Genetic Evaluation of Isolated Populations for Use in Reintroductions Reveals Significant Genetic Bottlenecks in Potential Stocks of Sacramento Perch

References

• Belkhir , K. , Borsa , P. , Chikhi , L. , Raufaste , N. and Bonhomme , F. 2004 . GENETIX 4.05, logiciel sous Windows pour la génétique des populations Montpellier, France : Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II .
   Google Scholar
• Cavalli-Sforza , L. L. and Edwards , A. W. F. 1967 . Phylogenetic analysis: Models and estimation procedures . Evolution , 21 : 550 – 570 .
   PubMed Web of Science ®Google Scholar
• Cornuet , J. M. and Luikart , G. 1996 . Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data . Genetics , 144 : 2001 – 2014 .
   PubMed Web of Science ®Google Scholar
• Coughlin , W. D. , Echelle , A. A. , Van Den Bussche , R. A. , Cofer , L. M. and Fisher , W. L. 2003 . Genetic structure of spotted bass (Micropterus punctulatus) in the Red and Arkansas River basins: Microsatellite and mitochondrial DNA variation . Southwestern Naturalist , 48 : 526 – 533 .
   Web of Science ®Google Scholar
• DeYoung , R. W. , Demarais , S. , Honeycutt , R. L. , Rooney , A. P. , Gonzales , R. A. and Gee , K. L. 2003 . Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi . Molecular Ecology , 12 : 3237 – 3252 .
   PubMed Web of Science ®Google Scholar
• Edmands , S. 1999 . Heterosis and outbreeding depression in interpopulation crosses spanning a wide range of divergence . Evolution , 53 : 1757 – 1768 .
   PubMed Web of Science ®Google Scholar
• Edmands , S. and Timmerman , C. C. 2003 . Modeling factors affecting the severity of outbreeding depression . Conservation Biology , 17 : 883 – 892 .
   Web of Science ®Google Scholar
• England , P. R. , Cornuet , J. M. , Berthier , P. , Tallmon , D. A. and Luikart , G. 2006 . Estimating effective population size from linkage disequilibrium: Severe bias in small samples . Conservation Genetics , 7 : 303 – 308 .
   Web of Science ®Google Scholar
• Falk , D. A. , Knapp , E. and Guerrant , E. O. 2001 . An introduction to restoration genetics Tucson, Arizona : Society for Ecological Restoration for U.S. Environmental Protection Agency, Plant Conservation Alliance, and Bureau of Land Management . Prepared by the
   Google Scholar
• Fischer , M. and Matthies , D. 1997 . Mating structure and inbreeding and outbreeding depression in the rare plant Gentianella germanica (Gentianaceae) . American Journal of Botany , 84 : 1685 – 1692 .
   PubMed Web of Science ®Google Scholar
• Franklin , I. R. 1980 . “ Evolutionary change in small populations ” . In Conservation biology: An evolutionary–ecological perspective Edited by: Soulé , M. E. and Wilcox , B. A. 135 – 149 . Sunderland, Massachusetts : Sinauer .
   Google Scholar
• Garza , J. C. and Williamson , E. G. 2001 . Detection of reduction in population size using data from microsatellite loci . Molecular Ecology , 10 : 305 – 318 .
   PubMed Web of Science ®Google Scholar
• Gharrett , A. J. , Smoker , W. W. , Reisenbichler , R. R. and Taylor , S. G. 1999 . Outbreeding depression in hybrids between odd- and even-brood year pink salmon . Aquaculture , 173 : 117 – 129 .
   Web of Science ®Google Scholar
• Gobalet , K. W. , Schulz , P. D. , Wake , T. A. and Siefkin , N. 2004 . Archaeological perspectives on native American fisheries of California, with emphasis on steelhead and salmon . Transactions of the American Fisheries Society , 133 : 801 – 833 .
   Web of Science ®Google Scholar
• Goudet , J. 2001 . FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3) Switzerland : University of Lausanne . Available: www2.unil.ch/popgen/softwares/fstat.htm. (July 2005)
   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
• Hill , W. G. 1981 . Estimation of effective population size from data on linkage disequilibrium . Genetical Research , 38 : 209 – 216 .
   Web of Science ®Google Scholar
• Holsinger , K. E. and Vitt , P. 1997 . “ The future of conservation biology: What's a geneticist to do? ” . In The ecological basis of conservation: Heterogeneity, ecosystems, and biodiversity Edited by: Pickett , S. T. 202 – 216 . New York : Chapman and Hall .
   Google Scholar
• IUBMB (International Union of Biochemistry and Molecular Biology) . 1992 . Enzyme nomenclature 1992 San Diego, California : Academic Press .
