Investigating phylogenetic relationships of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes

Molecular Phylogenetics and Evolution

Volumn 32, Issue 1, 2004, Pages 344-357

  Near, Thomas J ^a,b   Bolnick, Daniel I ^a   Wainwright, Peter C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Black bass; Lepomis; Micropterus; mtDNA; Nuclear gene phylogeny; Sunfish

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BASS; CELL NUCLEUS; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PERCIFORMES; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BASS; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; PERCIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ACANTHARCHUS POMOTIS; ACTINOPTERYGII; AMBLOPLITES; ARCHOPLITES; CENTRARCHIDAE; CENTRARCHUS; ENNEACANTHUS; LEPOMIS; MICROPTERUS; PERCIFORMES; PISCES; POMOXIS;

EID: 3042783269     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.12.010     Document Type: Article

References (52)

1. Avise J.C, Smith M.H. Gene frequency comparisons between sunfish (Centrarchidae) populations at various stages of evolutionary divergence. Syst. Zool. 26:1977;319-335
2. Avise J.C, Straney D.O, Smith M.H. Biochemical genetics of sunfish IV. Relationships of centrarchid genera. Copeia. 1977:1977;250-258
3. Bailey, R.M., 1938. A systematic revision of the centrarchid fishes with a discussion of their distribution, variations, and probable interrelationships. Ph.D. Dissertation, University of Michigan, Ann Arbor, MI
4. Branson B.A, Moore G.A. The lateralis components of the acoustico-lateralis system in the sunfish family Centrarchidae. Copeia. 1962:1962;1-108
5. Brown W.M, George M.G, Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA. 76:1979;1971-1976
6. Cavender T.M. Review of the fossil history of North American freshwater fishes. Hocutt C.H, Wiley E.O. The Zoogeography of North American freshwater fishes. 1986;699-724 Wiley, New York
7. Chang, C.-H.M., 1988. Systematics of the Centrarchidae (Perciformes: Percoidei) with notes on the haemal-anal-axial character complex. Ph.D. Dissertation, The City University of New York, New York, NY
8. Childers W.F. Hybridization of four species of sunfishes (Centrarchidae). Ill. Nat. Hist. Sur. Bull. 29:1967;159-214
9. Chow S, Hazama K. Universal PCR primers for S7 ribosomal protein genes in fish. Mol. Ecol. 7:1998;1255-1256
10. Doyle J.J. Trees within trees: genes and species, molecules and morphology. Syst. Biol. 46:1997;537-553
11. Farris J.S, Kallersjo M, Kluge A.G, Bult C. Testing significance of incongruence. Cladistics. 10:1994;315-319
12. Goldman N, Anderson J.P, Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:2000;652-670
13. Goldman N, Whelan S. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol. Biol. Evol. 17:2000;975-978
14. Hubbs C.L. Hybridization between fish species in nature. Syst. Zool. 4:1955;1-20
15. Hubbs C.L, Bailey R.M. A revision of the black basses (Micropterus and Huro) with descriptions of four new forms. Miscell. Publ. Mus. Zool. Univ. Michigan. 48:1940;1-51
16. Hubbs C.L, Hubbs L.C. Experimental verification of natural hybridization between distinct genera of sunfishes. Pap. Mich. Acad. Sci. Arts Lett. 15:1932;427-437
17. Hudson R.R, Turelli M. Stochasticity overrules the Three-Times Rule: genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution. 57:2003;182-190
18. Huelsenbeck J.P, Crandall K.A. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:1997;437-466
19. Huelsenbeck J.P, Ronquist F, Nielsen R, Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2001;2310-2314
20. Jackman T.R, Larson A, De Queiroz K, Losos J.B. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst. Biol. 48:1999;254-285
21. Johnson R.L, Magee J.B, Hodge T.A. Phylogenetics of freshwater black basses (Centrarchidae: Micropterus) inferred from restriction endonuclease analysis of mitochondrial DNA. Biochem. Genet. 39:2001;395-406
22. Jones W.J, Quattro J.M. Phylogenetic affinities of pygmy sunfishes (Elassoma) inferred from mitochondrial DNA sequences. Copeia. 1999:1999;470-474
