traditional phylogenetic analysis. Genetics 156 (2000) 879-891
68. Schluter D. Ecology and the origin of species. Trends Ecol. Evol. 16 (2001) 372-380
69. Sites Jr. J.W., and Marshall J.C. Operational criteria for delimiting species. Annu. Rev. Ecol. Evol. Syst. 35 (2004) 199-227
70. Sota T., and Vogler A.P. Reconstructing species phylogeny of the carabid beetles Ohomopterus using multiple nuclear DNA sequences: heterogenous information content and the performance of simultaneous analyses. Mol. Phyl. Evol. 26 (2003) 139-154
71. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4.0b10 (2003), Sinauer Associates, Sunderland, Massachusetts
72. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
73. 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
74. 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
75. Vanzolini P.E. O gênero Coleodactylus (Sauria, Gekkonidae). Pap. Avulsos Dep. Zool. (São Paulo) 13 (1957) 1-17
76. Vanzolini P.E. Lagartos brasileiros da família Gekkonidae (Sauria). Pap. Avulsos Dep. Zool. (São Paulo) 17 (1968) 1-84
77. Vanzolini P.E. Geography of the South American Gekkonidae (Sauria). Arq. Zool. (São Paulo) 17 (1968) 85-112
78. 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
79. 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
80. Vogler A.P., and Monaghan M.T. Recent advances in DNA taxonomy. J. Zool. Syst. Evol. Res. 45 (2007) 1-10
81. 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
82. Wiens J.J. Systematics and herpetology in the age of genomics. BioScience 58 (2008) 297-307
83. Wiens J.J., and Penkrot T.A. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51 (2002) 69-91
84. Willett C.E., Cherry J.J., and Steiner L.A. Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45 (1997) 394-404
85. Zamudio K.R., and Greene H.W. Phylogeography of the bushmaster (Lachesis muta:Viperidae): implications for neotropical biogeography, systematics, and conservation. Biol. J. Linn. Soc. 62 (1997) 421-442
86. Zink R.M., and Barrowclough G.F. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 17 (2008) 2107-2121