Molecular phylogenetics and evolution of the cytochrome b gene in the cyprinid genus Lythrurus (Actinopterygii: Cypriniformes)

Copeia

Volumn , Issue 1, 1998, Pages 14-22

  Schmidt, Timothy R ^a   Bielawski, Joseph P ^b   Gold, John R ^b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0032477781     PISSN: 00458511     EISSN: None     Source Type: Journal    
DOI: 10.2307/1447697     Document Type: Article

References (47)

1. ADELL, J. C., AND J. DOPAZO. 1994. Monte Carlo simulations in phylogenies: an application to test the constancy of evolutionary rates. J. Mol. Evol. 38: 305-309.
2. ALLARD, M. W., D. L. ELLSWORTH, AND R. L. HONEYCUTT. 1991. The production of single-stranded DNA suitable for sequencing using the polymerase chain reaction. BioTechniques 10:24-26.
3. AMEMIYA, G. T., AND J. R. GOLD. 1988. Chromosomal NORs as taxonomic characters in North American cyprinid fishes. Genetica 76:81-90.
4. ARAYA, A., R. AMTHAUER, G. LEON, AND M. KRAUSKOPF. 1984. Cloning, physical mapping and genome organization of mitochondrial DNA from Cyprinus carpio oocytes. Mol. Gen. Genet. 196:43-52.
5. BREMER, K. 1988. The limits of amino acid sequence data in Angiosperm phylogenetic reconstruction. Evolution 42:795-803.
6. BROWN, J. R., T. L. GILBERT, D. J. KOWBEL, P. J. O'HARA, N. E. BUROKER, A. T. BECKENBACK, AND M. J. SMITH. 1989. Nucleotide sequence of the apocytochrome b gene in white sturgeon mitochondrial DNA. Nucleic Acids Res. 11:4389.
7. CAVENDER, T. M., AND M. M. COBURN. 1992. Phylogenetic relationships of North American Cyprinidae, p. 293-327. In: Systematics, historical ecology, and North American freshwater fishes. R. L. Mayden (ed.). Stanford Univ. Press, Stanford, CA.
8. CHANG, Y.-S., F.-L. HUANG, AND T.-B. Lo. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38:138-155.
9. COBURN, M. M., AND T. M. CAVENDER. 1992. Interrelationships of North American cyprinid fishes, p. 328-373. In: Systematics, historical ecology, and North American freshwater fishes. R. L. Mayden (ed.). Stanford Univ. Press, Stanford, CA.
10. COOK, M. L., AND B. C. BROWN. 1974. Variation in the genus Desmognathus (Amphibia: Plethodontidae) in the western limits of its range. J. Herpetol. 8:93-105.
11. DESJARDINS, P., AND R. MORAIS. 1990. Sequence and gene organization of the chicken mitochondrial ge- nome: a novel gene order in higher vertebrates. J. Mol. Biol. 212:599-634.
12. DIMMICK, W. W., K. L. FIORINO, AND B. M. BURR. 1996. Reevaluation of the Lythrurus ardens (cypriniformes: cyprinidae) complex with recognition of three evolutionary species. Copeia 1996:813-823.
13. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
14. _. 1989. PHYLIP: phylogeny inference package. Vers. 3.2. Cladistics 5:164-166.
15. _, AND G. CHURCHILL. 1996. A hidden markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
16. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
17. HOBBS, H. H., JR., AND H. W. ROBISON. 1982. A new crayfish from the Ouachita River basin in Arkansas (Decapoda: Cambaridae). Proc. Biol. Soc. Wash. 95:804-811.
18. IRWIN, D. M., T. D. KOCHER, AND A. C. WILSON. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128-144.
19. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Ibid. 29:170-179.
20. KOCHER, T. D., W. K. THOMAS, A. MEYER, S. V. EDWARDS, S. PÄÄBO, F. X. VILLABLANCA, AND A. C. WIL- SON. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Nat. Acad. Sci. USA 86:6196-6200.
21. KORNEGAY, J. R., T. D. KOCHER, L. A. WILLIAMS, AND A. C. WILSON. 1994. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. J. Mol. Evol. 37:367-379.
22. KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal rates. Mol. Biol. Evol. 11:459-468.
23. LOCKHART, J. P., M. A. STEELE, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Ibid. 11:605-612.
24. MARTIN, A. P., AND S. R. PALUMBI. 1994. Protein evolution in different cellular environments: cyto- chrome b in sharks and mammals. Ibid. 10:873-891.
25. MATTHEWS, W. J., AND H. W. ROBISON. 1982. Addition of Etheostoma collettei (Perchidae) to the fish fauna of Oklahoma and the Red River drainage in Arkansas. Southwest. Nat. 27:215-216.
26. MAYDEN, R. L. 1985. Biogeography of Ouachita highland fishes. Ibid. 30:195-211.
27. _. 1988. Vicariance biogeography, parsimony, and evolution in North American freshwater fishes. Syst. Zool. 37:329-355.
28. _. 1989. Phylogenetic studies of North American minnows, with emphasis on the genus Cyprinella (Teleostei: Cypriniformes). Misc. Publ. Mus. Nat. Hist., Univ. Kan. 80:1-189.
29. MEYER, A. 1993. Evolution of mitochondrial DNA in fishes, p. 1-38. In: Biochemistry and molecular biology of fishes. Vol. 2. P. W. Hochachka and P. Mommsen (eds.). Elsevier Press, Amsterdam, The Netherlands.
30. _, AND A. C. WILSON. 1990. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J. Mol. Evol. 31:359-364.
31. _, T. D. KOCHER, P. BASASIBWAKI, AND A. C. WILSON. 1990. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347:550-553.
32. NIXON, K. C., AND J. M. CARPENTER. 1993. On outgroups. Cladistics 9:413-426.
33. RAMBAUT, A., AND N. C. CRASSLY. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238
34. RICE, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
35. ROBISON, H. W. 1985. Notropis snelsoni, a new cyprinid from the Ouachita Mountains of Arkansas and Oklahoma. Copeia 1985:126-134.
36. SAMBROOK, J., E. F. FRITSCH, AND T. MANIATIS. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. SANGER, F., S. NICKLEN, AND A. R. COULSON. 1977. DNA sequencing with chain terminating inhibitors. Proc. Nat. Acad. Sci. USA 74:5463-5467.
38. SMITH, M. F., AND J. L. PATTON. 1991. Variation in mitochondrial cytochrome b sequences in natural populations of South American akodontine rodents (Muridae: Sigmodontinae). Mol. Biol. Evol. 8:85-103.
39. SNELSON, F. F., JR. 1972. Systematics of the subgenus Lythrurus, genus Notropis (Pisces: Cyprinidae). Bull. Fla. State Mus. Biol. Sci. 17:1-92.
40. _. 1973. Systematics and distribution of the ribbon shiner, Notropis fumeus (Cyprinidae), from the central United States. Am. Midl. Nat. 89:166-191.
41. _. 1980. Systematic review of the cyprinid fish, Notropis lirus. Copeia 1980:323-334.
42. TAJIMA, F. 1993. Simple methods of testing the molecular evolutionary clock hypothesis. Genetics 135: 559-607.
43. TZENG, C.-S., C.-F, HUI, S.-C. SHEN, AND P.-C. HUANG. 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res. 20:4853-4858.
44. WHEELER, W. C. 1990. Nucleic acid sequence and phylogeny and random outgroups. Cladistics 6: 363-367.
45. WHITEMORE, D. H, T. H. THAI, AND C. M. CRAFT. 1994. The largemouth bass cytochrome b gene. J. Fish Biol. 44:637-645.
46. WILEY, E. O., AND R. L. MAYDEN. 1985. Species and speciation in phylogenetic Systematics, with examples from the North American fish fauna. Ann. MO. Bot. Gard. 72:596-635.
47. _, AND D. SIEGEL-CAUSEY. 1994. A phylogenetic analysis of the Lythrurus roseipinnis species group, with comments on the relationship of other Lythrurus. Occ. Pap. Mus. Nat. Hist., Univ. Kan. 171:1-20.