Proopiomelanocortin (POMC) and testing the phylogenetic position of turtles (Testudines);Proopiomelanocortin (POMC) und die Untersuchung der Phylogenetischen Position der Schildkröten (Testudines)

Journal of Zoological Systematics and Evolutionary Research

Volumn 49, Issue 2, 2011, Pages 148-159

  Becker, Rosemary E ^a   Valverde, Roldán A ^a   Crother, Brian I ^a  

^a SOUTHEASTERN LOUISIANA UNIVERSITY   (United States)

Author keywords

Bayesian; Direct optimization; Likelihood; Parsimony; Partitions; POMC; Testudines

Indexed keywords

BAYESIAN ANALYSIS; CLADISTICS; FUNCTIONAL MORPHOLOGY; GENETIC ANALYSIS; HORMONE; MOLECULAR ANALYSIS; OPTIMIZATION; PARSIMONY ANALYSIS; PEPTIDE; REPTILE; TAXONOMY;

AMNIOTA; ARCHOSAURIA; CROCODYLIDAE (ALL CROCODILES); LEPIDOSAURIA; MAMMALIA; SAURIA; TESTUDINES;

EID: 79953653437     PISSN: 09475745     EISSN: 14390469     Source Type: Journal    
DOI: 10.1111/j.1439-0469.2010.00589.x     Document Type: Article

References (63)

