Population Structure and Evolutionary History of Southern Flounder in the Gulf of Mexico and Western Atlantic Ocean

REFERENCES

• Alter , S. E. , Rynes , E. and Palumbi , S. R. 2007 . DNA evidence for historic population size and past ecosystem impacts of gray whales . Proceedings of the National Academy of Sciences of the USA , 104 : 15162 – 15167 .
   PubMed Web of Science ®Google Scholar
• Anderson , J. D. 2007 . Systematics of the North American menhadens: molecular evolutionary reconstructions in the genus Brevoortia (Clupeiformes: Clupeidae) . U.S. National Marine Fisheries Service Fishery Bulletin , 205 : 368 – 378 .
   Google Scholar
• Aris-Brosou , S. and Excoffier , L. 1996 . The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism . Molecular Biology and Evolution , 13 : 494 – 504 .
   PubMed Web of Science ®Google Scholar
• Avise , J. C. 1992 . Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology . Oikos , 63 : 62 – 76 .
   Web of Science ®Google Scholar
• Avise , J. C. , Walker , D. and Johns , G. C. 1998 . Speciation durations and Pleistocene effects on vertebrate phylogeography . Proceedings of the Royal Society of London B , 265 : 1707 – 1712 .
   Web of Science ®Google Scholar
• Beerli , P. 2008 . Migrate version 3.0 – a maximum likelihood and Bayesian estimator of gene flow using the coalescent . Available: popgen.sc.fsu.edu/Migrate/Migrate-n.html. (June 2010)
   Google Scholar
• Beerli , P. 2009 . “ How to use Migrate or why are Markov chain Monte Carlo programs so difficult to use? ” . In Population genetics for animal conservation , Edited by: Bertorelle , G. , Bruford , M. W. , Hauffe , H. C. , Rizzoli , A. and Vernesi , C. 42 – 79 . Cambridge , , UK : Cambridge University Press .
   Google Scholar
• Beerli , P. and Felsenstein , J. 1999 . Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach . Genetics , 152 : 762 – 773 .
   Web of Science ®Google Scholar
• Beerli , P. and Felsenstein , J. 2001 . Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach . Proceedings of the National Academy of Sciences of the USA , 98 : 4563 – 4568 .
   PubMed Web of Science ®Google Scholar
• Bertorelle , G. and Slatkin , M. 1995 . The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters . Molecular Biology and Evolution , 12 : 887 – 892 .
   PubMed Web of Science ®Google Scholar
• Birky , C. W. Jr. , Maruyama , T. and Fuerst , P. 1983 . An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results . Genetics , 103 : 513 – 527 .
   PubMed Web of Science ®Google Scholar
• Blandon , I. R. , Ward , R. , King , T. L. , Karel , W. J. and Monaghan , J. P. 2001 . Preliminary genetic population structure of southern flounder, Paralichthys lethostigma, along the Atlantic coast and Gulf of Mexico . U.S. National Marine Fisheries Service Fishery Bulletin , 99 : 671 – 678 .
   Web of Science ®Google Scholar
• Cass-Calay , S. L. and Schmidt , T. W. 2003 . Standardized catch rates of juvenile goliath grouper, Epinephelus itajara, from the Everglades National Park creel survey, 1973–1999 , Washington , D.C : National Oceanic and Atmospheric Administration . Southeast Data, Assessment and Review, Sustainable Fisheries Division Contribution SFD-2003–0016
   Google Scholar
• Clayton , L. and Moran , S. R. 1982 . Chronology of late Wisconsinan glaciation in middle North America . Quaternary Science Reviews , 1 : 55 – 82 .
   Google Scholar
• Crandall , K. A. , Bininda-Emonds , O. R. P. , Mace , G. M. and Wayne , R. K. 2000 . Considering evolutionary processes in conservation biology . Trends in Ecology and Evolution , 15 : 290 – 295 .
   PubMed Web of Science ®Google Scholar
• Donaldson , K. A. and Wilson , R. R. 1999 . Amphi-panamic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes . Molecular Phylogenetics and Evolution , 13 : 208 – 213 .
   PubMed Web of Science ®Google Scholar
• Excoffier , L. , Laval , G. and Schneider , S. 2005 . Arlequin version 3.0: an integrated software package for population genetics data analysis . Evolutionary Bioinformatics Online , 1 : 47 – 50 .
