11 Unsampled subpopulations

Typically, in most studies, sampling only take place in some of the populations, whereas no information is available about the gene frequencies in surrounding subpopulations. One way of handling this is simply to ignore the problem. A more satisfactory solution, perhaps somewhat experimental, is to compute the covariances for the entire population system, including unsampled populations, and then compute the likelihood of the data based on the appropriate covariance submatrix. Similarly, in the simulations, the process of genetic drift in the entire system should be simulated to produce bootstrap replicates of the data in the sampled regions of the population.

To incorporate unsampled subpopulations, Ne should be set up contain the effective size of all subpopulations. In addition, the elements of the boolean vector sampled should be set up to specify which subpopulations are sampled and which are not, for example:

   > sampled <- c(F,F,F,T,T,T,T,F,F)

Also note that the length of Ns and Nh should match the number of true elements in sampled.