TY - JOUR
T1 - De Novo Mutation Rates in Sticklebacks
AU - Zhang, Chaowei
AU - Reid, Kerry
AU - Sands, Arthur F.
AU - Fraimout, Antoine
AU - Schierup, Mikkel Heide
AU - Merilä, Juha
N1 - Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
PY - 2023/9
Y1 - 2023/9
N2 - Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
AB - Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
KW - divergence time
KW - genetic diversity
KW - germline mutation rate
KW - mutation rate
KW - ninespine stickleback
UR - http://www.scopus.com/inward/record.url?scp=85171601285&partnerID=8YFLogxK
U2 - 10.1093/molbev/msad192
DO - 10.1093/molbev/msad192
M3 - Journal article
C2 - 37648662
AN - SCOPUS:85171601285
SN - 0737-4038
VL - 40
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 9
M1 - msad192
ER -