   Google Scholar
• Kalinowski , S. T. 2004 . Counting alleles with rarefaction: Private alleles and hierarchical sampling designs . Conservation Genetics , 5 : 539 – 543 .
   Web of Science ®Google Scholar
• Kalinowski , S. T. 2005 . HP-RARE 1.0: A computer program for performing rarefaction on measures of allelic richness . Molecular Ecology Notes , 5 : 187 – 189 .
   Web of Science ®Google Scholar
• Kumar , S. , Tamura , K. and Nei , M. 2004 . MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment . Briefings in Bioinformatics , 5 : 150 – 163 .
   PubMed Web of Science ®Google Scholar
• Lambert , D. M. , King , T. , Shepherd , L. D. , Livingston , A. , Anderson , S. and Craig , J. L. 2005 . Serial population bottlenecks and genetic variation: Translocated populations of the New Zealand Saddleback (Philesturnus carunculatus rufusater) . Conservation Genetics , 6 : 1 – 14 .
   Web of Science ®Google Scholar
• Lande , R. 1995 . Mutation and conservation . Conservation Biology , 9 : 782 – 791 .
   Web of Science ®Google Scholar
• Luikart , G. , Allendorf , F. W. , Cornuet , J. M. and Sherwin , W. B. 1998 . Distortion of allele frequency distributions provides a test for recent population bottlenecks . Journal of Heredity , 89 : 238 – 247 .
   PubMed Web of Science ®Google Scholar
• Lutz-Carrillo , D. J. , Nice , C. C. , Bonner , T. H. , Forstner , M. R. J. and Fries , L. T. 2006 . Admixture analysis of Florida largemouth bass and northern largemouth bass using microsatellite loci . Transactions of the American Fisheries Society , 135 : 779 – 791 .
   Web of Science ®Google Scholar
• Marchetti , M. P. 1999 . An experimental study of competition between the native Sacramento perch (Archoplites interruptus) and introduced bluegill (Lepomis macrochirus) . Biological Invasions , 1 : 55 – 65 .
   Google Scholar
• Maudet , C. , Miller , C. , Bassano , B. , Breitenmoser-Würsten , C. , Gauthier , D. , Obexer-Ruff , G. , Michallet , J. , Taberlet , P. and Luikart , G. 2002 . Microsatellite DNA and recent statistical methods in wildlife conservation management: Applications in Alpine ibex [Capra ibex (ibex)] . Molecular Ecology , 11 : 421 – 436 .
   PubMed Web of Science ®Google Scholar
• Moyle , P. B. 2002 . Inland fishes of California, , 2nd edition Berkeley : University of California Press .
   Google Scholar
• Moyle , P. B. , Pine , R. , Brown , L. R. , Hanson , C. H. , Herbold , B. , Lentz , K. M. , Meng , L. , Smith , J. J. , Sweetnam , D. A. and Winternitz , L. 1996 . Recovery plan for the Sacramento–San Joaquin Delta native fishes Portland, Oregon : U.S. Fish and Wildlife Service .
   Google Scholar
• Neff , B. D. , Fu , P. and Gross , M. R. 1999 . Microsatellite evolution in sunfish (Centrarchidae) . Canadian Journal of Fisheries and Aquatic Sciences , 56 : 1198 – 1205 .
   Web of Science ®Google Scholar
• Nei , M. 1972 . Genetic distance between populations . American Naturalist , 106 : 283 – 292 .
   Web of Science ®Google Scholar
• O'Grady , J. J. , Brook , B. W. , Reed , D. H. , Ballou , J. D. , Tonkyn , D. W. and Frankham , R. 2006 . Realistic levels of inbreeding depression strongly affect extinction risk in wild populations . Biological Conservation , 133 : 42 – 51 .
   Web of Science ®Google Scholar
• Peer , K. and Taborsky , M. 2004 . Female ambrosia beetles adjust their offspring sex ratio according to outbreeding opportunities for their sons . Journal of Evolutionary Biology , 17 : 257 – 264 .
   PubMed Web of Science ®Google Scholar
• Peer , K. and Taborsky , M. 2005 . Outbreeding depression, but no inbreeding depression in haplodiploid ambrosia beetles with regular sibling mating . Evolution , 59 : 317 – 323 .
   PubMed Web of Science ®Google Scholar
• Perkins , D. L. , Fitzsimons , J. D. , Marsden , J. E. , Krueger , C. C. and May , B. 1995 . Differences in reproduction among hatchery strains of lake trout at eight spawning areas in Lake Ontario: Genetic evidence from mixed-stock analysis . Journal of Great Lakes Research , 21 : 364 – 374 .
