Pedigree-based germline mutation rate in sticklebacks
by Chaowei Zhang | Kerry Reid | Arthur F. Sands | Antoine Fraimout | Mikkel Heide Schierup | Juha Merilä | The University of Hong Kong | The University of Hong Kong | The University of Hong Kong | The University of Hong Kong | Aarhus University | The University of Hong Kong
Abstract ID: 22
Event: The 3rd AsiaEvo Conference
Topic: The genomics of adaptation and speciation
Presenter Name: Chaowei Zhang

Germline mutations, transmitted from parents to offspring, constitute the ultimate source of genetic variability. The rates at which these de novo mutations (DNM) occur are important for demographic, phylogenetic and population genetic inference, yet accurate estimates of DNM rates are still scarce, even for popular model systems in evolutionary biology. We estimated DNM rates for two populations of marine nine-spined sticklebacks (Pungitius pungitius) from deep coverage whole genome resequencing data for 128 individuals, representing 106 parent-offspring trios. After mapping the data to the species’ latest reference genome version and applying stringent filtering, 308 DNMs were discovered. These DNMs translated to DNM rate of 4.56e-09 per base pair per generation, which is 3.1 times lower than the commonly used substitution rate in phylogenetic dating of sticklebacks. Replacement of the latter with our DNM rate resulted in substantial increases in estimated divergence times among different stickleback lineages and better aligned with the known fossil record. Moreover, we also observed a relatively high parental mosaicism at around 20% in comparison to humans, apes and mice. The accurate estimate of DNM rate should provide a useful resource for teleost fish research, and that of sticklebacks in particular.