Abstract
Tandem repeat (TR) sequences occur when short DNA motifs are repeated head-to-tail along chromosomes and are a major source of genetic variation. Population genetic models of TR evolution have focused on large, randomly mating, haploid populations. Yet many organisms reproduce partially through self-fertilisation ('selfing'), which increases homozygosity and thus may alter the evolutionary processes shaping TR sequences. Here we use mathematical modelling and simulations to study the evolution of homologous TR sequences in partially selfing, diploid populations under four different selective regimes that may be relevant to TRs: (i) additive purifying selection, (ii) truncation-like purifying selection, (iii) selection against heterozygotes due to misalignment costs, and (iv) stabilising selection favouring an intermediate TR sequence length. We show that selfing influences TR evolution primarily by increasing homozygosity, with two main consequences: (1) it enhances the variation produced by unequal recombination within individuals, and (2) it increases variation between individuals. Consequently, selection on TRs becomes more effective under partial selfing across all modes of selection considered, resulting in lower genetic load, despite higher genetic drift. Overall, our results suggest that mating systems and inbreeding are important factors shaping variation in TR sequences.