Genetics and Juvenile Abundance Dynamics Show Congruent Patterns of Population Structure for Depleted River Herring Populations in the Upper Chesapeake Bay

REFERENCES

• ASMFC (Atlantic States Marine Fisheries Commission). 2012. River herring benchmark stock assessment, volume I. ASMFC, Stock Assessment Report 12-02, Arlington, Virginia.
   Google Scholar
• Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme. 2004. GENETIX 4.05, logiciel sous WINDOWS pour la genetique des populations. Université de Montpellier II, Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Montpellier, France.
   Google Scholar
• Bethoney, N. D., K. D. E. Stokesbury, B. P. Schondelmeier, W. S. Hoffman, and M. P. Armstrong. 2013. Characterization of river herring bycatch in the northwest Atlantic midwater trawl fisheries. North American Journal of Fisheries Management 34:828–838.
   Web of Science ®Google Scholar
• Carlson, S. M., and W. H. Satterthwaite. 2011. Weakened portfolio effect in a collapsed salmon population complex. Canadian Journal of Fisheries and Aquatic Sciences 68:1579–1589.
   Web of Science ®Google Scholar
• Durell, E. Q., and C. Weedon. 2015. Striped Bass seine survey juvenile index web page. Maryland Department of Natural Resources, Fisheries Service. Available: http://dnr2.maryland.gov/fisheries/Pages/juvenile-index.aspx. ( May 2017).
   Google Scholar
• Ellis, D., and J. C. Vokoun. 2009. Earlier spring warming of coastal streams and implications for Alewife migration timing. North American Journal of Fisheries Management 29:1584–1589.
   Web of Science ®Google Scholar
• Evanno, G., S. Regnaut, and J. Goudet. 2005. Detection of the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611–2620.
   PubMed Web of Science ®Google Scholar
• Falush, D., M. Stephens, and J. K. Pritchard. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587.
   PubMed Web of Science ®Google Scholar
• Gauthier, D. T., C. A. Audemard, J. E. L. Carlsson, T. L. Darden, M. R. Denson, K. S. Reece, and J. Carlsson. 2013. Genetic population structure of U.S. Atlantic coastal Striped Bass (Morone saxatilis). Journal of Heredity 104:510–520.
   PubMed Web of Science ®Google Scholar
• Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices, version 2.9.3. Available: http://www2.unil.ch/popgen/softwares/fstat.html. ( May 2012).
   Google Scholar
• Hall, C. J., A. Jordaan, and M. G. Frisk. 2012. Centuries of anadromous forage fish loss: consequences for ecosystem connectivity and productivity. BioScience 62:723–731.
   Web of Science ®Google Scholar
• Hasselman, D. J., E. C. Anderson, E. E. Argo, N. D. Bethony, S. G. Gephard, D. M. Post, B. P. Schondelmeier, T. F. Schultz, T. V. Willis, and E. P. Palkovacs. 2016. Genetic stock composition of marine bycatch reveals disproportional impacts on depleted river herring genetic stocks. Canadian Journal of Fisheries and Aquatic Sciences 73:951–963.
   Web of Science ®Google Scholar
• Hasselman, D. J., E. E. Argo, M. C. McBride, P. Bentzen, T. F. Schultz, A. A. Perez-Umphrey, and E. P. Palkovacs. 2014. Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species. Molecular Ecology 23:1137–1152.
   PubMed Web of Science ®Google Scholar
• Hasselman, D. J., and K. E. Limburg. 2012. Alosine restoration in the 21st century: challenging the status quo. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science [online serial] 4:174–187.
   Web of Science ®Google Scholar
• Hasselman, D. J., D. Ricard, and P. Bentzen. 2013. Genetic diversity and differentiation in a wide ranging anadromous fish, American Shad (Alosa sapidissima), is correlated with latitude. Molecular Ecology 22:1558–1573.
   PubMed Web of Science ®Google Scholar
• Hendrick, P. W. 2005. A standardized genetic differentiation measure. Evolution 59:1633–1638.
   PubMed Web of Science ®Google Scholar
• Holm, S. 1979. A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6:65–70.
   Web of Science ®Google Scholar
• Jolly, M. T., M. W. Aprahamian, S. J. Hawkins, P. A. Henderson, R. Hillman, N. O’Maoileidigh, P. S. Maitland, R. Piper, and M. J. Genner. 2012. Population genetic structure of protected Allis Shad (Alosa alosa) and Twaite Shad (Alosa fallax). Marine Biology 159:675–687.
   Web of Science ®Google Scholar
• Klauda, R. J., S. A. Fischer, L. W. Hall Jr., and J. A. Sullivan. 1991. Alewife and Blueback Herring; Alosa pseudoharengus and Alosa aestivalis. Pages 10.1–10.29 in S. L. Funderburk, J. A. Mihursky, S. J. Jordan, and D. Riley, editors. Habitat requirements for Chesapeake Bay living resources, 2nd edition. Chesapeake Bay Program, Living Resources Subcommittee, Annapolis, Maryland.