   PubMed Web of Science ®Google Scholar
• Excoffier , L. , Smouse , P. and Quattro , J. 1992 . Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction data . Genetics , 131 : 479 – 491 .
   PubMed Web of Science ®Google Scholar
• Fisher , M. 2000 . “ Stock assessment of southern flounder (Paralichthys lethostigma) in Texas waters ” . In The flounder fishery of the Gulf of Mexico, United States: a regional management plan , Edited by: Vanderkooy , S. J. 14.11 – 14.17 . Mississippi : Ocean Springs . . Gulf States Marine Fisheries Commission
   Google Scholar
• Fu , Y. X. 1997 . Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection . Genetics , 147 : 915 – 925 .
   PubMed Web of Science ®Google Scholar
• Gelman , A. , Carlin , J. B. , Stern , H. S. and Rubin , D. B. 2004 . Bayesian data analysis , 3rd edition , London : Chapman and Hall .
   Google Scholar
• Ginsburg , I. 1952 . Flounders of the genus Paralichthys and related genera in American waters . U.S. Fish and Wildlife Service Fishery Bulletin , 52 : 267 – 351 .
   Google Scholar
• Gold , J. R. and Richardson , L. R. 1998 . Mitochondrial DNA diversification and population structure in fishes from the Gulf of Mexico and western Atlantic . Journal of Heredity , 89 : 404 – 414 .
   Web of Science ®Google Scholar
• Goodyear , C. P. 1994 . An analysis of generation time and the influence of natural mortality on the status and recovery of Gulf of Mexico red snapper , Miami : U.S. National Marine Fisheries Service, Southeast Fisheries Center . Publication MIA-94/95-11, Miami Laboratory
   Google Scholar
• Hare , M. P. , Nunney , L. , Schwartz , M. K. , Ruzzante , D. E. , Burford , B. , Waples , R. S. , Ruegg , K. and Palstra , F. 2011 . Understanding and estimating effective population size for practical application in marine species management . Conservation Biology , 25 : 438 – 449 .
   PubMed Web of Science ®Google Scholar
• Hauser , L. and Seeb , J. E. 2008 . Advances in molecular technology and their impact on fisheries genetics . Fish and Fisheries , 9 : 473 – 486 .
   Web of Science ®Google Scholar
• Hoarau , G. , Boon , E. , Jongma , D. N. , Ferber , S. , Palsson , J. , Van der Veer , H. W. , Rijnsdorp , A. D. , Stam , W. T. and Olsen , J. L. 2005 . Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.) . Proceedings of the Royal Society Biological Sciences , 272 : 497 – 503 .
   PubMed Web of Science ®Google Scholar
• Hudson , R. R. 1990 . “ Gene genealogies and the coalescent process ” . In Oxford surveys in evolutionary biology , Edited by: Futuyama , D. and Antonovics , J. 1 – 44 . New York : Oxford University Press .
   Google Scholar
• Jukes , T. H. and Cantor , C. R. 1969 . Evolution of protein molecules. , 21 – 132 . New York : Academic Press . in H. N. Munro, editor. Mammalian protein metabolism.
   Google Scholar
• Kimura , M. A. 1980 . Simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences . Journal of Molecular Evolution , 16 : 111 – 120 .
   PubMed Web of Science ®Google Scholar
• Kuhner , M. K. 2008 . Coalescent genealogy samplers: windows into population history . Trends in Ecology and Evolution , 24 : 86 – 93 .
   PubMed Web of Science ®Google Scholar
• Kumar , S. , Dudley , J. , Nei , M. and Tamura , K. 2008 . MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences . Briefings in Bioinformatics , 9 : 299 – 306 .
   PubMed Web of Science ®Google Scholar
• Moritz , C. 1994 . Defining ‘evolutionarily significant units’ for conservation . Trends in Ecology and Evolution , 9 : 373 – 375 .
   PubMed Web of Science ®Google Scholar
• NCDMF (North Carolina Division of Marine Fisheries) . 2005 . North Carolina fishery management plan, southern flounder (Paralichthys lethostigma) , Morehead City , North Carolina : NCDMF .
   Google Scholar
• Nei , M. 1987 . Molecular evolutionary genetics , New York : Columbia University Press .
