Protein sequences indicate that turtles branched off from the amniote tree after mammals

Journal of Molecular Evolution

Volumn 42, Issue 5, 1996, Pages 580-586

  Caspers, Gert Jan ^a   Reinders, Geert Jan ^a   Leunissen, Jack A M ^b   Wattel, Jan ^c   De Jong, Wilfried W ^a,c  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

crystallin; Molecular evolution; Testudines; Tetrapod phylogeny; Trachemys scripta elegans

Indexed keywords

CRYSTALLIN;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; DNA SEQUENCE; EVOLUTION; MAMMAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; TURTLE;

ANIMALS; BIRDS; CRYSTALLINS; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; MAMMALS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; TURTLES; VERTEBRATES;

EID: 0029998015     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02352288     Document Type: Article

References (58)

1. Adachi J, Hasegawa M (1992) Computer science monographs, no. 27: MOLPHY: programs for molecular phylogenetics. I. - PROTML: maximum likelihood inference of protein phylogeny. Institute of Statistical Mathematics, Tokyo
2. Auffray C, Rougeon F (1980) Purification of mouse immunoglobulin heavy chain mRNAs from total myeloma tumor RNA. Eur J Biochem 107:303-314
3. Ax P (1984) Das phylogenetische System. G Fischer Verlag, Stuttgart, pp 101-114
4. Benton MJ (1990) Phylogeny of the major tetrapod groups: morphological data and divergence dates. J Mol Evol 30:409-424
5. Bishop MJ, Friday AE (1985) Evolutionary trees from nucleic acid and protein sequences. Proc R Soc B 226:271-302
6. Bishop MJ, Friday AE (1988) Estimating the interrelationships of tetrapod groups on the basis of molecular sequence data. In: Benton MJ (ed) The phylogeny and classification of the tetrapods. Vol 1: amphibians, reptiles, birds. Clarendon Press, Oxford, pp 33-58
7. Carroll RL (1987) Vertebrate paleontology and evolution. WH Freeman, New York, pp 1-15, 192-216
8. Cascone O, Turyn D, Dellacha JM, Machado VLA, Marques M, Vita N, Cassan C, Ferrara P, Guillemot JC (1991) Isolation, purification, and primary structure of insulin from the turtle Chrysemys dorbigni. Gen Comp Endocrinol 84:355-359
9. Caspers G-J, Leunissen JAM, de Jong WW (1995) The expanding small heat-shock protein family, and structure predictions of the conserved "α-crystallin domain." J Mol Evol 40:238-248
10. Caspers G-J, Wattel J, de Jong WW (1994) αA-Crystallin sequences group tinamou with ratites. Mol Biol Evol 11:711-713
11. Chaline J (1990) Paleontology of vertebrates. Springer Verlag, Berlin
12. DeBry RW, Abele LG (1995) The relationship between parsimony and maximum-likelihood analyses: tree scores and confidence estimates for three real data sets. Mol Biol Evol 12:291-297
13. de Jong WW, Zweers A, Versteeg M, Dessauer HC, Goodman M (1995) α-Crystallin A sequences of Alligator mississippiensis and the lizard Tupinambis teguixin: molecular evolution and reptilian phylogeny. Mol Biol Evol 2:484-493
14. Devereux J, Haeberli P, Smithies O (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12: 387-395
15. 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
16. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
17. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
18. Felsenstein J (1993) PHYLIP: phylogeny inference package, version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle, WA
19. Gaffney ES (1980) Phylogenetic relationship of the major groups of amniotes. In: Panchen AL (ed) The terrestrial environment and the origin of the land vertebrates. Academic Press, London, pp 593-610
20. Gardiner BG (1982) Tetrapod classification. Zool J Linn Soc 74:207-232
21. Gardiner BG (1993) Haematothermia: warm-blooded amniotes. Cladistics 9:369-395
22. Gauthier J, Kluge AG, Rowe T (1988) Amniote phylogeny and the importance of fossils. Cladistics 4:105-209
23. Goodman M, Miyamoto MM, Czelusniak J (1987) Pattern and process in vertebrate phylogeny revealed by coevolution of molecules and morphologies. In: Patterson C (ed) Molecules and morphology in evolution: conflict or compromise? Cambridge University Press, Cambridge, pp 141-176
24. Graur D, Hide WA, Li W-H (1991) Is the guinea-pig a rodent? Nature 351:649-652
