Impacts of Marker Class Bias Relative to Locus-Specific Variability on Population Inferences in Chinook Salmon: A Comparison of Single-Nucleotide Polymorphisms with Short Tandem Repeats and Allozymes

References

• Aebersold , P. B. , Winans , G. A. , Teel , D. J. , Milner , G. B. and Utter , F. M. 1987 . Manual for starch gel electrophoresis: A method for the detection of genetic variation. NOAA Technical Report NMFS 61
   Google Scholar
• Akey , J. M. , Zhang , K. , Xiong , M. and Jin , L. 2003 . The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium . Molecular Biology and Evolution , 20 : 232 – 242 .
   PubMed Web of Science ®Google Scholar
• Allendorf , F. W. and Seeb , L. W. 2000 . Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers . Evolution , 54 : 640 – 651 .
   PubMed Web of Science ®Google Scholar
• Anderson , T. J. , Nair , S. , Sudimack , D. , Williams , J. T. , Mayxay , M. , Newton , P. N. , Guthmann , J. P. , Smithuis , F. M. , Tran , T. H. , van den Broek , I. V. , White , N. J. and Nosten , F. 2005 . Geographical distribution of selected and putatively neutral SNPs in Southeast Asian malaria parasites . Molecular Biology and Evolution , 22 : 2362 – 2374 .
   PubMed Web of Science ®Google Scholar
• Banks , M. A. , Blouin , M. S. , Baldwin , B. A. , Rashbrook , V. K. , Fitzgerald , H. A. , Blankenship , S. M. and Hedgecock , D. 1999 . Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha) . Journal of Heredity , 90 : 281 – 288 .
   Web of Science ®Google Scholar
• Beaumont , M. A. and Nichols , R. A. 1996 . Evaluating loci for use in the genetic analysis of population structure . Proceedings of the Royal Society London B , 263 : 1619 – 1626 .
   Web of Science ®Google Scholar
• Brumfield , R. T. , Beerli , P. , Nickerson , D. A. and Edwards , S. V. 2003 . The utility of single nucleotide polymorphisms in inferences of population history . Trends in Ecology and Evolution , 18 : 249 – 256 .
   Web of Science ®Google Scholar
• Cappuccio , I. , Pariset , L. , Ajmone-Marsan , P. , Dunner , S. , Cortes , O. , Erhardt , G. , Lühken , G. , Gutscher , K. , Joost , S. , Nijman , I. J. , Lenstra , J. A. , England , P. R. , Zundel , S. , Obexer-Ruff , G. , Beja-Pereira , A. , Valentini , A. and Econogene Consortium . 2006 . Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds . Molecular Ecology Notes , 6 : 992 – 997 .
   Web of Science ®Google Scholar
• Cavalli-Sforza , L. L. and Edwards , A. W. 1967 . Phylogenetic analysis: Models and estimation procedures . American Journal of Human Genetics , 19 : 233 – 257 .
   PubMed Web of Science ®Google Scholar
• Cockerham , C. C. and Weir , B. S. 1993 . Estimation of gene flow from F-statistics . Evolution , 47 : 855 – 863 .
   PubMed Web of Science ®Google Scholar
• Estoup , A. , Presa , P. , Krieg , F. , Vaiman , D. and Guyomard , R. 1993 . (CT) n and (GT) n microsatellites: A new class of genetic markers for Salmo trutta L. (brown trout) . Heredity , 71 : 488 – 496 .
   PubMed Web of Science ®Google Scholar
• Excoffier , L. , Laval , G. and Balding , D. 2003 . Gametic phase estimation over large genomic regions using an adaptive window approach . Human Genomics , 1 : 7 – 19 .
   PubMedGoogle 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 . Available: la-press.com. (October 2007)
   PubMed Web of Science ®Google Scholar
• Excoffier , L. , Smouse , P. E. and Quattro , J. M. 1992 . Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data . Genetics , 131 : 479 – 491 .
   PubMed Web of Science ®Google Scholar
• Felsenstein , J. 1989 . PHYLIP: Phylogeny inference package (version 3.2) . Cladistics , 5 : 164 – 166 .
   Google Scholar
• Ford , M. J. 2000 . Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among Chinook salmon (Oncorhynchus tshawytscha) populations . Molecular Ecology , 9 : 843 – 855 .
