This chapter reviews theoretical models and statistical methods for inference from genetic data in subdivided populations. With few exceptions, these methods are based on neutral models of genetic differentiation and have been mainly concerned with estimation of dispersal rates. However, simulation-based methods allow to draw inferences under models involving additional demographic processes such as changes in dispersal rates over time. The formulation and main results of migration matrix, island, and isolation-by-distance models, are briefly described. The definition and basic properties of F -statistics are reviewed, and moment methods for their estimation are contrasted with likelihood methods. Then, the application of the different methodologies to simple biological scenarios is reviewed. Their practical performance is discussed in light of comparisons with demographic estimates, as well as of their robustness to different assumptions and of concepts of separation of timescale.
INTRODUCTIONSince the advent of molecular markers in population genetics, there have been many efforts to define methods of inference from the spatial genetic structure of populations. This chapter can only review a small selection of them including, in particular, some recent developments of simulation-based likelihood methods, and also of less sophisticated methods in so far as they provide analytical insight and proven performance in realistic conditions. With few exceptions, I will focus on allele frequency data; some methods for other types of data are described in Chapter 29.The perspective taken in this review is that studies of spatial population structure are conducted in order to make inferences about parameters considered important for the evolution of natural populations, for example, for the dynamics of adaptation. Thus, 945 Handbook of Statistical Genetics, Third Edition . E dited by D . J. Balding, M . Bishop and C. Cannings. © 2007 John Wiley & Sons, L td. I SBN: 978-0-470-05830-5 946 F. ROUSSETall such analyses should ultimately be based on models of evolution in subdivided populations. This would lead to the identification of important parameters in such processes and to the formulation of appropriate statistical models to estimate them (assuming it is useful to estimate them in order to test the models). In this perspective, the material reviewed below may seem imperfect not only because the statistical models are approximate but also because the important evolutionary parameters are not always clearly identified.In all inferences, we will consider a total sample from a population structured by restricted dispersal in a number of demes (a technical term used in the analysis of the models) or subpopulations (a somewhat looser term). The population concept must be carefully distinguished from another concept of 'population' often considered in statistics, which actually refers to the probability distribution of samples under some model. In general the value of a variable in the biological population is not the expected...