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Volumn 38, Issue 3, 2006, Pages 719-730

Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae)

Author keywords

Alignment; Direct optimization; Mabuya; Molecular phylogeny; Oceanic dispersal

Indexed keywords

PRIMER DNA;

EID: 33244484354     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.11.011     Document Type: Article
Times cited : (67)

References (45)
  • 1
    • 0011886353 scopus 로고    scopus 로고
    • The Fernando de Noronha archipelago
    • Schobbenhaus, C., Campos, D.A., Queiroz, E.T., Winge, M., Berbert-Born, M. (Eds.)
    • Almeida, F.F.M., 2000. The Fernando de Noronha archipelago. In: Schobbenhaus, C., Campos, D.A., Queiroz, E.T., Winge, M., Berbert-Born, M. (Eds.), Sítios Geológicos e Paleontológicos do Brasil. < http://www.unb.br/ig/sigep/witio066/sitio066.htm〉.
    • (2000) Sítios Geológicos e Paleontológicos Do Brasil
    • Almeida, F.F.M.1
  • 2
    • 0002349384 scopus 로고
    • Fossil reptiles from Aldabra Atoll, Indian Ocean
    • E.N. Arnold Fossil reptiles from Aldabra Atoll, Indian Ocean Bull. Brit. Mus. (Nat. Hist.) 29 1976 83 116
    • (1976) Bull. Brit. Mus. (Nat. Hist.) , vol.29 , pp. 83-116
    • Arnold, E.N.1
  • 3
    • 0000710277 scopus 로고    scopus 로고
    • Using fossils and phylogenies to understand evolution of reptile communities on islands
    • E.N. Arnold Using fossils and phylogenies to understand evolution of reptile communities on islands Bonner Zoologische Beiträge 46 2000 309 323
    • (2000) Bonner Zoologische Beiträge , vol.46 , pp. 309-323
    • Arnold, E.N.1
  • 4
    • 0002142792 scopus 로고
    • Lizards of Brazilian Amazonia (Reptilia: Squamata)
    • T.C.S. Ávila-Pires Lizards of Brazilian Amazonia (Reptilia: Squamata) Zool. Verhand. Leiden 299 1995 1 706
    • (1995) Zool. Verhand. Leiden , vol.299 , pp. 1-706
    • Ávila-Pires, T.C.S.1
  • 5
    • 8444232854 scopus 로고    scopus 로고
    • On the identity of Lacerta punctata Linnaeus, 1758, the type species of the genus Euprepis Wagler, 1830, and the generic assignment of Afro-Malagasy skinks
    • A.M. Bauer On the identity of Lacerta punctata Linnaeus, 1758, the type species of the genus Euprepis Wagler, 1830, and the generic assignment of Afro-Malagasy skinks Afr. J. Herpetol. 52 2003 1 7
    • (2003) Afr. J. Herpetol. , vol.52 , pp. 1-7
    • Bauer, A.M.1
  • 6
    • 0036829156 scopus 로고    scopus 로고
    • Specializations of the chorioallantoic placent in the Brazilian scincid lizard, Mabuya heathi: A new placental morphotype
    • D.G. Blackburn, and L.J. Vitt Specializations of the chorioallantoic placent in the Brazilian scincid lizard, Mabuya heathi: a new placental morphotype J. Morph. 254 2002 121 131
    • (2002) J. Morph. , vol.254 , pp. 121-131
    • Blackburn, D.G.1    Vitt, L.J.2
  • 7
    • 85010526802 scopus 로고    scopus 로고
    • Investigating the origin of transoceanic distributions: MtDNA shows Mabuya lizards (Reptilia, Scincidae) crossed the Atlantic twice
    • S. Carranza, and E.N. Arnold Investigating the origin of transoceanic distributions: mtDNA shows Mabuya lizards (Reptilia, Scincidae) crossed the Atlantic twice Syst. Biodivers. 1 2003 275 282
    • (2003) Syst. Biodivers. , vol.1 , pp. 275-282
    • Carranza, S.1    Arnold, E.N.2
  • 8
    • 30344466673 scopus 로고    scopus 로고
    • Systematics, biogeography, and evolution of Hemidactylus geckos (Reptilia: Gekkonidae) elucidated using mitochondrial DNA sequences
    • in press. doi:10.1016/j.mpev.2005.07.012
    • Carranza, S., Arnold, E.N., in press. Systematics, biogeography, and evolution of Hemidactylus geckos (Reptilia: Gekkonidae) elucidated using mitochondrial DNA sequences. Mol. Phylogenet. Evol. in press, doi: doi:10.1016/j.mpev.2005.07.012.
    • Mol. Phylogenet. Evol.
    • Carranza, S.1    Arnold, E.N.2
  • 9
    • 0034616188 scopus 로고    scopus 로고
    • Long-distance colonization and radiation in gekkonid lizards, Tarentola (Reptilia: Gekkonidae), revealed by mitochondrial DNA sequences
    • S. Carranza, E.N. Arnold, J.A. Mateo, and L.-F. López-Jurado Long-distance colonization and radiation in gekkonid lizards, Tarentola (Reptilia: Gekkonidae), revealed by mitochondrial DNA sequences Proc. R. Soc. B 267 2000 637 649
