Molecular phylogenetics and evolution of turtles

Molecular Phylogenetics and Evolution

Volumn 37, Issue 1, 2005, Pages 178-191

  Krenz, James G ^a,c   Naylor, Gavin J P ^a,d   Shaffer, H Bradley ^b   Janzen, Fredric J ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c OREGON STATE UNIVERSITY   (United States)

^d FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Evolution; Molecular phylogeny; RAG 1; Turtles

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; TURTLE;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TURTLES; VARIATION (GENETICS);

CARETTOCHELYIDAE; CARETTOCHELYS; CHELYDRIDAE; CRYPTODIRA; PLATYSTERNIDAE; SUS SCROFA; TESTUDINES; TRIONYCHIDAE;

EID: 25144515857     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.04.027     Document Type: Article

References (54)

1. R.M. Bernstein, S.F. Schluter, H. Bernstein, and J.J. Marchalonis Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases Proc. Natl. Acad. Sci. USA 93 1996 9454 9459
2. J.W. Bickham, and J.L. Carr Taxonomy and phylogeny of the higher categories of cryptodiran turtles based on a cladistic analysis of chromosomal data Copeia 1983 1983 918 932
3. L.M. Carlson, M.A. Oettinger, D.G. Schatz, E.L. Masteller, E.A. Hurley, W.T. McCormack, D. Baltimore, and C. Thompson Selective expression of RAG-2 in chicken B cells undergoing immunoglobulin gene conversion Cell 64 1991 201 208
4. B.-Y. Chen, S.-H. Mao, and Y.-H. Ling Evolutionary relationships of turtles suggested by immunological cross-reactivity of albumins Comp. Biochem. Physiol. B 66 1980 421 425
5. J. Claude, P.C.H. Pritchard, H. Tong, E. Paradis, and J.-C. Auffray Ecological correlates and evolutionary divergence in the skull of turtles: a geometric morphometric assessment Syst. Biol. 53 2004 933 948
6. R. Dalton Mock turtles Nature 423 2003 219 220
7. Danilov, I., 1998. Phylogenetic relationships of platysternid turtles. In: Third Asian Herpetological Meeting Abstracts, p. 14.
8. Dumeril, A.M.C., 1806. Zoologie Analytique, ou Methode Naturelle de Classification des Animaux, Allais Libraire, Paris.
9. Dumeril, A.M.C., Bibron, G., 1835. Erpetologie General ou Histoire Naturelle Complete des Reptiles, Paris.
10. T.N. Engstrom, H.B. Shaffer, and W.P. McCord Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae) Syst. Biol. 53 2004 693 710
11. C.H. Ernst, and R.W. Barbour Turtles of the World 1989 Smithsonian Institution Press Washington, DC
12. J. Felsenstein Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 1985 783 791
13. W. Frair Taxonomic relationships among chelydrid and kinosternid turtles elucidated by serological tests Copeia 1972 1972 97 108
14. W. Frair Serological survey of softshells with other turtles J. Herpetol. 17 1983 75 79
15. M.K. Fujita, T.N. Engstrom, D.E. Starkey, and H.B. Shaffer Turtle phylogeny: insights from a novel nuclear intron Mol. Phylogenet. Evol. 31 2004 1031 1040
16. E.S. Gaffney A phylogeny and classification of the higher categories of turtles Bull. Am. Mus. Nat. Hist. 155 1975 387 436
17. E.S. Gaffney Historical analyses of theories of chelonian relationship Syst. Zool. 33 1984 283 301
18. E.S. Gaffney The comparative osteology of the Triassic turtle Proganochelys Bull. Am. Mus. Nat. Hist. 194 1990 1 263
19. E.S. Gaffney, and P.A. Meylan A phylogeny of turtles M.J. Benton The phylogeny and classification of Tetrapods 1988 Clarendon Press Oxford 157 219
20. E.S. Gaffney, P.A. Meylan, and A.R. Wyss A computer assisted analysis of the relationships of the higher categories of turtles Cladistics 7 1991 313 335
21. J.W. Gibbons, D.E. Scott, T.J. Ryan, K.A. Buhlmann, T.D. Tuberville, B.S. Metts, J.L. Greene, T. Mills, Y. Leiden, S. Poppy, and C.T. Winne The global decline of reptiles, déjà vu amphibians BioScience 50 2000 653 666
22. J.G. Groth, and G.F. Barrowclough Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene Mol. Phylogenet. Evol. 12 1999 115 123
23. M.W. Haiduk, and J.W. Bickham Chromosomal homologies and evolution of testudinoid turtles with emphasis on the systematic placement of Platysternon Copeia 1982 1982 60 66
24. R. Hirayama Oldest known sea turtle Nature 392 1998 705 708
25. J.P. Huelsenbeck Performance of phylogenetic methods in simulation Syst. Biol. 44 1995 17 48
