# Bibliography

Anderson, Marti J. 2001. “Permutation Tests for Univariate or Multivariate Analysis of Variance and Regression.” Can. J. Fish Aquatic Scis. 58: 626–39.

Black, W. C., IV, and E. S. Krafsur. 1985. “A FORTRAN Program for the Calculation and Analysis of Two-Locus Linkage Disequilibrium Coefficients.” Theor. Appl. Genetics 70: 491–96.

Brookfield, J. F. Y. 1996. “A Simple New Method for Estimating Null Allele Frequency from Heterozygote Deficiency.” Mol. Ecol 5: 453–55.

Brooks, Stephen, and Andrew Gelman. 1998. “General Methods for Monitoring Convergence of Iterative Simulations.” J. Comput. Graphical Statistics 7: 434–55.

Chakraborty, R., M. de Andrade, S.P. Daiger, and B. Budowle. 1992. “Apparent Heterozygote Deficiencies Observed in DNA Typing Data and Their Implications in Forensic Applications.” Ann. Hum. Genetics 56: 45–57.

Cockerham, C. Clark. 1973. “Analyses of Gene Frequencies.” Genetics 74: 679–700.

Cockerham, C. Clark, and Bruce S. Weir. 1987. “Correlations, Descent Measures: Drift with Migration and Mutation.” PNAS 84: 8512–4.

Cox, D. R., and D. V. Hinkley. 1974. Theoretical Statistics. London: Chapman & Hall.

Dempster, A. P., N. M. Laird, and D. B. Rubin. 1977. “Maximum Likelihood from Incomplete Data via the EM Algorithm (with Discussion).” JRSSB 39: 1–38.

DiCiccio, Thomas J., and Bradley Efron. 1996. “Bootstrap Confidence Intervals (with Discussion).” Stat. Sci. 11: 189–228.

Felsenstein, J. 2005. “PHYLIP (Phylogeny Inference Package) Version 3.6.”

Fisher, Ronald Aylmer. 1935. “The Logic of Inductive Inference (with Discussion).” JRSS 98: 39–82.

Garnier-Géré, P., and C. Dillmann. 1992. “A Computer Program for Testing Pairwise Linkage Disequilibria in Subdivided Populations.” J. Hered. 83: 239.

Goudet, J. 1995. “FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics.” J. Hered. 86: 485–86.

Goudet, Jérome, Michel Raymond, Thierry de Meeüs, and François Rousset. 1996. “Testing Differentiation in Diploid Populations.” Genetics 144: 1931–8.

Guillot, G., and François Rousset. 2013. “Dismantling the Mantel Tests.” Methods Ecol. Evol. 4: 336–44.

Guo, Sun Wei, and Elizabeth A. Thompson. 1992. “Performing the Exact Test of Hardy-Weinberg Proportion for Multiple Alleles.” Biometrics 48: 361–72.

Haldane, John Burdon Sanderson. 1954. “An Exact Test for Randomness of Mating.” Journal of Genetics 52: 631–35.

Hartl, Daniel L., and Andrew G. Clark. 1989. Principles of Population Genetics. Second. Sunderland, Mass.: Sinauer.

Hastings, W. K. 1970. “Monte Carlo Sampling Methods Using Markov Chains and Their Applications.” Biometrika 57: 97–109.

Kalinowski, Steven T., and Mark L. Taper. 2006. “Maximum Likelihood Estimation of the Frequency of Null Alleles at Microsatellite Loci.” Conserv. Genetics 7: 991–95.

Leblois, R., P. Pudlo, J. Néron, F. Bertaux, C. R. Beeravolu, R. Vitalis, and F Rousset. 2014. “Maximum Likelihood Inference of Population Size Contractions from Microsatellite Data.” Mol. Biol. Evol. 31: 2805–23.

Leblois, Raphael, Arnaud Estoup, and François Rousset. 2003. “Influence of Mutational and Sampling Factors on the Estimation of Demographic Parameters in a ‘Continuous’ Population Under Isolation by Distance.” Mol. Biol. Evol. 20: 491–502.

Legendre, Pierre, and Marie-Josée Fortin. 2010. “Comparison of the Mantel Test and Alternative Approaches for Detecting Complex Multivariate Relationships in the Spatial Analysis of Genetic Data.” Mol. Ecol. Resources 10 (5): 831–44.

Legendre, Pierre, Marie-Josée Fortin, and Daniel Borcard. 2015. “Should the Mantel Test Be Used in Spatial Analysis?” Methods Ecol. Evol. 6: 1239–47.

Lehmann, E. L. 1994. Testing Statistical Hypotheses. Second. New York: Chapman & Hall.

Levene, Howard. 1949. “On a Matching Problem Arising in Genetics.” Annals of Mathematical Statistics 20: 91–94.

Loiselle, Bette A., Victoria L. Sork, John Nason, and Catherine Graham. 1995. “Spatial Genetic Structure of a Tropical Understory Shrub Psychotria Officinalis (Rubiaceae).” Am. J. Bot. 82: 1420–5.

