When selection deceives phylogeographic interpretation: The case of the Mediterranean house gecko, Hemidactylus turcicus (Linnaeus, 1758)

Molecular Phylogenetics and Evolution

Volumn 58, Issue 2, 2011, Pages 365-373

  Rato, C ^a,b,c   Carranza, S ^c   Harris, D J ^a,b  

^a CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^b UNIVERSITY OF PORTO   (Portugal)

^c INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Hemidactylus turcicus; MtDNA; NDNA; Phylogeography; Selective sweep

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETIC SELECTION; GENETICS; HAPLOTYPE; LIZARD; MOLECULAR EVOLUTION; PHYLOGEOGRAPHY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SOUTHERN EUROPE;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HAPLOTYPES; LIZARDS; MEDITERRANEAN REGION; MODELS, GENETIC; PHYLOGEOGRAPHY; SELECTION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

GEKKONIDAE; HEMIDACTYLUS TURCICUS; TARENTOLA MAURITANICA;

EID: 79951580401     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.12.004     Document Type: Article

References (61)

1. Akaike H. A new look at the statistical model identification. IEEE Trans. Automat. Control 1974, 19:716-723.
2. Arnold E.N., Vasconcelos R., Harris D.J., Mateo J.A., Carranza S. Systematics, biogeography and evolution of the endemic Hemidactylus geckos (Reptilia, Squamata, Gekkonidae) of the Cape Verde Islands: based on morphology and mitochondrial and nuclear DNA sequences. Zool. Scripta 2008, 37:619-636.
3. Bandelt H.-J., Forster P., Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
4. Bansal R., Karanth K.P. Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos. Mol. Phylogenet. Evol. 2010, 57:459-465.
5. Bauer A.M., Jackman T.R., Greenbaum E., Giri V.B., de Silva A. South Asia supports a major endemic radiation of Hemidactylus geckos. Mol. Phylogenet. Evol. 2010, 57:343-352.
6. Bons, J., Geniez, P., 1996. Amphibians and Reptiles of Morocco. Asociación Herpetológica Española, Barcelona, Spain, pp. 319.
7. Braverman J.M., Hudson R.R., Kaplan N.L., Langley C.H., Stephan W. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 1995, 140:783-796.
8. Carranza S., Arnold E.N. Systematics, biogeography, and evolution of Hemidactylus geckos (Reptilia: Gekkonidae) elucidated using mitochondrial DNA sequences. Mol. Phylogenet. Evol. 2006, 38:531-545.
9. Chiari Y., Vences M., Vieites D.R., Rabemananjara F., Bora P., Ravoahangimalala O.R., Meyer A. New evidence for parallel evolution of colour patterns in Malagasy poison frogs (Mantella). Mol. Ecol. 2004, 13:3763-3774.
10. Corander J., Sirén J., Arjas E. Bayesian spatial modelling of genetic population structure. Comput. Stat. 2008, 23:111-129.
11. Fay J.C., Wu C.-I. Hitchhiking under positive Darwinian selection. Genetics 2000, 155:1405-1413.
12. Flot J.-F. SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Mol. Ecol. Resources 2010, 10:162-166.
13. Fu Y.-X., Li W.-H. Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709.
14. Gamble T., Bauer A.M., Greenbaum E., Jackman T.R. Out of the blue: a novel, trans-Atlantic clade of geckos (Gekkota, Squamata). Zool. Scripta 2008, 37:355-366.
15. Gamble T., Bauer A.M., Greenbaum E., Jackman T.R. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. J. Biogeogr. 2008, 35:88-104.
16. Geniez, P., 2002. Hemidactylus turcicus. In: Pleguezuelos, J.M., Márquez, R., Lizana, M. (Eds.), Atlas y Libro Rojo de los anfibios y reptiles de España. Dirección General de Conservación de la Naturaleza, Asociación Herpetológica Española, Madrid, pp. 584.
17. Godinho R., Crespo E.G., Ferrand N. The limits of mtDNA phylogeography: complex patterns of population history in a highly structured Iberian lizard are only revealed by the use of nuclear markers. Mol. Ecol. 2008, 17:4670-4683.
18. Hall T.A. Bioedit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acid Symp. Ser. 1999, 41:95-98.
19. Hamilton M.B. Population Genetics 2009, Blackwell Publishing, Chichester, West Sussex, UK, pp. 407.
20. Harris D.J., Arnold E.N., Thomas R.H. Relationships of the lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. Roy. Soc. London B 1998, 265:1939-1948.
21. Harris D.J., Batista V., Carretero M.A., Ferrand N. Genetic variation in Tarentola mauritanica (Reptilia: Gekkonidae) across the Strait of Gibraltar derived from mitochondrial and nuclear DNA sequences. Amphibia-Reptilia 2004, 25:451-459.
22. Harris, D.J., Batista, V., Lymberakis, P., Carretero, M.A., 2004b. Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequence. Mol. Phylogenet. Evol. 30, 855-859.
23. Harris D.J., Carretero M.A., Corti C., Lo Cascio P. Genetic affinities of Tarentola mauritanica (Reptilia: Gekkonidae) from Lampedusa and Conigli islet (SW Italy). North-West J. Zool. 2009, 5:197-205.
24. Hoegg S., Vences M., Brinkmann H., Meyer A. Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes. Mol. Biol. Evol. 2004, 21:1188-1200.
25. Hudson R.R. A new statistic for detecting genetic differentiation. Genetics 2000, 155:2011-2014.
26. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
