Mutation, Gene Conversion, and Migration

Chapter 4 focuses on forward and reverse mutation, gene duplication and functional divergence, gene conversion, and equilibrium heterozygosity. It includes an introduction to the coalescent as well as the Wright–Fisher and Moran models of random genetic drift, measures of nucleotide polymorphism and diversity, and how these may be estimated from sequence data. Biased gene conversion is discussed in regard to its effects on homogeneity of nucleotide sequence across the genome. Several distinct types of effective population number are compared and contrasted including the inbreeding, variance, and coalescent effective numbers. Various models of migration are also examined including one-way migration, the island model, and stepping-stone models.

FST between Archaic and Present-Day Samples

The increasing abundance of DNA sequences obtained from fossils calls for new population genetics theory that takes account of both the temporal and spatial separation of samples. Here we exploit the relationship between Wright’s FST and average coalescence times to develop an analytic theory describing how FST depends on both the distance and time separating pairs of sampled genomes. We apply this theory to several simple models of population history. If there is a time series of samples, partial population replacement creates a discontinuity in pairwise FST values. The magnitude of the discontinuity depends on the extent of replacement. In stepping-stone models, pairwise FST values between archaic and present-day samples reflect both the spatial and temporal separation. At long distances, an isolation by distance pattern dominates. At short distances, the time separation dominates. Analytic predictions fit patterns generated by simulations. We illustrate our results with applications to archaic samples from European human populations. We compare present-day samples with a pair of archaic samples taken before and after a replacement event.