Abstract
DNA repeats are common in eukaryotic genomes, and recombination between copies can occur. This recombination can result in concerted evolution, where within-genome repeats are more similar to each other than to orthologous repeats in related species. We investigated the tandemly-repeated keratin-associated protein (KAP) gene family, KRTAP1, which encodes proteins that are important components of hair and wool in mammals. Comparison of KRTAP1 gene repeats across the mammalian phylogeny shows strongly contrasting evolutionary patterns between the coding regions, that have a concerted evolution pattern, and the flanking regions, that have a normal, radiating pattern of evolution. This dichotomy transitions abruptly at the start and stop codons, and is not the result of purifying selection, codon adaptation, or reverse transcription of KRTAP1-n mRNA. Instead, our results suggest that short-tract gene conversion events coupled with selection for these events in the coding region drives the contrasting KRTAP1 repeat evolutionary patterns. Our work shows the power that repeat recombination has to complement selection and shape the evolution of repetitive genes, and this interplay may be a more common mechanism than currently appreciated for achieving adaptive outcomes in eukaryotic multi-gene families. Thus, our work argues for greater emphasis on exploring the evolution of these families.
