How many SNPs do we expect to observe in a sample of genes? This can be computed by modeling the evolution of a population of diploid individuals with genes by drawing the next generation of genes with replacement from the previous generation. Such a scenario is known among biologists as the Wright-Fisher model of evolution. You can interactively simulate populations under this model here. Notice that each gene has a single ancestor. This contrasts with family histories, where each individual has two ancestors, a mother and a father. However, our genes also follow the single-parent genealogies described by the Wright-Fisher model. Under this model, the expected number of SNPs is given by the following simple equation :the mutation rate.
In the past we have generalized equation (1) for alignments of arbitrary topology and looked at the distribution of SNPs in humans . In addition, we have analyzed the microevolutionary implications of localized SNP patterns in the model plant Arabidopsis thaliana .
The analysis of A. thaliana relied, like much of modern population genetics, on a data structure known as the coalescent. This describes a random genealogy of a sample of homologous genes [7,6]. We have used the coalescent to explore the effect of sampling on the frequency spectrum of nucleotide polymorphisms in expanding subdivided populations  and to quantify historical population size changes .