Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: A catchment analysis of mitochondrial DNA sequences and nuclear microsatellites

Journal of Fish Biology

Volumn 75, Issue 9, 2009, Pages 2244-2268

  Haponski, A E ^a   Bollin, T L ^a   Jedlicka, M A ^b,c   Stepien, C A ^a  

^a UNIVERSITY OF TOLEDO   (United States)

^b CLEVELAND STATE UNIVERSITY   (United States)

^c LERNER RESEARCH INSTITUTE   (United States)

Author keywords

Etheostoma caeruleum; Freshwater fish; Lake Erie; Landscape genetics; Ohio River; Pleistocene glaciations

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; DNA SEQUENCE; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR EVOLUTION; PERCH; POPULATION GENETICS; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; PERCHES; SEQUENCE ANALYSIS, DNA;

ETHEOSTOMA CAERULEUM; MYA; PERCIDAE; TELEOSTEI;

EID: 68349151036     PISSN: 00221112     EISSN: 10958649     Source Type: Journal    
DOI: 10.1111/j.1095-8649.2009.02414.x     Document Type: Article

References (91)

1. Avise, J. C. (2000). Phylogeography: The History and Formation of Species. Cambridge : Harvard University Press.
2. Avise, J. C. (2004). Molecular Markers, Natural History, and Evolution, 2nd edn. Sunderland : Sinauer Associates, Inc.
3. Bailey, R. M. & Smith, G. R. (1981). Origin and geography of the fish fauna of the Laurentian Great Lakes basin. Canadian Journal of Fisheries and Aquatic Sciences 38, 1539 1561.
4. Benjamini, Y. & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B 57, 289 300.
5. Benzecri, J. P. (1973). L'analyse Des Donnees, Tome II: L'analyse Des Correspondances. Paris : Dunod Press.
6. Berendzen, P. B., Simons, A. M. & Wood, R. M. (2003). Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River. Journal of Biogeography 30, 1139 1152.
7. Bernatchez, L. & Dodson, J. J. (1991). Phylogeographic structure in mitochondrial DNA of the lake whitefish (Coregonus clupeaformis) and its relation to the Pleistocene glaciations. Evolution 45, 1016 1035.
8. Bernatchez, L. & Wilson, C. C. (1998). Comparative phylogeography of Nearctic and Palearctic fishes. Molecular Ecology 7, 431 452.
9. Billington, N. & Hebert, P. D. N. (1991). Mitochondrial DNA diversity in fishes and its implications for introductions. Canadian Journal of Fisheries and Aquatic Sciences 48, 80 94.
10. Billington, N., Barrette, R. J. & Hebert, P. D. N. (1992). Management implications of mitochondrial DNA variation in walleye stocks. North American Journal of Fisheries Management 12, 276 284.
11. Cavalli-Sforza, L. L. & Edwards, A. W. (1967). Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics 19, 233 257.
12. Cavender, T. M. (1986). Review of the fossil history of North American freshwater fishes. In The Zoogeography of North American Freshwater Fishes (Hocutt, C. H. & Wiley, E. O., (eds), pp. 699 724. New York, NY : Wiley Interscience Publishing.
13. Clement, M., Posada, D. & Crandall, K. A. (2000). TCS: a computer program to estimate gene genealogies. Molecular Ecology 9, 1657 1660.
14. Costello, A. B., Down, T. E., Pollard, S. M., Pacas, C. J. & Taylor, E. B. (2003). The influence of history and contemporary stream hydrology on the evolution of genetic diversity within species: an examination of microsatellite DNA variation in bull trout, Salvelinus confluentus (Pisces: Salmonidae). Evolution 57, 328 344.
15. Danzmann, R. G., Morgan, R. P., Jones, M. W., Bernatchez, L. & Ihssen, P. H. (1998). A major sextet of mitochondrial DNA phylogenetic assemblages extant in eastern North American brook trout (Salvelinus fontinalis): distribution and postglacial dispersal patterns. Canadian Journal of Fisheries and Aquatic Sciences 76, 1300 1318.
16. Dyke, A. S. & Prest, V. K. (1987). Late Wisconsinan and Holocene history of the Laurentide Ice Sheet. Géographie physique et Quaternaire 41, 237 263.
17. Esmond, E. F. & Stauffer, J. R. (1983). Taxometric comparison of the Atlantic Slope and Ohio River populations of Etheostoma caeruleum Storer. American Midland Naturalist 109, 390 397.