    • (2000) Proc. R. Soc. B , vol.267 , pp. 637-649
    • Carranza, S.1    Arnold, E.N.2    Mateo, J.A.3    López-Jurado, L.-F.4
  • 10
    • 12344290679 scopus 로고    scopus 로고
    • The resurrection of oceanic dispersal in historical biogeography
    • A. de Queiroz The resurrection of oceanic dispersal in historical biogeography Trends Ecol. Evol. 20 2005 68 73
    • (2005) Trends Ecol. Evol. , vol.20 , pp. 68-73
    • De Queiroz, A.1
  • 11
    • 2542439906 scopus 로고    scopus 로고
    • Single copy nuclear DNA markers characterized for comparative phylogeography in Australian Wet Tropics rainforest skinks
    • G. Dolman, and B. Phillips Single copy nuclear DNA markers characterized for comparative phylogeography in Australian Wet Tropics rainforest skinks Mol. Ecol. Notes 4 2004 185 187
    • (2004) Mol. Ecol. Notes , vol.4 , pp. 185-187
    • Dolman, G.1    Phillips, B.2
  • 13
    • 33244469607 scopus 로고    scopus 로고
    • Generating implied alignments under direct optimization using POY
    • G. Giribet Generating implied alignments under direct optimization using POY Cladistics 21 2005 396 402
    • (2005) Cladistics , vol.21 , pp. 396-402
    • Giribet, G.1
  • 14
    • 0001046581 scopus 로고
    • A subfamilial classification of scincid lizards
    • A.E. Greer A subfamilial classification of scincid lizards Bull. Mus. Comp. Zool. 139 1970 151 183
    • (1970) Bull. Mus. Comp. Zool. , vol.139 , pp. 151-183
    • Greer, A.E.1
  • 15
    • 0000094136 scopus 로고    scopus 로고
    • The systematic significance of the number of presacral vertebrae in the scincid lizard genus Mabuya
    • A.E. Greer, C. Arnold, and E.N. Arnold The systematic significance of the number of presacral vertebrae in the scincid lizard genus Mabuya Amphibia-Reptilia 21 2000 121 126
    • (2000) Amphibia-Reptilia , vol.21 , pp. 121-126
    • Greer, A.E.1    Arnold, C.2    Arnold, E.N.3
  • 17
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • J.P. Huelsenbeck, and F.R. Ronquist MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.R.2
  • 18
    • 0002410257 scopus 로고    scopus 로고
    • Parametric bootstrapping in molecular phylogenetics: Applications and performance
    • J.D. Ferraris S.R. Palumbi Wiley-Liss New York, NY
    • J.P. Huelsenbeck, D.M. Hillis, and R. Jones Parametric bootstrapping in molecular phylogenetics: applications and performance J.D. Ferraris S.R. Palumbi Molecular Zoology: Advances, Strategies, and Protocols 1996 Wiley-Liss New York, NY 19 42
    • (1996) Molecular Zoology: Advances, Strategies, and Protocols , pp. 19-42
    • Huelsenbeck, J.P.1    Hillis, D.M.2    Jones, R.3
  • 21
    • 0032904538 scopus 로고    scopus 로고
    • Development of comparative anchor tagged sequences (CATS) for canine genome mapping
    • L.A. Lyons, J.S. Kehler, and S.J. O'Brien Development of comparative anchor tagged sequences (CATS) for canine genome mapping J. Hered. 90 1999 15 26
    • (1999) J. Hered. , vol.90 , pp. 15-26
    • Lyons, L.A.1    Kehler, J.S.2    O'Brien, S.J.3
  • 23
    • 0036814634 scopus 로고    scopus 로고
    • Phylogenetic affinities of Mabuya atlantica Schmidt, 1945, endemic to the Atlantic Ocean archipelago of Fernando de Noronha (Brazil): Necessity of partitioning the genus Mabuya Fitzinger, 1826 (Scincidae: Lygosominae)
    • P. Mausfeld, A. Schmitz, W. Bohme, B. Misof, D. Vrcibradic, and C.F.D. Rocha Phylogenetic affinities of Mabuya atlantica Schmidt, 1945, endemic to the Atlantic Ocean archipelago of Fernando de Noronha (Brazil): necessity of partitioning the genus Mabuya Fitzinger, 1826 (Scincidae: Lygosominae) Zool. Anz. 241 2002 281 293
    • (2002) Zool. Anz. , vol.241 , pp. 281-293
    • Mausfeld, P.1    Schmitz, A.2    Bohme, W.3    Misof, B.4    Vrcibradic, D.5    Rocha, C.F.D.6
  • 25
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa
    • D.A. Morrison, and J.T. Ellis Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa Mol. Biol. Evol. 14 1997 428 441
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 27
    • 0142167519 scopus 로고    scopus 로고
    • The problem with the "paleoptera problem: Sense and sensitivity
    • T.H. Ogden, and M.F. Whiting The problem with the "Paleoptera problem: sense and sensitivity Cladistics 19 2003 379 448