27. Jesus J., Brehm A., Harris D.J. Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequences. Mol. Phylogenet. Evol. 2005, 34:480-485.
28. Kasapidis K., Magoulas A., Mylonas M., Zouros E. The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago. Mol. Phylogenet. Evol. 2005, 35:612-623.
29. Katoh T. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008, 9:286-298.
30. Kim Y. Allele frequency distribution under recurrent selective sweeps. Genetics 2006, 172:1967-1978.
31. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 1989, 86:6196-6200.
32. Librado P., Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
33. Locey K.J., Stone P.A. Factors affecting range expansion in the introduced Mediterranean gecko, Hemidactylus turcicus. J. Herpetol. 2006, 40:526-530.
34. Luo Y., Gao W., Gao Y., Tang S., Huang Q., Tan X., Chen J., Huang T. Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation. Mitochondrion 2008, 8:352-357.
35. Mateus O., Jacinto J.J. Hemidactylus turcicus (Linnaeus, 1758). Atlas de Anfíbios e Répteis de Portugal 2008, 134-135. Instituto da Conservação da Natureza e da Biodiversidade, Lisbon. A. Loureiro, N. Ferrand de Almeida, M.A. Carretero, O.S. Paulo (Eds.).
36. Maynard-Smith J., Haigh J. The hitch-hiking effect of a favourable gene. Genet. Res. 1974, 23:23-35.
37. Perera A., Harris D.J. Genetic diversity in the gecko Tarentola mauritanica within the Iberian Peninsula. Amphibia-Reptilia 2008, 29:583-588.
38. Perera A., Harris D.J. Genetic variability within the Oudri's fan-footed gecko Ptyodactylus oudrii in North Africa assessed using mitochondrial and nuclear DNA sequences. Mol. Phylogenet. Evol. 2010, 54:634-639.
39. Pianka E.R., Vitt L.J. Lizards, Windows to the Evolution of Diversity 2003, University of California Press, Berkeley, pp. 348.
40. Pinho C., Harris D.J., Ferrand N. Comparing patterns of nuclear and mitochondrial divergence in a cryptic species complex: the case of Iberian and North African wall lizards (Podarcis, Lacertidae). Biol. J. Linn. Soc. 2007, 91:121-133.
41. Pinho C., Harris D.J., Ferrand N. Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species. BMC Evol. Biol. 2008, 8:1-20.
42. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
43. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer.
44. Ramos-Onsins S.E., Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 2002, 19:2092-2100.
45. Rato C., Carranza S., Perera A., Carretero M.A., Harris D.J. Conflicting patterns of nucleotide diversity between mtDNA and nDNA in the Moorish gecko, Tarentola mauritanica. Mol. Phylogenet. Evol. 2010, 56:962-971.
46. Rato C., Zuffi M.A.L., Corti C., Fornasiero S., Gentilli A., Razzetti E., Scali S., Carretero M.A., Harris D.J. Phylogeography of the European Whip Snake, Hierophis viridiflavus (Colubridae), using mtDNA and nuclear DNA sequences. Amphibia-Reptilia 2009, 30:283-289.
47. Renoult J.P., Geniez P., Bacquet P., Benoit L., Crochet P.-A. Morphology and nuclear markers reveal extensive mitochondrial introgressions in the Iberian Wall Lizard species complex. Mol. Ecol. 2009, 18:4298-4315.
48. Rocha S., Carretero M.A., Harris D.J. Diversity and phylogenetic relationships of Hemidactylus geckos from the Comoro islands. Mol. Phylogenet. Evol. 2005, 35:292-299.
49. Rocha S., Carretero M.A., Harris D.J. On the diversity, colonization patterns and status of Hemidactylus spp. (Reptilia: Gekkonidae) from the Western Indian Ocean islands. Herpetol. J. 2010, 20:83-89.
50. Rödder D., Lötters S. Niche shift versus niche conservatism? Climatic characteristics of the native and invasive ranges of the Mediterranean house gecko (Hemidactylus turcicus). Glob. Ecol. Biogeogr. 2009, 18:674-678.
51. Sindaco R., Jeremcenko V. The Reptiles of the Western Paleartic 2008, Societas Herpetologica Italica, Latina, Italy, pp. 579.
52. Smith H.M. Handbook of Lizards, Lizards of the United States and Canada 1946, Comstock Publishing, Ithaca and New York, pp. 557.
53. Stephens M., Donnelly P. A comparison of bayesian methods for haplotype reconstruction. Am. J. Hum. Genet. 2003, 73:1162-1169.
54. Stephens M., Smith N.J., Donnelly P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 2001, 68:978-989.
55. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts, USA.
56. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
57. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
58. Velo-Antón G., Martínez-Solano I., García-París M. β-Fibrinogen intron 7 variation in Discoglossus (Anura: Discoglossidae): implications for the taxonomic assessment of morphologically cryptic species. Amphibia-Reptilia 2008, 29:523-533.
59. Vences M., Wanke S., Vieites D.R., Branch W.R., Glaw F., Meyer A. Natural colonization or introduction? Phylogeographical relationships and morphological differentiation of house geckos (Hemidactylus) from Madagascar. Biol. J. Linn. Soc. 2004, 83:115-130.
60. White G., Tumlison R. Hemidactylus turcicus (Mediterranean gecko). Herpet. Rev. 1999, 30:110.
61. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas, Austin. http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html.