18. Evanno, G., Regnaut, S. & Goudet, J. (2005). Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology 14, 2611 2620.
19. Excoffier, L., Smouse, P. & Quattro, J. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479 491.
20. Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin ver 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47 50.
21. Faber, J. E. & White, M. M. (2001). Comparison of gene flow estimates between species of darters in different streams. Journal of Fish Biology 57, 1465 1473.
22. Farris, J. S., Kallersjo, M., Kluge, A. G. & Bult, C. (1994). Testing significance of congruence. Cladistics 10, 315 320.
23. Farris, J. S., Kallersjo, M., Kluge, A. G. & Bult, C. (1995). Constructing a significance test for incongruence. Systematic Biology 44, 570 572.
24. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783 791.
25. Guindon, S. & Gascuel, O. (2003). PhyML: a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696 704.
26. Haponski, A. E. & Stepien, C. A. (2008). Molecular, morphological, and biogeographic resolution of cryptic taxa in the greenside darter Etheostoma blennioides complex. Molecular Phylogenetics and Evolution 49, 69 83.
27. Hasegawa, M., Kishino, H. & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160 174.
28. Heithaus, M. R. & Laushman, R. H. (1997). Genetic variation and conservation of stream fishes: influence of ecology, life history, and water quality. Canadian Journal of Fisheries and Aquatic Sciences 54, 1822 1836.
29. Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnaean Society 58, 247 276.
30. Holcik, J. & Hensel, K. (1974). A new species of Gymnocephalus (Pisces: Percidae) from the Danube, with remarks on the genus. Copeia 1974, 481 486.
31. Jenkins, R. E. & Burkhead, N. M. (1994). Freshwater Fishes of Virginia. Bethesda, MD : American Fisheries Society.
32. Larson, G. & Schaetzl, R. (2001). Origin and evolution of the Great Lakes. Journal of Great Lakes Research 27, 518 546.
33. Lebedev, V. D. (1952). Fishes from alate-paleolithic settlement at Murzak-Koba in Crimea. Bulletin of the Society of Natural History, Moscow 51, 46 51.
34. LeClerc, E., Mailhot, Y., Mingelbier, M. & Bernatchez, L. (2008). The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem. Molecular Ecology 17, 1702 1717.
35. Lewis, C. F. M., Karrow, P. F., Blasco, S. M., McCarthy, F. M. G., King, J. W., Moore, T. C. & Rea, D. K. (2008). Evolution of the lakes in the Huron basin: deglaciation to present. Aquatic Ecosystem Health and Management 11, 127 168.
36. Mandrak, N. E. & Crossman, E. J. (1992). Postglacial dispersal of freshwater fishes into Ontario. Canadian Journal of Zoology 70, 2247 2259.
37. Manel, S., Schwartz, M. K., Luikart, G. & Taberlet, P. (2003). Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution 18, 189 197.
38. Mantel, N. (1967). The detection of disease clustering and generalized regression approach. Cancer Research 27, 209 220.
39. Martin, A. P., Humphreys, R. & Palumbi, S. R. (1992). Population genetic structure of the Armorhead, Pseudopentaceros wheeleri, in the North Pacific Ocean: application to fisheries problems. Canadian Journal of Fisheries and Aquatic Sciences 49, 2386 2391.
40. Mayden, R. M. (1988). Vicariance biogeography, parsimony, and evolution in North American freshwater fishes. Systematic Zoology 37, 329 355.
41. Monmonier, M. (1973). Maximum-difference barriers: an alternative numerical regionalization method. Geographical Analysis 3, 245 261.
42. Murdoch, M. M. & Hebert, P. D. N. (1997). Mitochondrial DNA evidence of distinct glacial refugia for brown bullhead (Ameirus nebulosus) in the Great Lakes. Canadian Journal of Fisheries and Aquatic Sciences 54, 1450 1460.
43. Near, T. J. (2002). Phylogenetic relationships of the genus Percina (Percidae: Etheostomatinae). Copeia 2002, 1 14.
