Detecting past changes of effective population size.

Area of Science:

• Population genetics
• Evolutionary biology
• Conservation genetics

Background:

• Estimating population abundance and predicting future numbers are significant scientific challenges.
• Genetic models using microsatellite markers estimate current and ancestral effective population sizes.
• Understanding population evolution necessitates tracing past fluctuations in population size.

Purpose of the Study:

• To develop a novel model for estimating past effective population size changes from microsatellite data.
• To enhance the understanding of population evolutionary history by reconstructing past demographic events.
• To provide a tool for detecting transient population size changes.

Main Methods:

• Developed a new model integrating coalescence theory and approximate likelihoods within a Monte Carlo Markov Chain framework.
• Utilized simulated data to assess model efficiency, sensitivity to gene flow, and mutational process assumptions.
• Applied the method to real datasets from Atlantic salmon populations.

Main Results:

• The developed model, VarEff, effectively estimates past changes in effective population size.
• The model provides evidence for transient population size fluctuations in historical demographic events.
• Analysis revealed limitations in detecting very ancient events and discussed the risk of false bottleneck detection due to gene flow.

Conclusions:

• The VarEff method offers a valuable approach for reconstructing historical population dynamics.
• The R package VarEff facilitates the application of this method in population genetics research.
• This tool aids in understanding long-term population trends and evolutionary trajectories.