    • (2003) Cladistics , vol.19 , pp. 379-448
    • Ogden, T.H.1    Whiting, M.F.2
  • 28
    • 27544515936 scopus 로고    scopus 로고
    • Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: A reply to Kjer
    • T.H. Ogden, M.F. Whiting, and W.C. Wheeler Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: a reply to Kjer Cladistics 21 2005 295 302
    • (2005) Cladistics , vol.21 , pp. 295-302
    • Ogden, T.H.1    Whiting, M.F.2    Wheeler, W.C.3
  • 29
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 30
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: And application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • A. Rambaut, and N.C. Grassly Seq-Gen: and application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Comput. Appl. Biosci. 13 1997 235 238
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 32
    • 0009554557 scopus 로고    scopus 로고
    • A new species of Mabuya (Squamata: Scincidae) from the semiarid Caatingas of northeastern Brazil
    • M.T. Rodrigues A new species of Mabuya (Squamata: Scincidae) from the semiarid Caatingas of northeastern Brazil Papeis Avulsos de Zoologia 41 2000 313 328 Museu de Zoologia da Universidade de Sao Paulo
    • (2000) Papeis Avulsos de Zoologia , vol.41 , pp. 313-328
    • Rodrigues, M.T.1
  • 33
    • 0000248681 scopus 로고
    • The evolution of viviparity in reptiles: An ecological analysis
    • C. Gans F. Billett John Wiley and Sons New York
    • R. Shine The evolution of viviparity in reptiles: an ecological analysis C. Gans F. Billett Biology of the Reptilia 1985 John Wiley and Sons New York 605 694
    • (1985) Biology of the Reptilia , pp. 605-694
    • Shine, R.1
  • 35
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D.M. Hillis C. Moritz B.K. Mable second ed. Sinauer Associates Sunderland, MA
    • D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis Phylogenetic inference D.M. Hillis C. Moritz B.K. Mable Molecular Systematics second ed. 1996 Sinauer Associates Sunderland, MA 407 514
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 36
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • J.D. Thompson, D.G. Higgins, and T.J. Gibson 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
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 37
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 24 1997 4876 4882
    • (1997) Nucleic Acids Res. , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 38
    • 25744447830 scopus 로고
    • Nota sobre a "mabuya" da Ilha Fernando de Noronha (Squamata: Scincidae)
    • H. Travassos Nota sobre a "Mabuya" da Ilha Fernando de Noronha (Squamata: Scincidae) Rev. Brasil. Biol. 8 1948 201 208
    • (1948) Rev. Brasil. Biol. , vol.8 , pp. 201-208
    • Travassos, H.1
  • 40
    • 0001857390 scopus 로고    scopus 로고
    • Optimization alignment: The end of multiple sequence alignment in phylogenetics?
    • W.C. Wheeler Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12 1996 1 10
    • (1996) Cladistics , vol.12 , pp. 1-10
    • Wheeler, W.C.1
  • 41
    • 0043211946 scopus 로고    scopus 로고
    • Implied alignment: A synapomorphy-based multiple-sequence alignment method and its use in cladogram search
    • W.C. Wheeler Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search Cladistics 19 2003 261 268
    • (2003) Cladistics , vol.19 , pp. 261-268
    • Wheeler, W.C.1
  • 44
    • 0344287479 scopus 로고    scopus 로고
    • Phylogenetic relationships and limb loss in southern African scincine lizards (Squamata: Scincidae)
    • A.S. Whiting, A.M. Bauer, and J.W.J. Sites Phylogenetic relationships and limb loss in southern African scincine lizards (Squamata: Scincidae) Mol. Phylogenet. Evol. 29 2003 582 598
    • (2003) Mol. Phylogenet. Evol. , vol.29 , pp. 582-598
    • Whiting, A.S.1    Bauer, A.M.2    Sites, J.W.J.3
  • 45
    • 33745078845 scopus 로고    scopus 로고
    • Molecular phylogenetics of Malagasy skinks (Squamata: Scincidae)
    • A.S. Whiting, J.W.J. Sites, and A.M. Bauer Molecular phylogenetics of Malagasy skinks (Squamata: Scincidae) Afr. J. Herpetol. 53 2004 135 146
    • (2004) Afr. J. Herpetol. , vol.53 , pp. 135-146
    • Whiting, A.S.1    Sites, J.W.J.2    Bauer, A.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.