De Novo Mutation Rates in Sticklebacks.

Area of Science:

• Population Genetics
• Evolutionary Biology
• Genomics

Background:

• Mutation rate is a key parameter in population genetics, influencing genetic diversity and demographic inference.
• Accurate de novo mutation rate estimates are scarce for wild organisms, hindering population genetic studies.
• The nine-spined stickleback (Pungitius pungitius) is an important model for ecological and evolutionary research.

Purpose of the Study:

• To estimate the de novo mutation rate (µ) in two wild marine populations of the nine-spined stickleback.
• To provide a more accurate mutation rate for recalibrating evolutionary timescales in stickleback species.
• To offer a valuable resource for fish population genetics research.

Main Methods:

• Utilized 2- and 3-generational family pedigrees from Pungitius pungitius populations.
• Performed deep whole-genome resequencing (>50× coverage) of individuals.
• Applied stringent filtering to identify germline mutations from high-quality reference genomes.

Main Results:

• Identified 308 germline mutations across 106 offspring.
• Estimated mutation rates of µ = 4.83 × 10⁻⁹ and µ = 4.29 × 10⁻⁹ per base per generation.
• Observed up to 20% of mutations shared by full-sibs, indicating significant parental mosaicism.

Conclusions:

• The estimated de novo mutation rates are substantially lower (3.1 times) than commonly used substitution rates.
• Recalibration using these new mutation rates significantly increases estimated divergence times between stickleback species.
• These findings provide crucial data for population genetics and evolutionary studies of sticklebacks and other fish.