Evaluation of Genetic Population Structure of Smallmouth Bass in the Susquehanna River Basin, Pennsylvania

References

• Allendorf, F. W., G. Luikart, and S. N. Aitken. 2013. Conservation and the genetics of populations, 2nd edition. Wiley-Blackwell, West Sussex, UK.
   Google Scholar
• Arway, J. A., and G. Smith. 2013. The Susquehanna River—a fishery in decline. Fisheries 38:235–236.
   Web of Science ®Google Scholar
• Barthel, B. L., S. J. Cooke, J. H. Svec, C. D. Suski, C. M. Bunt, F. J. S. Phelan, and D. P. Phillipp. 2008. Divergent life histories among Smallmouth Bass Micropterus dolomieu inhabiting a connected river–lake system. Journal of Fish Biology 73:829–852.
   Web of Science ®Google Scholar
• Beyer, B. K. 1957. The Chenango Canal and the campaign for its construction. New York History 38:257–275.
   Google Scholar
• Blazer, V. S., D. D. Iwanowicz, H. L. Walsh, A. J. Sperry, L. R. Iwanowicz, D. A. Alvarez, R. A. Brightbill, G. Smith, W. T. Foreman, and R. Manning. 2014. Reproductive health indicators of fishes from Pennsylvania watersheds: association with chemicals of emerging concern. Environmental Monitoring Assessment 186:6471–6491.
   PubMed Web of Science ®Google Scholar
• Borden, W. C., and R. A. Krebs. 2009. Phylogeography and postglacial dispersal of Smallmouth Bass (Micropterus dolomieu) into the Great Lakes. Canadian Journal of Fisheries and Aquatic Sciences 66:2142–2156.
   Web of Science ®Google Scholar
• Borden, W. C., and C. A. Stepien. 2006. Discordant population genetic structuring of Smallmouth Bass, Micropterus dolomieu Lacèpede, in Lake Erie based on mitochondrial DNA sequences and nuclear DNA microsatellites. Journal of Great Lakes Research 32:242–257.
   Web of Science ®Google Scholar
• Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570.
   PubMed Web of Science ®Google Scholar
• DeWoody, J. A., D. E. Fletcher, S. D. Wilkins, W. S. Nelson, and J. C. Avise. 1998. Molecular genetic dissection of spawning, parentage, and reproductive tactics in a population of Redbreast Sunfish, Lepomis auritus. Evolution 52:1802–1810.
   PubMed Web of Science ®Google Scholar
• DeWoody, J. A., D. E. Fletcher, S. D. Wilkins, W. S. Nelson, and J. C. Avise. 2000. Genetic monogamy and biparental care in an externally fertilizing fish, the Largemouth Bass (Micropterus salmoides). Proceedings of the Royal Society of London 267:2431–2437.
   Google Scholar
• Do, C., R. S. Waples, D. Peel, G. M. Macbeth, B. J. Tillett, and J. R. Ovenden. 2014. NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14:209–214.
   PubMed Web of Science ®Google Scholar
• Earl, D. A., and B. M. vonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4:359–361.
   Web of Science ®Google Scholar
• Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611–2620.
   PubMed Web of Science ®Google Scholar
• Excoffier, L., and H. E. L. Lischer. 2010. Arlequin suite version 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564–567.
   PubMed Web of Science ®Google Scholar
• Faircloth, B. C. 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8:92–94.
   PubMed Web of Science ®Google Scholar
• Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. University of Washington, Seattle. Available: http://evolution.genetics.washington.edu/phylip.html. ( June 2017).
   Google Scholar
• Goldsborough, E. L., and H. W. Clark. 1908. Fishes of West Virginia. Government Printing Office, Bulletin of the Bureau of Fisheries, Washington, D.C.
   Google Scholar
• Goslee, S. C., and D. L. Urban. 2007. The ecodist package for dissimilarity-based analysis of ecological data. Journal of Statistical Software 22:1–19.
   Web of Science ®Google Scholar
• Goudet, J. 2002. FSTAT, a program to estimate and test gene diversities and fixation indices, version 2.9.3.2. Available: http://www.unil.ch/izea/softwares/fstat.html. ( June 2017).
   Google Scholar
• Gross, M. L., A. R. Kapuscinski, and A. J. Faras. 1994. Nest-specific DNA fingerprints of Smallmouth Bass in Lake Opeongo, Ontario. Transactions of the American Fisheries Society 123:449–459.
   Web of Science ®Google Scholar
• Hallerman, E. M., N. Johnson, and D. Dutton. 2015. Implications of microsatellite DNA variation upon management of Virginia Smallmouth Bass populations. Pages 615–633 in M. D. Tringali, J. M. Long, T. W. Birdsong, and M. S. Allen, editors. Black bass diversity: multidisciplinary science for conservation. American Fisheries Society, Symposium 82, Bethesda, Maryland.
   Google Scholar
• Hӓnfling, B. 2007. Understanding the establishment success of non-indigenous fishes: lessons from population genetics. Journal of Fish Biology 71:115–135.
   Web of Science ®Google Scholar
• Hawkins, S. J., K. Bohn, D. W. Sims, P. Ribeiro, J. Faria, P. Presa, A. Pita, G. M. Martins, A. I. Neto, M. T. Burrows, and M. J. Genner. 2016. Fisheries stocks from an ecological perspective: disentangling ecological connectivity from genetic interchange. Fisheries Research 179:333–341.
   Google Scholar
• Henshall, J. A. 1881. Book of the black bass. Robert Clarke Company, Cincinnati, Ohio.