   Web of Science ®Google Scholar
• Petit , R. J. , El Mousadik , A. and Pons , O. 1998 . Identifying populations for conservation on the basis of genetic markers . Conservation Biology , 12 : 844 – 855 .
   Web of Science ®Google Scholar
• Piry , S. , Luikart , G. and Cornuet , J. M. 1999 . BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data . Journal of Heredity , 90 : 502 – 503 .
   Web of Science ®Google Scholar
• Pyron , M. 1999 . Relationships between geographical range size, body size, local abundance, and habitat breadth in North American suckers and sunfishes . Journal of Biogeography , 26 : 549 – 558 .
   Web of Science ®Google Scholar
• Ramey , R. R. , Luikart , G. and Singer , F. J. 2000 . Genetic bottlenecks resulting from restoration efforts: The case of bighorn sheep in Badlands National Park . Restoration Ecology , 8 : 85 – 90 .
   Web of Science ®Google Scholar
• Raymond , M. and Rousset , F. 1995 . Genepop (version-1.2): Population-genetics software for exact tests and ecumenicism . Journal of Heredity , 86 : 248 – 249 .
   Web of Science ®Google Scholar
• Reed , D. H. and Frankham , R. 2003 . Correlation between fitness and genetic diversity . Conservation Biology , 17 : 230 – 237 .
   Web of Science ®Google Scholar
• Reed , D. H. , Nicholas , A. C. and Stratton , G. E. 2007a . Genetic quality of individuals impacts population dynamics . Animal Conservation , 10 : 275 – 283 .
   Web of Science ®Google Scholar
• Reed , D. H. , Nicholas , A. C. and Stratton , G. E. 2007b . Inbreeding levels and prey abundance interact to determine fecundity in natural populations of two species of wolf spider . Conservation Genetics , 8 : 1061 – 1071 .
   Web of Science ®Google Scholar
• Rice , W. R. 1989 . Analyzing tables of statistical tests . Evolution , 43 : 223 – 225 .
   PubMed Web of Science ®Google Scholar
• Robichaux , R. H. , Friar , E. A. and Mount , D. W. 1997 . Molecular genetic consequences of a population bottleneck associated with reintroduction of the Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense [Asteraceae]) . Conservation Biology , 11 : 1140 – 1146 .
   Web of Science ®Google Scholar
• Rodriguez-Ramilo , S. T. , Moran , P. and Caballero , A. 2006 . Relaxation of selection with equalization of parental contributions in conservation programs: An experimental test with Drosophila melanogaster . Genetics , 172 : 1043 – 1054 .
   PubMed Web of Science ®Google Scholar
• Rowe , G. , Beebee , T. J. C. and Burke , T. 1999 . Microsatellite heterozygosity, fitness and demography in natterjack toads Bufo calamita . Animal Conservation , 2 : 85 – 92 .
   Web of Science ®Google Scholar
• Schwartz , R. S. and May , B. 2004 . Characterization of microsatellite loci in Sacramento perch (Archoplites interruptus) . Molecular Ecology Notes , 4 : 694 – 697 .
   Web of Science ®Google Scholar
• Skinner , J. 1962 . A historical review of the fish and wildlife resources of the San Francisco Bay area Sacramento : California Department of Fish and Game, Water Projects Branch . Report 1
   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
• Stepien , C. A. , Murphy , D. J. and 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 .
   PubMed Web of Science ®Google Scholar
• Stockwell , C. A. , Mulvey , M. and Vinyard , G. L. 1996 . Translocations and the preservation of allelic diversity . Conservation Biology , 10 : 1133 – 1141 .
   Web of Science ®Google Scholar
• Waples , R. S. 1991 . Genetic methods for estimating the effective size of cetacean populations . International Whaling Commission Report of the Commission , 13 : 279 – 300 .
   Google Scholar
• Waples , R. S. 2006 . A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci . Conservation Genetics , 7 : 167 – 184 .
   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
• Williamson-Natesan , E. G. 2005 . Comparison of methods for detecting bottlenecks from microsatellite loci . Conservation Genetics , 6 : 551 – 562 .
   Web of Science ®Google Scholar
• Wright , S. 1965 . The interpretation of population structure by F-statistics with special regard to systems of mating . Evolution , 19 : 395 – 420 .
   Web of Science ®Google Scholar
• Zhu , B. , Zhou , F. , Cao , H. , Shao , Z. , May , B. and Chang , J. 2002 . Analysis of genetic variation in the Chinese sturgeon, Acipenser sinensis: Estimating the contribution of artificially produced larvae in a wild population . Journal of Applied Ichthyology , 18 : 301 – 306 .
   Web of Science ®Google Scholar