   PubMed Web of Science ®Google Scholar
• Guo , S. W. and Thompson , E. A. 1992 . Performing the exact test of Hardy-Weinberg proportion for multiple alleles . Biometrics , 48 : 361 – 372 .
   PubMed Web of Science ®Google Scholar
• Heath , D. D. , Shrimpton , J. M. , Hepburn , R. I. , Jamieson , S. K. , Brode , S. K. and Docker , M. F. 2006 . Population structure and divergence using microsatellite and gene locus markers in Chinook salmon (Oncorhynchus tshawytscha) populations . Canadian Journal of Fisheries and Aquatic Sciences , 63 : 1370 – 1383 .
   Web of Science ®Google Scholar
• Hedrick , P. W. 2005 . A standardized genetic differentiation measure . Evolution , 59 : 1633 – 1638 .
   PubMed Web of Science ®Google Scholar
• Hedrick , P. W. 1999 . Perspective: Highly variable loci and their interpretation in evolution and conservation . Evolution , 53 : 313 – 318 .
   PubMed Web of Science ®Google Scholar
• IUBMB (International Union of Biochemistry and Molecular Biology) . 1992 . Enzyme nomenclature 1992 San Diego , California : Academic Press .
   Google Scholar
• Kruglyak , L. 1997 . The use of a genetic map of biallelic markers in linkage studies . Nature Genetics , 17 : 21 – 24 .
   PubMed Web of Science ®Google Scholar
• Kwok , P. Y. 2003 . Single nucleotide polymorphisms—methods and protocols Totowa , New Jersey : Humana Press .
   Google Scholar
• Luikart , G. , England , P. R. , Tallmon , D. , Jordan , S. and Taberlet , P. 2003 . The power and promise of population genomics: From genotyping to genome typing . Nature Reviews Genetics , 4 : 981 – 994 .
   PubMed Web of Science ®Google Scholar
• Mantel , N. 1967 . The detection of disease clustering and a generalized regression approach . Cancer Research , 27 : 209 – 220 .
   PubMed Web of Science ®Google Scholar
• Miller , K. M. , Withler , R. E. and Beacham , T. D. 1997 . Molecular evolution at MHC genes in two populations of Chinook salmon Oncorhynchus tshawytscha . Molecular Ecology , 6 : 937 – 954 .
   PubMed Web of Science ®Google Scholar
• Morin , P. A. , Luikart , G. , Wayne , R. K. and SNP workshop group . 2004. SNPs in ecology, evolution and conservation . Trends in Ecology and Evolution , 19 208 – 216 . and
   Web of Science ®Google Scholar
• Mountain , J. L. and Cavalli-Sforza , L. L. 1994 . Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms . Proceedings of the National Academy of Sciences of the USA , 91 : 6515 – 6519 .
   PubMed Web of Science ®Google Scholar
• Narum , S. R. , Powell , M. S. and Talbot , A. J. 2004 . A distinctive microsatellite locus that differentiates ocean-type from stream-type Chinook salmon in the interior Columbia River basin . Transactions of the American Fisheries Society , 133 : 1051 – 1055 .
   Web of Science ®Google Scholar
• Nei , M. 1973 . Analysis of gene diversity in subdivided populations . Proceedings of the National Academy of Sciences of the USA , 70 : 3321 – 3323 .
   PubMed Web of Science ®Google Scholar
• Nelson , R. J. and Beacham , T. D. 1999 . Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon . Animal Genetics , 30 : 228 – 229 .
   PubMed Web of Science ®Google Scholar
• Nelson , R. J. , Beacham , T. D. and Small , M. P. 1998 . Microsatellite analysis of the population structure of a Vancouver Island sockeye salmon (Oncorhynchus nerka) stock complex using nondenaturing gel electrophoresis . Molecular Marine Biology and Biotechnology , 7 : 312 – 319 .
   PubMedGoogle Scholar
• Nielsen , R. and Signorovitch , J. 2003 . Correcting for ascertainment biases when analyzing SNP data: Applications to the estimation of linkage disequilibrium . Theoretical Population Biology , 63 : 245 – 255 .
   PubMed Web of Science ®Google Scholar
• Ohta , T. 1982 . Linkage disequilibrium with the island model . Genetics , 101 : 139 – 155 .
   PubMed Web of Science ®Google Scholar
• Olsen , J. B. , Wilson , S. L. , Kretschmer , E. J. , Jones , K. C. and Seeb , J. E. 2000 . Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon . Molecular Ecology , 9 : 2185 – 2187 .