23. Kassler T.W, Koppelman J.B, Near T.J, Dillman C.B, Levengood J.M, Swofford D.L, VanOrman J.L, Claussen J.E, Philipp D.P. Molecular and morphological analyses of the black basses (Micropterus): implications for taxonomy and conservation. Am. Fish. Soc. Symp. 31:2002;291-322
24. Kocher T.D, Conroy J.A, McKaye K.R, Stauffer J.R, Lockwook S.F. Evolution of NADH dehydrogenase subunit 2 in East African cichlid fish. Mol. Phylogenet. Evol. 4:1995;420-432
25. Kraus F, Miyamoto M.M. Rapid cladogenesis among the pecoran ruminants: evidence from mitochondrial DNA sequences. Syst. Zool. 40:1991;117-130
26. Larget B, Simon D.L. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:1999;750-759
27. Lauder G.V. Functional and morphological bases of trophic specializations in sunfishes (Teleostei, Centrarchidae). J. Morphol. 178:1983;1-21
28. Lauder G.V. Homology, analogy, and the evolution of behavior. Nitecki M.H, Kitchell J.A. Evolution of Animal Behavior. 1986;9-40 Oxford University Press, New York
29. Lee D.S, Gilbert C.R, Hocutt C.H, Jenkins R.E, McAllister D.E, Stauffer J.R Jr. Atlas of North American freshwater fishes. 1980;North Carolina State Museum of Natural History, Raleigh, NC
30. Li W.-H. Molecular evolution. 1997;Sinauer, Sunderland, MA
31. Mabee P.M. An empirical rejection of the ontogenetic polarity criterion. Cladistics. 5:1989;409-416
32. Mabee P.M. Phylogenetic interpretation of ontogenetic change: sorting out the actual and artefactual in an empirical case study of centrarchid fishes. Zool. J. Linn. Soc. 107:1993;175-291
33. Maddison D.R, Maddison W.P. MacClade 4: Analysis of Phylogeny and Character Evolution. 4.0 ed. 2000;Sinauer, Sunderland, MA
34. Mok H.-K. The phylogenetic implications of centrarchid kidneys. Bull. Inst. Zool. Acad. Sin. 20:1981;59-67
35. Moore W.S. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution. 49:1995;718-726
36. Near T.J, Kassler T.W, Koppelman J.B, Dillman C.B, Philipp D.P. Speciation in North American black basses, Micropterus. Evolution. 57:2003;1610-1621
37. Page L.M, Burr B.M. A Field Guide to Freshwater Fishes, North America North of Mexico. 1991;Houghton Mifflin Company, Boston
38. Pamilo P, Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:1988;568-583
39. Parker H.R, Philipp D.P, Whitt G.S. Gene regulatory divergence among species estimated by altered development patterns in interspecific hybrids. Mol. Biol. Evol. 2:1985;217-250
40. Posada D, Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:1998;817-818
41. Ramsey J.S. Taxonomic history and systematic relationships among species of Micropterus. Stroud R.H, Clepper H. Black Bass Biology and Management. 1975;47-53 Sport Fishing Institute, Washington, DC
42. Roe K.J, Harris P.M, Mayden R.L. Phylogenetic relationships of the genera of North American sunfishes and basses (Percoidei: Centrarchidae) as evidenced by the mitochondrial cytochrome b gene. Copeia. 2002:2002;897-905
43. Ronquist F, Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:2003;1572-1574
44. Schlaikjer E.M. New fishes from the continental Tertiary of Alaska. Bull. Am. Mus. Nat. Hist. 74:1937;1-23
45. Shaffer H.B, Meylan P, McKnight M.L. Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Syst. Biol. 46:1997;235-268
46. Slowinski J.B. Molecular polytomies. Mol. Phylogenet. Evol. 19:2001;114-120
47. Smith C.L, Bailey R.M. Evolution of the dorsal-fin supports of percoid fishes. Pap. Mich. Acad. Sci. Arts Lett. 46:1961;345-363
48. Swofford D.L. PAUP*. Phylogenetic Analysis using Parsimony (*and Other Methods). Version 4.0b4. 2001;Sinauer Associates, Sunderland, MA
49. Thompson J.D, Gibson T.J, Plewniak F, Jeanmougin F, Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 22:1997;4673-4680
50. Wainwright P.C, Lauder G.V. The evolution of feeding biology in sunfishes (Centrarchidae). Mayden R.L. Systematics, Historical Ecology, and North American Freshwater Fishes. 1992;472-491 Stanford University Press, Stanford
51. Warren M.L Jr. Variation of the spotted sunfish, Lepomis punctatus complex (Centrarchidae): meristics, morphometrics, pigmentation and species limits. Bull. Alabama Mus. Nat. Hist. 12:1992;1-47
52. Werner E.E, Hall D.J. Foraging efficiency and habitat switching in competing sunfishes. Ecology. 60:1979;256-264