   Google Scholar
• Humston, R., B. M. Priest, W. C. Hamilton, and P. E. Bugas Jr. 2010. Dispersal between tributary and main-stem rivers by juvenile Smallmouth Bass evaluated using otolith microchemistry. Transactions of the American Fisheries Society 139:171–184.
   Google Scholar
• Jackson, D. A. 2002. Ecological effects of Micropterus introductions: the dark side of black bass. Pages 221–232 in D. P. Phillipp and M. S. Ridgway, editors. Black bass: ecology, conservation, and management. American Fisheries Society, Symposium 31, Bethesda, Maryland.
   Google Scholar
• Jakobsson, M., and N. A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806.
   PubMed Web of Science ®Google Scholar
• Jeschke, J. M., and D. L. Strayer. 2006. Determinants of vertebrate invasion success in Europe and North America. Global Change Biology 12:1608–1619.
   Web of Science ®Google Scholar
• Keefer, M. L., and C. C. Caudill. 2014. Homing and straying by anadromous salmonids: a review of mechanisms and rates. Reviews in Fish Biology and Fisheries 24:333–368.
   Web of Science ®Google Scholar
• Langhurst, R. W., and D. L. Schoenike. 1990. Seasonal migration of Smallmouth Bass in the Embarrass and Wolf rivers, Wisconsin. North American Journal of Fisheries Management 10:224–227.
   Google Scholar
• Lewis, P. O., and D. Zaykin. 2001. Genetic Data Analysis: computer program for the analysis of allelic data, version 1.0 (d16c). Available: http://lewis.eeb.uconn.edu/lewishome/software.html. ( June 2017).
   Google Scholar
• Malloy, T. P. Jr., R. A. Van Den Bussche, W. D. Coughlin, and A. A. Echelle. 2000. Isolation and characterization of microsatellite loci in Smallmouth Bass, Micropterus dolomieu (Teleostei: Centrarchidae), and cross-species amplification in Spotted Bass, M. punctulatus. Molecular Ecology 9:1919–1952.
   Google Scholar
• Milner, J. W. 1874. The progress of fish-culture in the United States. Pages 524–536 in Report of the U.S. Commission of Fish and Fisheries 1872–1873. Government Printing Office, Washington, D.C.
   Google Scholar
• Page, R. D. M. 1996. TreeView: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12:357–358.
   PubMedGoogle Scholar
• Palsboll, P. J., M. Berube, and F. W. Allendorf. 2006. Identification of management units using population genetic data. Trends in Ecology and Evolution 22:11–16.
   PubMed Web of Science ®Google Scholar
• Piry, S., A. Alapetite, J. M. Cornuet, D. Paetkau, L. Baudouin, and A. Estoup. 2004. GENECLASS2: A software for genetic assignment and first-generation migrant detection. Journal of Heredity 95:536–539.
   PubMed Web of Science ®Google Scholar
• Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.
   PubMed Web of Science ®Google Scholar
• Quinn, T. P., M. J. Unwin, and M. T. Kinnison. 2000. Evolution of temporal isolation in the wild: genetic divergence in timing of migration and breeding by introduced Chinook Salmon populations. Evolution 54:1372–1385.
   PubMed Web of Science ®Google Scholar
• R Core Team. 2013. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Available: http://www.R-project.org/. ( June 2017).
   Google Scholar
• Rannala, B., and J. L. Mountain. 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the USA 94:9197–9201.
   Google Scholar
• Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
   PubMed Web of Science ®Google Scholar
• Ridgway, M. S., J. A. MacLean, and J. C. MacLeod. 1991. Nest-site fidelity in a centrarchid fish, the Smallmouth Bass (Micropterus dolomieu). Canadian Journal of Zoology 69:3103–3015.
   Web of Science ®Google Scholar
• Rosenberg, N. A. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4:137–138.
   Web of Science ®Google Scholar
• Rousset, F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228.
   PubMed Web of Science ®Google Scholar
• Smith, H. M. 1907. Our fish immigrants. National Geographic 18:385–400.
   Google Scholar
• Stark, W. J., and A. A. Echelle. 1998. Genetic structure and systematics of Smallmouth Bass, with emphasis on interior highlands populations. Transactions of the American Fisheries Society 127:393–416.
   Web of Science ®Google Scholar
• Stepien, C. A., D. J. Murphy, and R. M. Strange. 2007. Broad- to fine-scale population genetic patterning in the Smallmouth Bass Micropterus dolomieu across the Laurentian Great Lakes and beyond: an interplay of behavior and geography. Molecular Ecology 16:1605–1624.
   PubMed Web of Science ®Google Scholar
• Stillwell, S. B., H. C. Demuth, L. Streuber, H. C. Ford, J. A. Dale, and D. P. Corwin. 1895. Report of the state commissioners of fisheries, year 1895. Pages 215–220 in Fish Commissioners of Pennsylvania, Harrisburg.
   Google Scholar
• Todd, B. L., and C. F. Rabeni. 1989. Movement and habitat use by stream-dwelling Smallmouth Bass. Transactions of the American Fisheries Society 118:229–242.
   Web of Science ®Google Scholar
• Untergasser, A., I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth, M. Remm, and S. G. Rozen. 2012. Primer3—new capabilities and interfaces. Nucleic Acids Research [online serial] 40(15):e115.
   PubMed Web of Science ®Google Scholar
• Waples, R. S., and C. Do. 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 3:244–262.
   PubMed Web of Science ®Google Scholar
• Waples, R. S., and O. Gaggiotti. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15:1419–1439.
   PubMed Web of Science ®Google Scholar
• Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370.
   PubMed Web of Science ®Google Scholar