Moderately and Highly Polymorphic Microsatellites Provide Discordant Estimates of Population Divergence in Sockeye Salmon, Oncorhynchus nerka
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Mutation rate can vary widely among microsatellite loci. This variation may cause discordant single-locus and multi-locus estimates of FST, the commonly used measure of population divergence. We use 16 microsatellite and five allozyme loci from 14 sockeye salmon populations to address two questions about the affect of mutation rate on estimates of FST: (1) does mutation rate influence FST estimates from all microsatellites to a similar degree relative to allozymes?; (2) does the influence of mutation rate on FST estimates from microsatellites vary with geographic scale in spatially structured populations? For question one we find that discordant estimates of FST among microsatellites as well as between the two marker classes are correlated with mean within-population heterozygosity (HS) and thus are likely due to differences in mutation rate. Highly polymorphic microsatellites (HS > 0.84) provide significantly lower estimates of FST than moderately polymorphic microsatellites and allozymes (HS < 0.60). Estimates of FST from binned allele frequency data and RST provide more accurate measures of population divergence for highly polymorphic but not for moderately polymorphic microsatellites. We conclude it is more important to pool loci of like HS rather than marker class when estimating FST. For question two we find the FST values for moderately and highly polymorphic loci, while significantly different, are positively correlated for geographically proximate but not geographically distant population pairs. These results are consistent with expectations from the equilibrium approximation of Wright's infinite island model and confirm that the influence of mutation on estimates of FST can vary in spatially structured populations presumably because the rate of migration varies inversely with geographic scale.
- ABI (Applied Biosystems Inc.) 1996a. GeneScan 672 Users Manual Rev. A. Perkin-Elmer Corp., Foster City, CA. 337 pp.
- ABI (Applied Biosystems Inc.) 1996b. Genotyper 2.0 Users Manual. Perkin-Elmer Corp., Foster City, CA. 75 pp.
- Allendorf, F.W. & L.W. Seeb. 2000. Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54: 640–651.
- Balloux, F., H. Brünner, N. Lugon-Moulin, J. Hausser & J. Goudet. 2000. Micro-satellites can be misleading: An empirical and simulation study. Evolution 54: 1414–1422.
- Balloux, F. & J. Goudet. 2002. Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol. Ecol. 11: 771–783.
- Bowcock, A.M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J.R. Kidd & L.L. Cavalli-Sforza. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455–457. CrossRef
- Buonaccorsi,V.P., J.R. McDowell & J.E. Graves. 2001. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans). Mol. Ecol. 10: 1179–1196. CrossRef
- Charlesworth, B. 1998. Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15: 538–543.
- Estoup, A., F. Rousset, Y. Michalakis, J.-M. Cornuet, M. Adriamanga & R. Guyomard. 1998. Comparative analysis of microsatellite and allozyme markers: A case study investigating microgeographic differentiation in brown trout (Salmo trutta). Mol. Ecol. 7: 339–353. CrossRef
- Freville, H., F. Justy & I. Olvieri. 2001. Comparative allozyme and microsatellite population structure in a narrow endemic plant species, Centaurea corymbosa Pourret (Asteraceae). Mol. Ecol. 10: 879–889. CrossRef
- Goodman, S.J. 1997. RST Calc: A collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol. Ecol. 6: 881–886. CrossRef
- Hedrick, P.W. 1999. Perspectives: Highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313–318.
- Hendry, A.P., J.K. Wenburg, P. Bentzen, E.C. Volk & T.P. Quinn. 2000. Rapid evolution of reproductive isolation in the wild: Evidence from introduced salmon. Science 290: 516–518. CrossRef
- Hutchison, D.W. & A.R. Templeton. 1999. Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53: 1898–1914.
- Jarne, P. & J.L. Lagoda. 1996. Microsatellites, from molecules to populations and back. TREE 11: 424–429.
- Landry, C. & L. Bernatchez. 2001. Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar). Mol. Ecol. 10: 2525–2539. CrossRef
- Nei, M. 1987. Molecular Evolutionary Genetics, Columbia University Press, New York. 512 pp.
- Neigel, J.E. 2002. Is FST obsolete? Conserv. Genet. 3: 167–173. CrossRef
- Olsen, J.B., S.L.Wilson, E.J. Kretschmer, K.C. Jones & J.E. Seeb. 2000. Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon. Mol. Ecol. 9: 2155–2234.
- Rice, W.R. 1989. Analyzing tables of statistical tests. Evolution 43: 223–225.
- Seeb, L.W., C. Habicht, W.D. Templin, K.E. Tarbox, R.Z. Davis, L.K. Brannian & J.E. Seeb. 2000. Genetic diversity of sockeye salmon of Cook Inlet, Alaska, and its application to management of populations affected by the Exxon Valdez oil spill. Trans. Amer. Fish. Soc. 129: 1223–1249. CrossRef
- Shaw, P.W., C. Turan, J.M. Wright, M. O'Connell & G.R. Carvalho. 1999. Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analysis. Heredity 83: 4990–4499. CrossRef
- Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457–462.
- Wood, C.C. 1995. Life history variation and population structure in sockeye salmon. pp. 195–216. In: J.L. Nielsen (ed.) Evolution and the Aquatic Ecosystem: Defining Unique Units of Population Conservation, American Fisheries Society Symposium 17, Bethesda, Maryland.
- Wright, S. 1969. Evolution and the Genetics of Populations, The Theory of Gene Frequencies, The University of Chicago Press, Chicago, Illinois. 511 pp.
- Moderately and Highly Polymorphic Microsatellites Provide Discordant Estimates of Population Divergence in Sockeye Salmon, Oncorhynchus nerka
Environmental Biology of Fishes
Volume 69, Issue 1-4 , pp 261-273
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- Online ISSN
- Kluwer Academic Publishers
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- population genetics
- population structure
- Pacific salmon
- Author Affiliations
- 1. Gene Conservation Laboratory, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, AK, 99518-1599, U.S.A.
- 2. Division of Natural Resources, U.S. Fish & Wildlife Service, 1011 East Tudor Road, 99503, Anchorage, AK, USA