Microsatellites and minisatellites for molecular ecology: Theoretical and empirical considerations

Variable number of tandem repeat (VNTR) sequences include both microsatelli te and minisatellite loci. We describe qualitative and quantitative feature s of VNTRs as well as the methods used to isolate these loci and reveal the ir polymorphism. The relative advantages of VNTRs over other generic marker s and of microsatellites over minisatellites is addressed. A thorough under standing of the mutational events shaping VNTR evolution is necessary to co nstruct sound and accurate theoretical models from which population paramet ers can be estimated. We examine the mutation models usually considered for VNTR markers along with the statistical tests and experimental data that c an be used to evaluate the adequacy of these models. Important additional e volutionary features of VNTRs, namely mutational biases, allele size constr aints, size homoplasy and the existence of correlations between structural features and levels of polymorphism, are also examined. Finally, we provide an overview of applications and case studies of VNTR markers in molecular ecology, with particular emphasis on the most promising category of VNTRs i n molecular ecology, namely, microsatellites. The high variability of micro satellites presents new perspectives for analyses at the individual level i ncluding genetic tagging, classification of individuals to their population of origin, level of relatedness among individuals and parentage assignment . Application of VNTR markers at the population level is also addressed. Mo re specifically, we discuss the methods and statistics available to test an d measure population differentiation, to estimate effective population size (N-e), to detect non-equilibrium situations due to N-e fluctuations, and t o reconstruct phylogenetic relationships among populations.