26. J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 2001 754 755
27. F.J. Janzen, and J.G. Krenz Phylogenetics: which was first, GSD or TSD? N. Valenzuela V.A. Lance Temperature-dependent sex determination in vertebrates 2004 Smithsonian Books Washington, DC 121 130
28. M.W. Klemens Turtle conservation 2000 Smithsonian Institution Press Washington, DC
29. F. Kraus, and M.M. Miyamoto Rapid cladogenesis among the pecoran ruminants: evidence from mitochondrial DNA sequences Syst. Zool. 40 1991 117 130
30. A. Larson The comparison of morphological and molecular data in phylogenetic systematics B. Schierwater B. Streit G.P. Wagner R. DeSalle Molecular ecology and evolution: Approaches and applications 1994 Birkhäuser Basel 371 390
31. W.-H. Li Molecular evolution 1997 Sinauer Sunderland, MA
32. O. Madsen, M. Scally, C.J. Douady, D.J. Kao, R.W. DeBry, R. Adkins, H.M. Amrine, M.J. Stanhope, W.W. de Jong, and M.S. Springer Parallel adaptive radiations in two major clades of placental mammals Nature 409 2001 610 614
33. Maisey, J.G., Naylor, G.J.P., Ward, D.J., 2004. Mesozoic elasmobranches, neoselachian phylogeny and the rise of modern neoselachian diversity. In: Arratia, G., Tintori, A. (Eds.), Mesozoic Fishes 3. Systematics Paleoenvironments and Biodiversity. Verlag. F. Pfeil., Munchen, Germany, pp. 17-56.
34. P.A. Meylan Morphology and relationships of the early Cretaceous side-necked turtle, Araripemys barretoi (Testudines: Pelomedusoides: Araripemydidae) from the Santana Formation of Brazil J. Vert. Paleontol. 16 1996 20 33
35. P.A. Meylan, R.J.T. Moody, C.A. Walker, and S.D. Chapman Sandownia harrisi, a highly derived trionychoid turtle (Testudinata: Cryptodira) from the Early Cretaceous of the Isle Of Wright, England J. Vert. Paleontol. 20 2000 522 532
36. W.J. Murphy, E. Eizirik, W.E. Johnson, Y.P. Zhang, O.A. Ryder, and S.J. O'Brien Molecular phylogenetics and the origin of placental mammals Nature 409 2001 614 618
37. G.J.P. Naylor, and W.M. Brown Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences Syst. Biol. 47 1998 61 76
38. T.J. Near, P.A. Meylan, and H.B. Shaffer Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles Am. Nat. 165 2005 137 146
39. H.A. Orr The probability of parallel evolution Evolution 59 2005 216 220
40. D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
41. Rambaut, A., 1995. Sequence Alignment Program v1.d1, University of Oxford.
42. F. Rodriguez, J.L. Oliver, A. Marin, and J.R. Medina The general stochastic model of nucleotide substitution J. Theor. Biol. 142 1990 485 501
43. M.J. Sanderson, and H.B. Shaffer Troubleshooting molecular phylogenetic analyses Annu. Rev. Ecol. Syst. 33 2002 49 72
44. D.G. Schatz, M.A. Oettinger, and D. Baltimore The V(D)J recombination activating gene, RAG-1 Cell 59 1989 1035 1048
45. H.B. Shaffer, P. Meylan, and M.L. McKnight Tests of turtle phylogeny: molecular, morphological, and paleontological approaches Syst. Biol. 46 1997 235 268
46. H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
47. Swofford, D.L., 2001. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4, Sinauer, Sunderland, MA.
48. K. Tamura, and M. Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Mol. Biol. Evol. 10 1993 512 526
49. A.R. Templeton Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes Evolution 37 1983 221 244
50. T. Townsend, A. Larson, E. Louis, and J. Macey Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree Syst. Biol. 53 2004 735 757
51. D.W. Weisrock, and F.J. Janzen Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces Mol. Phylogenet. Evol. 14 2000 152 164
52. K.N. Whetstone Additional record of the fossil snapping turtle Macroclemys schmidti from the Marshland Formation (Miocene) of Nebraska with notes on interspecific skull variation within the genus Macroclemys Copeia 1978 1978 159 162
53. E.E. Williams Variation and selection of the cervical central articulations of living turtles Bull. Am. Mus. Nat. Hist. 94 1950 505 562
54. R. Zangerl The vertebrate fauna of the Selma Formation of Alabama. Part 3. The turtles of the family Protostegidae. Part 4. The turtles of the family Toxochelyidae Fieldiana Geol. Mem. 3-4 1953 61 277