44. Near, T. J., Kassler, T. W., Koppelman, J. B., Dillman, C. B. & Philipp, D. P. (2003). Speciation in North American black basses, Micropterus (Actinopterygii: Centrarchidae). Evolution 57, 1610 1621.
45. Neely, D. A. & George, A. L. (2006). Range extensions and rapid dispersal of Etheostoma blennioides (Teleostei: Percidae) in the Susquehanna River drainage. Northeastern Naturalist 13, 391 402.
46. van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. & Shipley, P. (2004). Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 2004, 535 538.
47. Page, L. M. (2000). Etheostomatinae. In Percid Fishes: Systematics, Ecology, and Exploitation (Craig, J. F., ed.), pp. 225 253. Oxford : Blackwell Science.
48. Page, L. M. & Burr, B. M. (1991). Freshwater Fishes. New York, NY : Houghton Mifflin Co.
49. Paine, M. D. (1984). Ecological and evolutionary consequences of early ontogenies of darters (Etheostomatini). Environmental Biology of Fishes 11, 97 106.
50. Pielou, E. C. (1991). After the Ice Age: The Return of Life to Glaciated North America. Chicago, IL : University of Chicago Press.
51. Poissant, J., Knight, T. W. & Ferguson, M. M. (2005). Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish. Molecular Ecology 14, 1321 1331.
52. Porter, B. A., Cavender, T. M. & Fuerst, P. A. (2002). Molecular phylogeny of the snubnose darters, subgenus Ulocentra (Genus Etheostoma, Family Percidae). Molecular Phylogenetics and Evolution 22, 64 374.
53. Posada, D. & Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817 818.
54. Ray, J. M., Wood, R. M. & Simons, A. M. (2006). Phylogeography and post-glacial colonization patterns of the rainbow darter, Etheostoma caeruleum (Teleostei: Percidae). Journal of Biogeography 33, 1550 1558.
55. Raymond, M. & Rousset, F. (1995a). An exact test for population differentiation. Evolution 49, 1280 1283.
56. Raymond, M. & Rousset, F. (1995b). Genepop (v1.2): population genetics software for exact tests and ecumenicism. Journal of Hereditary 86, 248 249.
57. Rice, R. M. (1989). Analyzing tables of statistical tests. Evolution 43, 223 225.
58. Rogers, A. R. & Harpending, H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552 569.
59. Saitou, N. & Nei, M. (1987). The neighbor joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406 425.
60. Sanderson, M. J. (2002). Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19, 101 109.
61. Sanderson, M. J. (2003). r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics Applications Notes 19, 301 302.
62. Schmidt, T. R. & Gold, J. R. (1993). Complete sequence of the mitochondrial cyt b gene in the Cherryfin Shiner, Lythurus roseipinnis (Teleostei: Cyprinidae). Copeia 1993, 880 883.
63. Scott, W. B. & Crossman, E. J. (1973). Freshwater fishes of Canada. Fisheries Research Board of Canada Bulletin 184, 1 966.
64. Sepulveda-Villet, O. J., Ford, A. M., Williams, J. & Stepien, C. A. (2009). Population genetic diversity and divergence patterns of yellow perch Perca flavescens. Journal of Great Lakes Research 35, 107 119.
65. Sloss, B. L., Billington, N. & Burr, B. M. (2004). A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution 32, 545 562.
66. Smith, C. L. (1985). Inland Fishes of New York State. Albany, NY : The New York State Department of Environmental Conservation.
67. Stepien, C. A. & Faber, J. E. (1998). Population genetic structure, phylogeography, and spawning philopatry in walleye (Stizostedion vitreum) from mtDNA control region sequences. Molecular Ecology 7, 1757 1769.
68. Stepien, C. A., Taylor, C. D. & Einhouse, D. (2004). An analysis of genetic risk to a native spawning stock of walleye Sander vitreus due to stocking in Cattaraugus Creek. In Proceedings of Percis III, the 3rd International Symposium on Percid Fishes (Barry, T. P. & Malison, J. A., (eds), pp 93 94. Madison, WI : University of Wisconsin Sea Grant Institute.
69. Stepien, C. A., Murphy, D. J. & Strange, R. M. (2007). Broad- to fine-scale population genetic patterning in the smallmouth bass Micropterus dolomieu across the Laurentian Great Lakes and beyond: an interplay of behaviour and geography. Molecular Ecology 16, 1605 1624.
