Genetic variation in structured populations

Sammanfattning: It is widely acknowledged that the process of speciation in the presence of gene flow between different ecotypes is common in nature. However, the mechanisms underlying speciation are not understood. In order to gain understanding of this process, one must identify loci which establish primary reproductive barriers between ecotypes and monitor how these barriers evolve towards completion. Since such loci are presumably under natural selection, they can be detected using neutral loci as markers in genome-wide scans. Therefore, the patterns of neutral genetic variation must be understood first. This thesis analyses genetic variation in structured populations. First it is shown how to compute the moments of the frequency spectrum of nucleotide polymorphisms under a varying population size. It is discussed how these results together with empirical data can be used to infer the underlying population size history. Moreover, the effect of sustained population size fluctuations on two-locus patterns of neutral genetic variation is analysed. It is shown that, under severe reductions of population size, pairs of loci can exhibit long-range association. Afterwards, neutral genetic variation in geographically structured populations is discussed. An important example are populations arising from a series of founder events. By describing such populations using a mainland-island model, it is shown how genetic variation decays as the distance from the mainland increases. The effect of multiple paternity is also discussed. It is shown that populations with high degree of multiple paternity have on average higher heterozygosity than the populations with low degree of multiple paternity. Finally, it is demonstrated that migration patterns between partly isolated populations can be represented in terms of a colonisation-migration ancestral tree. Inferring such a tree using gene trees of samples taken across different populations is related to inferring species tree using gene trees of samples taken across different species. Thereafter, the relatedness of species trees to their resulting gene trees under rapid speciations is discussed. The effects of the time between successive speciations, of the number of derived species, and of the symmetry of the species tree are analysed. The effect of the time scale of speciation remains to be taken into account.