   PubMed Web of Science ®Google Scholar
• Rasmussen , C. , Ostberg , C. O. , Clifton , D. R. and Rodriguez , R. J. 2003 . Identification of a genetic marker that discriminates ocean-type and stream-type Chinook salmon in the Columbia River basin . Transactions of the American Fisheries Society , 132 : 131 – 142 .
   Web of Science ®Google Scholar
• Raymond , M. and Rousset , F. 1997 . GENEPOP (version 3.1b), an updated version of GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism . Journal of Heredity , 86 : 248 – 249 .
   Web of Science ®Google Scholar
• Rice , W. R. 1989 . Analyzing tables of statistical tests . Evolution , 43 : 223 – 225 .
   PubMed Web of Science ®Google Scholar
• Saitou , N. and Nei , M. 1987 . The neighbor-joining method: A new method for reconstructing phylogenetic trees . Molecular Biology and Evolution , 4 : 406 – 425 .
   PubMed Web of Science ®Google Scholar
• Schlötterer , C. 2004 . The evolution of molecular markers: Just a matter of fashion? . Nature Reviews Genetics , 5 : 63 – 69 .
   PubMed Web of Science ®Google Scholar
• Schlötterer , C. and Harr , B. 2002 . Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster . Molecular Ecology , 11 : 947 – 950 .
   PubMed Web of Science ®Google Scholar
• Scribner , K. T. , Crane , P. A. , Spearman , W. J. and Seeb , L. W. 1998 . DNA and allozyme markers provide concordant estimates of population differentiation: Analyses of U.S. and Canadian populations of Yukon River fall-run chum salmon (Oncorhynchus keta) . Canadian Journal of Fisheries and Aquatic Sciences , 55 : 1748 – 1758 .
   Web of Science ®Google Scholar
• Scribner , K. T. , Gust , J. R. and Fields , R. L. 1996 . Isolation and characterization of novel salmon microsatellite loci: Cross-species amplification and population genetic applications . Canadian Journal of Fisheries and Aquatic Sciences , 53 : 833 – 841 .
   Web of Science ®Google Scholar
• Smith , C. T. , Elfstrom , C. M. , Seeb , J. E. and Seeb , L. W. 2005a . Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon . Molecular Ecology , 14 : 4193 – 4203 .
   PubMed Web of Science ®Google Scholar
• Smith , C. T. , Seeb , J. E. , Schwenke , P. and Seeb , L. W. 2005b . Use of the 5′-nuclease reaction for single nucleotide polymorphism genotyping in Chinook salmon . Transactions of the American Fisheries Society , 134 : 207 – 217 .
   Web of Science ®Google Scholar
• Teel , D. J. , Crane , P. A. , Guthrie , C. M. , Marshall , A. R. , Van Doornik , D. M. , Templin , W. D. , Varnavskaya , N. V. and Seeb , L. W. 1999 . Comprehensive allozyme database discriminates Chinook salmon around the Pacific Rim Anchorage : Alaska Department of Fish and Game, Division of Commercial Fisheries . North Pacific Anadromous Fish Commission Document 440
   Google Scholar
• Teel , D. J. , Milner , G. B. , Winans , G. A. and Grant , W. S. 2000 . Genetic population structure and origin of life history types in Chinook salmon in British Columbia, Canada . Transactions of the American Fisheries Society , 129 : 194 – 209 .
   Web of Science ®Google Scholar
• Utter , F. W. , Milner , G. , Stahl , G. and Teel , D. 1989 . Genetic population structure of Chinook salmon, Oncorhynchus tshawytscha, in the Pacific Northwest . U.S. National Marine Fisheries Service Fishery Bulletin , 87 : 239 – 264 .
   Web of Science ®Google Scholar
• Waples , R. S. , Teel , D. J. , Myers , J. M. and Marshall , A. R. 2004 . Life-history divergence in Chinook salmon: Historic contingency and parallel evolution . Evolution , 58 : 386 – 403 .
   PubMed Web of Science ®Google Scholar
• Weir , B. S. and Cockerham , C. C. 1984 . Estimating F-statistics for the analysis of population structure . Evolution , 38 : 1358 – 1370 .
   PubMed Web of Science ®Google Scholar
• Wright , S. 1951 . The genetical structure of populations . Annals of Eugenics , 15 : 323 – 354 .
   PubMedGoogle Scholar