Timing of Population Fragmentation in a Vulnerable Minnow, the Umpqua Chub, and the Role of Nonnative Predators

REFERENCES

• Allendorf , F. W. , Hohenlohe , P. A. and Luikart , G. 2010 . Genomics and the future of conservation genetics . Nature Reviews Genetics , 11 : 697 – 709 .
   PubMed Web of Science ®Google Scholar
• Ardren , W. R. , Amata , L. , Whelan , J. and DeHaan , P. W. 2007 . Characterization of 16 highly variable tetranucleotide microsatellite loci for Oregon Chub (Oregonichthys crameri) and cross amplification in Umpqua Chub (O. kalawatseti) . Molecular Ecology Notes , 7 : 808 – 810 .
   Web of Science ®Google Scholar
• 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 5171, Université de Montpellier II .
   Google Scholar
• Briggs , G. G. 1994 . Coastal crossing of the elastic strain zero-isobase, Cascadia margin, south-central Oregon coast. Master's thesis , Portland , Oregon : Portland State University .
   Google Scholar
• Cade , B. S. and Noon , B. R. 2003 . A gentle introduction to quantile regression for ecologists . Frontiers in Ecology and the Environment , 1 : 412 – 420 .
   Web of Science ®Google Scholar
• Cade , B. S. and Richards , J. D. 2005 . User manual for Blossom statistical software , Reston , Virginia : U.S. Geological Survey . Open-File Report 2005-1353, Available: www.fort.usgs.gov/products/software/blossom/blossom.asp. (April 2012)
   Google Scholar
• Cade , B. S. , Terrell , J. W. and Schroeder , R. L. 1999 . Estimating effects of limiting factors with regression quantiles . Ecology , 80 : 311 – 323 .
   Web of Science ®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
• DeHaan , P. W. , Scheerer , P. D. , Rhew , R. and Ardren , W. R. 2012 . Analyses of genetic variation in populations of Oregon Chub, a threatened floodplain minnow in a highly altered environment . Transactions of the American Fisheries Society , 141 : 533 – 549 .
   Web of Science ®Google Scholar
• Dunham , J. B. , Cade , B. S. and Terrell , J. W. 2002 . Influences of spatial and temporal variation on fish–habitat relationships defined by regression quantiles . Transactions of the American Fisheries Society , 131 : 86 – 98 .
   Web of Science ®Google Scholar
• Estoup , A. 1998 . “ Microsatellites and minisatellites for molecular ecology: theoretical and empirical considerations ” . In Advances in molecular ecology , Edited by: Carvalho , G. R. and Angers , B. 55 – 86 . Amsterdam : IOS Press .
   Google Scholar
• Evanno , G. , Regnaut , S. and Goudet , J. 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 Heckel , G. 2006 . Computer programs for population genetics data analysis: a survival guide . Nature Review Genetics , 7 : 745 – 758 .
   PubMed Web of Science ®Google Scholar
• Felsenstein , J. 2005 . PHYLIP (phylogenetic inference package), version 3.6 , Seattle : Department of Genome Sciences, University of Washington .
   Google Scholar
• Guo , Q. , Brown , J. H. and Enquist , B. J. 1998 . Using constraint lines to characterize plant performance . Oikos , 83 : 237 – 245 .
   Web of Science ®Google Scholar
• Hey , J. and Nielsen , R. 2004 . Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis . Genetics , 167 : 747 – 760 .
   PubMed Web of Science ®Google Scholar
• Hey , J. and Nielsen , R. 2007 . Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics . Proceedings of the National Academy of Sciences of the USA , 104 : 2785 – 2790 .
   PubMed Web of Science ®Google Scholar
• Ivanova , N. V. , deWaard , J. R. and Hebert , P. D. N. 2006 . An inexpensive, automation-friendly protocol for recovering high-quality DNA . Molecular Ecology Notes , 6 : 998 – 1002 .
   Web of Science ®Google Scholar
• Jakobsson , M. and Rosenberg , N. A. 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
• Jensen , J. L. , Bohonak , A. J. and Kelley , S. T. 2005 . Isolation by distance, web service. BMC Genetics . 6 : 13 [online serial]
   Google Scholar
• Lampman , B. H. 1946 . The coming of the pond fishes , Portland , Oregon : Binfords and Mort .