Louis, Edward J., and Everett R. Dempster. 1987. “An Exact Test for Hardy-Weinberg and Multiple Alleles.” Biometrics 43: 805–11.

Mantel, Nathan. 1967. “The Detection of Disease Clustering and a Generalized Regression Approach.” Cancer Research 27: 209–20.

Mehta, Cyrus R., and Nitin R. Patel. 1983. “A Network Algorithm for Performing Fisher’s Exact Test in \(r \times c\) Contingency Tables.” JASA 78: 427–34.

Michalakis, Yannis, and Laurent Excoffier. 1996. “A Generic Estimation of Population Subdivision Using Distances Between Alleles with Special Interest to Microsatellite Loci.” Genetics 142: 1061–4.

Oden, Neal L., and Robert R. Sokal. 1992. “An Investigation of Three-Matrix Permutation Tests.” J. Classif. 9: 275–90.

Ohta, Tomoko. 1982. “Linkage Disequilibrium Due to Random Genetic Drift in Finite Subdivided Populations.” PNAS 79: 1940–4.

Raufaste, Nathalie, and François Rousset. 2001. “Are Partial Mantel Tests Adequate?” Evolution 55: 1703–5.

Raymond, Michel, and François Rousset. 1995a. “An Exact Test for Population Differentiation.” Evolution 49: 1283–6.

———. 1995b. “GENEPOP Version 1.2: Population Genetics Software for Exact Tests and Ecumenicism.” J. Hered. 86: 248–49.

Robertson, Alan, and William G. Hill. 1984. “Deviations from Hardy-Weinberg Proportions: Sampling Variances and Use in Estimation of Inbreeding Coefficients.” Genetics 107: 703–18.

Rousset, François. 1996. “Equilibrium Values of Measures of Population Subdivision for Stepwise Mutation Processes.” Genetics 142: 1357–62.

———. 1997. “Genetic Differentiation and Estimation of Gene Flow from \(F\)-Statistics Under Isolation by Distance.” Genetics 145: 1219–28.

———. 1999. “Genetic Differentiation Within and Between Two Habitats.” Genetics 151: 397–407.

———. 2000. “Genetic Differentiation Between Individuals.” J. Evol. Biol. 13: 58–62.

———. 2002a. “Inbreeding and Relatedness Coefficients: What Do They Measure?” Heredity 88: 371–80.

———. 2002b. “Partial Mantel Tests: Reply to Castellano and Balletto.” Evolution 56: 1874–5.

———. 2007. “Inferences from Spatial Population Genetics.” In Handbook of Statistical Genetics, edited by D. J. Balding, M. Bishop, and C. Cannings, third, 945–79. Chichester, U.K.: Wiley.

Rousset, François, and Raphaël Leblois. 2007. “Likelihood and Approximate Likelihood Analyses of Genetic Structure in a Linear Habitat: Performance and Robustness to Model Mis-Specification.” Mol. Biol. Evol. 24: 2730–45.

Rousset, François, and Raphaël Leblois. 2012. “Likelihood-Based Inferences Under Isolation by Distance: Two-Dimensional Habitats and Confidence Intervals.” Mol. Biol. Evol. 29: 957–73.

Rousset, François, and Michel Raymond. 1995. “Testing Heterozygote Excess and Deficiency.” Genetics 140: 1413–9.

———. 1997. “Statistical Analyses of Population Genetic Data: Old Tools, New Concepts.” Tr. Ecol. Evol. 12: 313–17.

Slatkin, Montgomery. 1995. “A Measure of Population Subdivision Based on Microsatellite Allele Frequencies.” Genetics 139: 457–62.

Swofford, D. L., and R. B. Selander. 1989. BIOSYS-1. a Computer Program for the Analysis of Allelic Variation in Population Genetics and Biochemical Systematics. Release 1.7. Champaign: Illinois Natural History Survey.

Vekemans, X., and O. J. Hardy. 2004. “New Insights from Fine-Scale Spatial Genetic Structure Analyses in Plant Populations.” Mol. Ecol. 13: 921–34.

Watts, Phillip C., François Rousset, Ilik J. Saccheri, Raphaël Leblois, Stephen J. Kemp, and David J. Thompson. 2007. “Compatible Genetic and Ecological Estimates of Dispersal Rates in Insect (Coenagrion Mercuriale: Odonata: Zygoptera) Populations: Analysis of ‘Neighbourhood Size’ Using a More Precise Estimator.” Mol. Ecol. 16: 737–51.

Weir, B. S., and C. Clark Cockerham. 1984. “Estimating \(F\)-Statistics for the Analysis of Population Structure.” Evolution 38: 1358–70.

Weir, Bruce S. 1996. Genetic Data Analysis Ii. Sunderland, Mass.: Sinauer.

Whitlock, M. C. 2005. “Combining Probability from Independent Tests: The Weighted Z-Method Is Superior to Fisher’s Approach.” J. Evol. Biol. 18 (5): 1368–73.