   Google Scholar
• Latch, E. K., G. Dharmarajan, J. C. Glaubitz, and O. E. Rhodes. 2006. Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetics 7:295–302.
   Web of Science ®Google Scholar
• MacAvoy, S. E., S. A. Macko, S. P. McIninch, and G. C. Garman. 2000. Marine nutrient contributions to freshwater apex predators. Oecologia 122:568–573.
   PubMed Web of Science ®Google Scholar
• McBride, M. C., D. J. Hasselman, T. V. Willis, E. P. Palkovacs, and P. Bentzen. 2015. Influence of stocking history on the population genetic structure of anadromous Alewife (Alosa pseudoharengus) in Maine rivers. Conservation Genetics 16:1209–1223.
   Web of Science ®Google Scholar
• McBride, M. C., T. V. Willis, R. G. Bradford, and P. Bentzen. 2014. Genetic diversity and structure of two hybridizing anadromous fishes (Alosa pseudoharengus, Alosa aestivalis) across the northern portion of their ranges. Conservation Genetics 15:1281–1298.
   Web of Science ®Google Scholar
• McDermott, S. P., N. C. Bransome, S. E. Sutton, B. E. Smith, J. S. Link, and T. J. Miller. 2015. Quantifying alosine prey in the diets of marine piscivores in the Gulf of Maine. Journal of Fish Biology 86:1811–1829.
   PubMed Web of Science ®Google Scholar
• Meirmans, P. G. 2006. Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60:2399–2402.
   PubMed Web of Science ®Google Scholar
• Molecular Ecology Resources Primer Development Consortium. 2012. Permanent genetic resources added to Molecular Ecology Resources Database, 1 August 2011– 30 September 2011. Molecular Ecology Resources 12:185–189.
   PubMed Web of Science ®Google Scholar
• NMFS (National Marine Fisheries Service). 2016a. Fisheries of the northeastern United States; Atlantic Herring fishery; specification of management measures for Atlantic Herring for the 2016–2018 fishing years. Code of Federal Regulations, Title 50, Part 648. U.S. Government Printing Office, Washington, D.C.
   Google Scholar
• NMFS (National Marine Fisheries Service). 2016b. Fisheries of the northeastern United States; Atlantic Mackerel, squid, and Butterfish fisheries; specifications and management measures. Code of Federal Regulations, Title 50, Part 648. U.S. Government Printing Office, Washington, D.C.
   Google Scholar
• Ogburn, M. B., J. Spires, R. Aguilar, M. R. Goodison, K. Heggie, E. Kinnebrew, W. McBurney, K. D. Richie, P. M. Roberts, and A. H. Hines. 2017. Assessment of river herring spawning runs in a Chesapeake Bay coastal plain spawning stream using imaging sonar. Transactions of the American Fisheries Society 146:22–35.
   Web of Science ®Google Scholar
• Palkovacs, E. P., D. J. Hasselman, E. E. Argo, S. R. Gephard, K. E. Limburg, D. M. Post, T. F. Schultz, and T. V. Willis. 2014. Combining genetic and demographic information to prioritize conservation efforts for anadromous Alewife and Blueback Herring. Evolutionary Applications 7:212–226.
   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
• Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
   PubMed 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. 2008. Genepop’007: a complete re-implementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8:103–106.
   PubMed Web of Science ®Google Scholar
• Scott, W. B., and E. J. Crossman. 1973. Freshwater fishes of Canada. Fisheries Research Board of Canada Bulletin 184.
   Google Scholar
• Stence, C. P., M. W. Baldwin, M. T. Bowermaster, M. J. Porta, J. W. Gill, A. N. Horne, J. J. Newhard, and S. P. Minkinnen. 2015. Patapsco River herring and shad restoration: 2014 Progress Report. Maryland Department of Natural Resources, Stevensville.
   Google Scholar
• Turner, S. M., K. E. Limburg, and E. P. Palkovacs. 2015. Can different combinations of natural tags identify river herring natal origin at different levels of stock structure? Canadian Journal of Fisheries and Aquatic Sciences 72:845–854.
   Google Scholar
• Twining, C. W., E. P. Palkovacs, M. Friedman, D. J. Hasselman, and D. M. Post. 2017. Nutrient loading by anadromous fishes: species-specific contributions and the effects of diversity. Canadian Journal of Fisheries and Aquatic Sciences 74:609–619.
   Web of Science ®Google Scholar
• U.S. Bureau of Fisheries. 1916. Annual report. U.S. Bureau of Fisheries, Document 836, Washington, D.C.
   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
• Wilks, D. S. 2011. Statistical methods in the atmospheric sciences, 3rd edition. Academic Press, Waltham, Massachusetts.
   Google Scholar
• Yako, L. A., M. E. Mather, and F. Juanes. 2000. Assessing the contribution of anadromous herring to Largemouth Bass growth. Transactions of the American Fisheries Society 129:77–88.
   Web of Science ®Google Scholar