Abstract
Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.
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Kim KS, Sappington TW (2006) Molecular genetic variation of boll weevil populations in North America estimated with microsatellites: implications for patterns of dispersal. Genetica 127:143–161
Jiang X-F, Luo L-Z, Zhang L (2007) Amplified fragment length polymorphism analysis of Mythimna separata (Lepidoptera: Noctuidae) geographic and melanic laboratory populations in China. J Econ Entomol 100:1525–2532
Jiang X-F, Cao W-J, Zhang L, Luo L-Z (2010) Beet webworm (Lepidoptera: Pyralidae) migration in China: evidence from genetic markers. Environ Entomol 39:232–242
Nagoshi RN, Fleischer S, Meagher RL (2009) Texas is the overwintering source of fall armyworm in central Pennsylvania: implications for migration into the northeastern United States. Environ Entomol 38:1546–1554
Kim KS, Coates BS, Bagley MJ, Hellmich RL, Sappington TW (2011) Genetic structure and gene flow among European corn borer (Lepidoptera: Crambidae) populations from the Great Plains to the Appalachians of North America. Agric For Entomol 13:383–393
Kim KS, Bagley MJ, Coates BS, Hellmich RL, Sappington TW (2009) Spatial and temporal genetic analyses show high gene flow among European corn borer (Lepidoptera: Crambidae) populations across the central U.S. Corn Belt. Environ Entomol 38:1312–1323
Van Oosterhout C, Hutchinson W, Wills D, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Resour 4:535–538
Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. thesis, University of Dublin
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program Cervus accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106
Goudet J (1995) Fstat version 1.2: a computer program to calculate F statistics (version 2.9.03). J Hered 86:485–486
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Heredity 86:248–249
Cornuet J, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. Heredity 95:536–539
Harley EH (2001) AGARst. A programme for calculating allele frequencies, GST and RST from microsatellite data, version 2. University of Cape Town, Cape Town, South Africa
Ota T (1993) DISPAN: genetic distance and phylogenetic analysis. Pennsylvania State University, University Park, PA
Minch E (1998) MICROSAT version 1.5b. University of Stanford, Stanford, CA
Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763–773
Goodman SJ (1997) Rst Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and a determining their significance. Mol Ecol 6:881–885
Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Kim KS, Stolz U, Miller NJ, Waits ER, Guillemaud T, Sumerford DV, Sappington TW (2008) A core set of microsatellite markers for western corn rootworm (Coleoptera: Chrysomelidae) population genetics studies. Environ Entomol 37:293–300
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Slatkin M (1985) Gene flow in natural populations. Annu Rev Ecol Syst 16:393–430
Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159
Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA 98:4563–4568
Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39:53–65
Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 75:2868–2872
Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166–3170
Estoup A, Wilson IJ, Sullivan C, Cornuet JM, Moritz C (2001) Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus. Genetics 159:1671–1687
Luikart G, Allendorf FW, Cornuet JM, Sherwin B (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238–247
Garza JC, Williamson EG (2001) Detection of reduction of population size using data from microsatellite loci. Mol Ecol 10:305–318
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sneath PHA, Sokal RR (1973) Numerical taxonomy. W.H. Freedman and Co., San Francisco
Goudet J (1999) PCAGEN version 1.2. Population genetics laboratory, University of Lausanne, Lausanne, Switzerland
Felsenstein J (1993) PHYLIP-phylogenetic inference package, version 3.5c. University of Washington, Seattle, WA
Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989–2000
Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191
Paetkau D, Slade R, Burdens M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation based exploration of accuracy and power. Mol Ecol 13:55–65
Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429–446
Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201
Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354
Efron B (1983) Estimating the error rate of a prediction rule: improvement on cross-validation. J Am Stat Assoc 78:316–331
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620
Slatkin M (1993) Isolation by distance in equilibrium and nonequilibrium populations. Evolution 47:264–279
Wright S (1943) Isolation by distance. Genetics 28:114–138
Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228
de Sousa SN, Finkeldey R, Gailing O (2005) Experimental verification of microsatellite null alleles in Norway spruce (Picea abies [L.] Karst.): implications for population genetic studies. Plant Mol Biol Rep 23:113–119
Girard P, Angers B (2008) Assessment of power and accuracy of methods for detection and frequency-estimation of null alleles. Genetica 134:187–197
Slatkin M (1995) Hitchhiking and associative overdominance at a microsatellite locus. Mol Biol Evol 12:473–480
Paetkau D, Waits IP, Clarkson PL, Craighead I, Strobeck C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics 147:1943–1957
Pemberton JM, Slate J, Bancroft DR, Barrett JA (1995) Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252
Rice WR (1989) Analysing tables of statistical tests. Evolution 43:223–225
Benjamini Y, Yekutieli D (2001) The control of false discovery rate under dependency. Ann Stat 29:1165–1188
Acknowledgements
This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korean government (MEST) (No. 2009-0080227). Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.
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Appendix
Appendix
The figures in Appendix illustrate correctly formatted input files for most of the population genetics software programs described in this chapter. Instructions on formatting are provided on the programs’ respective websites (Table 1). Each input file contains the same genotype data for a total of ten individuals from four populations (two individuals for popA, three individuals for popB, two individuals for popC, three individuals for popD) at five microsatellite loci.
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Kim, K.S., Sappington, T.W. (2013). Microsatellite Data Analysis for Population Genetics. In: Kantartzi, S. (eds) Microsatellites. Methods in Molecular Biology, vol 1006. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-389-3_19
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DOI: https://doi.org/10.1007/978-1-62703-389-3_19
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