70. Stepien, C. A., Murphy, D. J., Lohner, R. N., Sepulveda-Villet, O. J. & Haponski, A. E. (2009). Signatures of vicariance, postglacial dispersal, and spawning philopatry: Population genetics and biogeography of the walleye Sander vitreus. Molecular Ecology 18, 3411 3428.
71. Strange, R. M. & Stepien, C. A. (2007). Genetic divergence and connectivity among river and reef spawning groups of walleye (Sander vitreus) in Lake Erie. Canadian Journal of Fisheries and Aquatic Sciences 64, 437 448.
72. Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512 526.
73. Todd, T. N. & Hatcher, C. O. (1993). Genetic variability and glacial origins of yellow perch (Perca flavescens) in North America. Canadian Journal of Fisheries and Aquatic Sciences 50, 1828 1834.
74. Tonnis, B. D. (2006). Microsatellite DNA markers for the rainbow darter, Etheostoma caeruleum (Percidae), and their potential utility for other darter species. Molecular Ecology Notes 6, 230 232.
75. Turgeon, J. & Bernatchez, L. (2001). Mitochondrial DNA phylogeography of lake cisco (Coregonus artedi): evidence supporting extensive secondary contacts between two glacial races. Molecular Ecology 10, 987 1001.
76. Underhill, J. C. (1986). The fish fauna of the Laurentian Great Lakes, the St. Lawrence lowlands, Newfoundland and Labrador. In The Zoogeography of North American Freshwater Fishes (Hocutt, C. H. & Wiley, E. O., (eds), pp. 105 136. New York, NY : John Wiley & Sons, Inc.
77. Ward, R. D., Woodwark, M. & Skibinski, D. O. F. (1994). A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. Journal of Fish Biology 44, 213 232.
78. Weir, B. S. & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358 1370.
79. Zar, J. H. (1999). Biostatistical Analysis, 4th edn. Upper Saddle River, NJ : Prentice Hall, Inc.
80. Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N. & Bonhomme, F. (2004). Genetix 4.05, logiciel sous Windows TM pour la genetique des populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000, Universite de Montpellier II, Montpellier, France. Available at http://www.genetix.univ-montp2.fr/genetix/genetix.htm
81. Clement, M., Posada, D. & Crandall, K. A. (2000). TCS : phylogenetic network estimation using statistical parsimony (v1.2). Available at http://darwin.uvigo.es/software/tcs.html
82. Environmental Protection Agency (2007). Biological Indicators of Watershed Health. Available at http://www.epa.gov/bioindicators/html/fish- perches.html
83. Excoffier, L. (2007). Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Available at http://cmpg.unibe.ch/ software/arlequin3
84. Felsenstein, J. (2005). Phylip (Phylogeny Inference Package) Version 3.6. Available at http://evolution.genetics.washington.edu/phylip.html
85. Goudet, J. (1995). Fstat version 1.2: a computer program to calculate Fstatistics. Journal of Hereditary 86, 485 486. Available at http://www2.unil.ch/popgen/softwares/fstat.htm
86. Hall, T. A. (2007). BioEdit (v1.09). Available at http://www.mbio.ncsu. edu/BioEdit/bioedit.html
87. Manni, F., Gu'erard, E. & Heyer, E. (2004). Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Human Biology 76, 173 190. Available at http://www.mnhn.fr/mnhn/ecoanthropologie/software/barrier.html
88. van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. & Shipley, P. (2004). Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 2004, 535 538. Available at http://www.microchecker.hull.ac.uk
89. Posada, D. & Crandall, K. A. (2009). Modeltest: a tool to select the bestfit model of nucleotide substitution v3.7. Available at http://darwin.uvigo. es/software/modeltest.html
90. Pritchard, J. K., Stephens, M. & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945 959. Available at http://pritch.bsd.uchicago.edu/software.html
91. Rousset, F. (2007). Genepop (v4.0). Available at http://kimura.univ- montp2.fr/%7Erousset/Genepop.htm