25. Groenen PJTA, Merck KB, de Jong WW, Bloemendal H (1994) Structure and modifications of the junior chaperone α-crystallin: from lens transparency to molecular pathology. Eur J Biochem 225:1-19
26. Haeckel E (1866) Generelle Morphologie der Organismen. G Reimer, Berlin, Tafel XII
27. Hasegawa M, Fujiwara M (1993) Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol Phylogen Evol 2:1-5
28. Hedges SB (1994) Molecular evidence for the origin of birds. Proc Natl Acad Sci USA 91:2621-2624
29. Hedges SB, Moberg KD, Maxson LR (1990) Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol Biol Evol 7:607-633
30. Hennig W (1983) Testudines. In: Hennig W (ed) Stammesgeschichte der Chordaten. P Parey, Hamburg, pp 132-139
31. Hillis DM, Allard MW, Miyamoto MM (1993) Analysis of DNA sequence data: phylogenetic inference. Methods Enzymol 224:456-487
32. Hillis DM, Huelsenbeck JP, Cunningham CW (1994) Application and accuracy of molecular phylogenies. Science 264:671-677
33. Huelsenbeck JP (1995) The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 12:843-849
34. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
35. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, p 75
36. King CR, Piatigorsky J (1983) Alternative RNA splicing of the murine αA crystallin gene: protein-coding information within an intron. Cell 32:707-712
37. Laurin M, Reisz RR (1995) A reevaluation of early amniote phytogeny. Zool J Linn Soc 113:165-223
38. Lee DC, Kim RY, Wistow GJ (1993) An avian αB-crystallin: non-lens expression and sequence similarities with both small (HSP27) and large (HSP70) heat shock proteins. J Mol Biol 232:1221-1226
39. Løvtrup S (1977) The phylogeny of the Vertebrata. J Wiley & Sons, London, pp 180-184
40. Løvtrup S (1985) On the classification of the taxon Tetrapoda. Syst Zool 34:463-470
41. Lu S-F, Pan F-M, Chiou S-H (1995) Sequence analysis of frog αB-crystallin cDNA: sequence homology and evolutionary comparison of αA, αB and heat shock proteins. Biochem Biophys Res Commun 216:881-891
42. Marshall CR (1992) Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences. Mol Biol Evol 9:370-373
43. Morrison R, Mason K, Frost-Mason S (1994) A cladistic analysis of the evolutionary relationships of the members of the tyrosinase gene family using sequence data. Pigment Cell Res 7:388-393
44. Owen R (1866) On the anatomy of vertebrates, vol I. Longmans, Green, London, p 7
45. Philippe H, Douzery E (1994) The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J Mamm Evol 2:133-152
46. Quax-Jeuken Y, Quax W, van Rens G, Meera Khan P, Bloemendal H (1985) Complete structure of the αB-crystallin gene: conservation of the exon-intron distribution in the two nonlinked α-crystallin genes. Proc Natl Acad Sci USA 82:5819-5823
47. Ridley M (1993) Evolution. Blackwell Scientific Publications, Boston
48. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
49. Seutin G, Lang BF, Mindell DP, Morais R (1994) Evolution of the WANCY region in amniote mitochondrial DNA. Mol Biol Evol 11:329-340
50. Stapel SO, Leunissen JAM, Versteeg M, Wattel J, de Jong WW (1984) Ratites as oldest offshoot of avian stem - evidence from α-crystallin A sequences. Nature 311:257-259
51. Steel MA, Lockhart PJ, Penny D (1993) Confidence in evolutionary trees from biological sequence data. Nature 364:440-442
52. Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular systematics. Sinauer, Sunderland, MA, pp 411-501
53. Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11:261-277
54. Van de Peer Y, Neefs J-M, De Rijk P, De Wachter R (1993) Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol 37:221-232
55. Van de Peer Y, De Wachter R (1994). TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569-570
56. Yamamoto H, Kudo T, Masuko N, Miura H, Sato S, Tanaka M, Tanaka S, Takeuchi S, Shibahara S, Takeuchi T (1992) Phylogeny of regulatory regions of vertebrate tyrosinase genes. Pigment Cell Res 5:284-294
57. Yasuda A, Kawauchi H, Papkoff H (1990) The complete amino acid sequence of prolactin from the sea turtle (Chelonia mydas). Gen Comp Endocrinol 80:363-371
58. Yasuda A, Yamaguchi K, Papkoff H, Yokoo Y, Kawauchi H (1989) The complete amino acid sequence of growth hormone from the sea turtle (Chelonia mydas). Gen Comp Endocrinol 73:242-251