   Google Scholar
• Nelson , D. M. , Monaco , M. E. , Irlandi , E. A. , Settle , L. R. and Coston-Clements , L. 1991 . Distribution and abundance of fishes and invertebrates in southeast estuaries , Silver Spring , Maryland : National Oceanic and Atmospheric Administration/National Ocean Service, Strategic Environmental Assessments Division . ELMR Report 9
   Google Scholar
• Palsbøll , P. J. , Bérubé , M. and Allendorf , F. W. 2006 . Identification of management units using population genetic data . Trends in Ecology and Evolution , 22 : 11 – 16 .
   PubMed Web of Science ®Google Scholar
• Palumbi , S. R. 2003 . Population genetics, demographic connectivity, and the design of marine reserves . Ecological Applications , 13 : S146 – S158 .
   Web of Science ®Google Scholar
• Pritchard , E. 2009 . Fisheries of the United States 2008 , Silver Spring , Maryland : U.S. National Marine Fisheries Service .
   Google Scholar
• Rogers , A. R. and Harpending , H. 1992 . Population growth makes waves in the distribution of pairwise genetic differences . Molecular Biology and Evolution , 9 : 552 – 569 .
   PubMed Web of Science ®Google Scholar
• Ryder , O. A. 1986 . Species conservation and systematics: the dilemma of subspecies . Trends in Ecology and Evolution , 1 : 9 – 10 .
   Web of Science ®Google Scholar
• Schwartz , M. K. , Luikart , G. and Waples , R. S. 2006 . Genetic monitoring as a promising tool for conservation and management . Trends in Ecology and Evolution , 22 : 25 – 33 .
   PubMed Web of Science ®Google Scholar
• Slatkin , M. 1995 . A measure of population subdivision based on microsatellite allele frequencies . Genetics , 139 : 457 – 462 .
   PubMed Web of Science ®Google Scholar
• Slatkin , M. and Hudson , R. R. 1991 . Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations . Genetics , 129 : 555 – 562 .
   PubMed Web of Science ®Google Scholar
• Smouse , P. E. , Long , J. C. and Sokal , R. R. 1986 . Multiple regression and correlation extensions of the Mantel Test of matrix correspondence . Systematic Zoology , 35 : 627 – 632 .
   Google Scholar
• Strom , D. G. and Graves , G. A. 1995 . A comparison of mercury in estuarine fish: Florida Bay and Indian River Lagoon , Port St. Lucie : Florida Department of Environmental Protection . Ecosystem Management Report
   Google Scholar
• Tajima , F. 1989 . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism . Genetics , 123 : 585 – 595 .
   PubMed Web of Science ®Google Scholar
• Tringali , M. D. and Bert , T. M. 1996 . The genetic stock structure of common snook (Centropomus undecimalis) . Canadian Journal of Fisheries and Aquatic Sciences , 53 : 974 – 984 .
   Web of Science ®Google Scholar
• Waples , R. S. 1991 . Pacific salmon, Oncorhynchus spp., and the definition of “species” under the Endangered Species Act . Marine Fisheries Review , 53 : 11 – 22 .
   Google Scholar
• Waples , R. S. and Gaggiotti , O. 2006 . What is a population? . Molecular Ecology , 15 : 1419 – 1439 .
   PubMed Web of Science ®Google Scholar
• Waples , R. S. , Punt , A. E. and Cope , J. M. 2008 . Integrating genetic data into management of marine resources: how can we do it better? . Fish and Fisheries , 9 : 423 – 449 .
   Web of Science ®Google Scholar
• Wenner , C. and Archambault , J. 2005 . Southern flounder: natural history and fishing techniques in South Carolina , Charleston : South Carolina Department of Natural Resources . Educational Report 20
   Google Scholar
• Wright , S. 1931 . Evolution in Mendelian populations . Genetics , 16 : 97 – 159 .
   PubMedGoogle Scholar
• Wright , S. 1938 . Size of population and breeding structure in relation to evolution . Science , 87 : 430 – 431 .
   Google Scholar
• Xia , X. and Xie , Z. 2001 . DAMBE: data analysis in molecular biology and evolution . Journal of Heredity , 92 : 371 – 373 .
   PubMed Web of Science ®Google Scholar