   Google Scholar
• Markle , D. F. , Pearsons , T. N. and Bills , D. T. 1991 . Natural history of Oregonichthys (Pisces: Cyprinidae), with a description of a new species from the Umpqua River of Oregon . Copeia , 1991 : 277 – 293 .
   Google Scholar
• Mesquita , N. , Hänfling , B. , Carvalho , G. R. and Coelho , M. M. 2005 . Phylogeography of the cyprinid Squalius aradensis and implications for conservation of the endemic freshwater fauna of southern Portugal . Molecular Ecology , 14 : 1939 – 1954 .
   PubMed Web of Science ®Google Scholar
• Nelson , A. R. 1992 . “ Holocene tidal-marsh stratigraphy in south-central Oregon: evidence for localized sudden submergence in the Cascadia subduction zone ” . In Quaternary coasts of the United States: marine and lacustrine systems , Edited by: Fletcher , C. H. III and Wehmiller , J. F. 287 – 301 . Tulsa , Oklahoma : Society for Sedimentary Geology . Special Publication 48
   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
• Parker , K. M. , Sheffer , R. J. and Hedrick , P. W. 1999 . Molecular variation and evolutionarily significant units in the endangered Gila topminnow . Conservation Biology , 13 : 108 – 116 .
   Web of Science ®Google Scholar
• Pritchard , J. K. , Stephens , M. and Donnelly , P. 2000 . Inference of population structure using multilocus genotype data . Genetics , 155 : 945 – 959 .
   PubMed Web of Science ®Google Scholar
• Raymond , M. and Rousset , F. 1995 . An exact test for population differentiation . Evolution , 49 : 1280 – 1283 .
   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
• Rieman , B. E. and Allendorf , F. W. 2001 . Effective population size and genetic conservation criteria for bull trout . North American Journal of Fisheries Management , 21 : 756 – 764 .
   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
• Scheerer , P. D. and McDonald , P. J. 2003 . Age, growth and timing of spawning of an endangered minnow, the Oregon Chub (Oregonichthys crameri), in the Willamette basin, Oregon . Northwestern Naturalist , 84 : 68 – 79 .
   Google Scholar
• Simon , D. C. and Markle , D. F. 1999 . Evidence of a relationship between Smallmouth Bass (Micropterus dolomeiu) and decline of Umpqua Chub (Oregonichthys kalawatseti) in the Umpqua basin, Oregon . Northwestern Naturalist , 80 : 110 – 113 .
   Google Scholar
• Sousa , V. , Penha , F. , Collares-Pereira , M. J. , Chikhi , L. and Coelho , M. M. 2008 . Genetic structure and signature of population decrease in the critically endangered freshwater cyprinid Chondrostoma lusitanicum . Conservation Genetics , 9 : 791 – 805 .
   Web of Science ®Google Scholar
• Terwilliger , M. R. , Reece , T. and Markle , D. F. 2010 . Historic and recent age structure and growth of endangered Lost River and shortnose suckers in Upper Klamath Lake, Oregon . Environmental Biology of Fishes , 89 : 239 – 252 .
   Web of Science ®Google Scholar
• USFWS (U.S. Fish and Wildlife Service) . 2010 . Endangered and threatened wildlife and plants; reclassification of the Oregon Chub from endangered to threatened . Federal Register 75 , 78 ( 23 April 2010 ) : 21179 – 21189 .
   Google Scholar
• Waples , R. S. and Gaggiotti , O. 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 Cockerham , C. C. 1984 . Estimating F-statistics for the analysis of population structure . Evolution , 38 : 1358 – 1370 .
   PubMed Web of Science ®Google Scholar
• Witter , R. C. , Kelsey , H. M. and Hemphill-Haley , E. 2003 . Great Cascadia earthquakes and tsunamis of the past 6700 years, Coquille River estuary, southern coastal Oregon . Geological Society of America Bulletin , 115 : 1289 – 1306 .
   Web of Science ®Google Scholar