1. deBraga M, Rieppel O (1997) Reptile phylogeny and the interrelationships of turtles. Zool J Linn Soc 120:281-354.
2. Brandley MC, Schmitz A, Reeder TW (2005) Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol 54:373-390.
3. Bremer K (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
4. Burnham KP, Anderson DR (1998) Model selection and Multimodel Inference: A Practical Information-theoretic Approach. Springer-Verlag, New York.
5. Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa M (2000) Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene 259:139-148.
6. Castoe TA, Parkinson CL (2006) Bayesian mixed models and the phylogeny of pitvipers (Viperidae:Serpentes). Mol Phylogenet Evol 39:91-110.
7. Castoe TA, Doan TM, Parkinson CL (2004) Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Syst Biol 53:448-469.
8. Cunningham CW, Zuh H, Hillis DM (1998) Best-fit maximum likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52:978-987.
9. Danielson PB, Dores RM (1999) Molecular evolution of the opioid/orphanin gene family. Gen Comp Endocrinol 113:169-186.
10. Dores RM (1990) The proopiomelanocortin family. Prog Clin Biol Res 342:22-27.
11. Dores RM, Rubin DA, Quinn TW (1996) Is it possible to construct phylogenetic trees using polypeptide hormone sequences? Gen Comp Endocrinol 103:1-12.
12. Dores RM, Sollars C, Danielson P, Lee J, Alrubanian J, Joss JMP (1999) Cloning of a POMC cDNA from the Pituitary of the Australian Lungfish, Neoceratodus forsteri: Analyzing Trends in the Organization of the Prohormone Precursor, Proopiomelanocortin. Gen Comp Endocrinol 116:433-444.
13. Eernisse DJ, Kluge AG (1993) Taxonomic congruence versus total evidence, and Amniote phylogeny inferred from fossils, molecules, and morphology. Mol Biol Evol 10:1170-1195.
14. Gaffney ES (1980) Phylogenetic relationships of the major groups of amniotes. In: Panchen AL (ed.), The Terrestrial Environment and The Origin of Land Vertebrates. Academic Press, London, pp 593-610.
15. Gauthier J, Kluge AG, Rowe T (1988a) The early evolution of the amniota. In: Benton MJ (ed.), The Phylogeny and Classification of the Tetrapods. Clarendon Press, Oxford, pp 103-153.
16. Gauthier J, Kluge AG, Rowe T (1988b) Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
17. Giribet G (2001) Exploring the behavior of POY, a program for direct optimization of molecular data. Cladistics 17:S60-S70.
18. Giribet G, Wheeler WC (1999) On gaps. Mol Phylogenet Evol 13:132-143.
19. Grant T, Kluge AG (2004) Transformation series as an ideographic character concept. Cladistics 20:23-31.
20. Gregory WK (1946) Pareiasaurs versus placodonts as near ancestors to turtles. Bull Am Mus Nat Hist 86:275-326.
21. Hedges SB (1994) Molecular evidence for the origin of birds. Proc Natl Acad Sci USA 91:2621-2624.
22. Hedges SB, Poling LL (1999) A molecular phylogeny of reptiles. Science 283:998-1001.
23. Hill RV (2005) Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling. Syst Biol 54:530-547.
24. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42:182-192.
25. Hillis DM, Pollack DD, McGuire JA, Zwickl DJ (2003) Is sparse taxon sampling a problem for phylogenetic inference? Syst Biol 52:124-126.
26. Huelsenbeck JP, Rannala B (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol 53:904-913.
27. Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, Miyata T, Katoh K (2005) Sister group relationship of turtles to the Bird-Crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol 22:810-813.
28. Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773-795.
29. Kluge AG (2007) Completing the neo-Darwinian synthesis with an event criterion. Cladistics 23:613-633.
30. Kumazawa Y, Nishida M (1999) Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles. Mol Biol Evol 16:784-792.
31. Lanyon SM (1985) Detecting internal inconsistencies in distance data. Syst Zool 34:397-403.
32. Laurin M, Resiz RR (1995) A reevaluation of early amniote phylogeny. Zool J Linn Soc 113:165-223.
33. Lee MSY (1993) The origin of the turtle body plan: bridging a famous morphological gap. Science 261:1716-1720.
34. Lee MSY (1997) Pareiasaur phylogeny and the origin of turtles. Zool J Linn Soc 120:197-280.
35. Lemmon AR, Moriarty EC (2004) The importance of proper model assumption in Bayesian phylogenetics. Syst Biol 53:265-277.
36. Maddison WP, Maddison DR (2003) MacClade4 v. 4.06. Sinauer Associates, Sunderland.
37. Mannen H, Li SS-L (1999) Molecular evidence for a clade of turtles. Mol Phylogenet Evol 13:144-148.
38. Meyer A, Zardoya R (2003) Recent advances in the (molecular) phylogeny of vertebrates. Ann Rev Ecol Evol Syst 34:311-338.
39. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53:47-67.
40. Ogden TH, Rosenberg MS (2007) How should gaps be treated in parsimony? A comparison of approaches using simulation. Mol Phylogenet Evol 42:817-826.
41. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808.
42. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
43. Posada D, Crandall KA (2001) Selecting the best-fit model of nucleotide substitution. Syst Biol 50:580-601.
44. Reisz RR (1997) The origin and early evolutionary history of amniotes. Trends Ecol Evol 12:218-222.
45. Reisz RR, Laurin M (1991) Owenetta and the origin of turtles. Nature 349:324-326.
46. Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP (2003) Molecular systematic of primary reptilian lineages and the tuatara mitochondrial genome. Mol Phylogenet Evol 29:289-297.
47. Rieppel O, deBraga M (1996) Turtles as diapsid reptiles. Nature 384:453-455.
48. Rieppel O, Reisz RR (1999) The origin and early evolution of turtles. Annu Rev Ecol Syst 30:1-22.
49. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
50. Shoureshi P, Baron A, Szynskie L, Dores RM (2007) Analyzing the evolution of beta-endorphin post-translational processing events: studies on reptiles. Gen Comp Endocrinol 153:148-154.
51. Siddall ME (1995) Another monophyly index: revisiting the jackknife. Cladistics 11:33-56.
52. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369-381.
53. Simmons MP, Ochoterena H, Carr TG (2001) Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst Biol 50:454-462.
54. Sorenson MD, Franzosa E (2007) TreeRot, Version 3. Boston University, Boston.
55. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland.
56. Varón A, Vinh LS, Bomash I, Wheeler WC (2008) POY 4.0 Beta 2602. American Museum of Natural History, New York. .
57. Weisrock DW, Shaffer HB, Storz BL, Storz SR, Voss SR (2006) Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders. Mol Ecol 15:2489-2503.
58. Werneburg I, Sánchez-Villagra MR (2009) Timing of organogenesis support basal position of turtles in the amniote tree of life. BMC Evol Biol 9:82.
59. Wheeler WC (1996) Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12:1-9.
60. Wiens JJ, Servedio MR (1998) Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods. Syst Biol 47:228-253.
61. Yang Z (1996) Maximum likelihood models for combined analyses of multiple sequence data. J Mol Evol 42:587-596.
62. Zardoya R, Meyer A (1998) Complete mitochondrial genome suggests diapsid affinities of turtles. Proc Natl Acad Sci USA 95:14226-14231.
63. Zwickl DJ (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.