Rate of de novo mutations in the three-spined stickleback

Abstract

As a fundamentally important genetic parameter and evolutionary force, germline mutation rates have many applications in evolutionary biology. However, accurate estimates of de novo mutation (DNM) rates are still relatively scarce, even for extensively studied evolutionary biology models. We estimated DNM rates for the three-spined stickleback (Gasterosteus aculeatus), the ‘supermodel’ of ecology and evolutionary biology. Using a large number of family trios sequenced to 45x coverage, we identified 115 unique mutations genome-wide and estimated the DNM rate at µ = 5.11 × 10−9/bp/gen without any detectable sex bias. The localised DNM rate was found to be positively correlated with the recombination rate, supporting the notion that recombination is a mutagenic process. Correlations between µ and genomic characteristics of studied species and the related nine-spined stickleback (Pungitius pungitius) revealed a high degree of similarity, suggesting that despite 17.5 million years of independent evolution, the mutational processes in the two species appear to have been conserved.