# Bibliography

Anderson, Marti J. 2001. “Permutation Tests for Univariate or Multivariate Analysis of Variance and Regression.” Can. J. Fish Aquatic Scis. 58: 626–39.
Andrews, Donald W. K. 2000. “Inconsistency of the Bootstrap When a Parameter Is on the Boundary of the Parameter Space.” Econometrica 68 (2): 399–405.
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: 8512–14.
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.
Efron, Bradley. 1987. “Better Bootstrap Confidence Intervals.” Journal of the American Statistical Association 82: 171–85.
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: 1931–38.
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., 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.
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.
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: 1420–25.
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: 1061–64.
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: 1940–44.
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: 1283–86.
———. 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: 1874–75.
———. 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.
———. 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: 1413–19.
———. 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.
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.