Structure of multilocus genetic diversity in predominantly selfing populations

Predominantly selfing populations are expected to have reduced effective population sizes due to nonrandom sampling of gametes, demographic stochasticity (bottlenecks or extinction–recolonization), and large scale hitchhiking (reduced effective recombination). Thus, they are expected to display low genetic diversity, which was confirmed by empirical studies. The structure of genetic diversity in predominantly selfing species is dramatically different from outcrossing ones, with populations often dominated by one or a few multilocus genotypes (MLGs) coexisting with several rare genotypes. Therefore, multilocus diversity indices are relevant to describe diversity in selfing populations. Here, we use simulations to provide analytical expectations for multilocus indices and examine whether selfing alone can be responsible for the high-frequency MLGs persistent through time in the absence of selection. We then examine how combining single and multilocus indices of diversity may be insightful to distinguish the effects of selfing, population size, and more complex demographic events (bottlenecks, migration, admixture, or extinction–recolonization). Finally, we examine how temporal changes in MLG frequencies can be insightful to understand the evolutionary trajectory of a given population. We show that combinations of selfing and small demographic sizes can result in high-frequency MLGs, as observed in natural populations. We also show how different demographic scenarios can be distinguished by the parallel analysis of single and multilocus indices of diversity, and we emphasize the importance of temporal data for the study of predominantly selfing populations. Finally, the comparison of our simulations with empirical data on populations of Medicago truncatula confirms the pertinence of our simulation framework.