Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and...

Area of Science:

• Population genetics
• Genomics
• Evolutionary biology

Background:

• Effective population size (Ne) and mutation rate (u) are not uniform across genomes.
• Ignoring this heterogeneity can lead to inaccurate inferences of past population demographics.

Purpose of the Study:

• To develop novel methods for simultaneously inferring demographic history and detecting genomic variation in Ne and u.
• To provide tools for analyzing sex chromosome and autosomal data to understand evolutionary processes.

Main Methods:

• Development of statistical methods utilizing polymorphism data alone or combined polymorphism and divergence data.
• Application of methods to analyze multilocus sequence data, including comparisons between sex chromosomes and autosomes.
• Implementation of methods in a user-friendly software package.

Main Results:

• Simulations confirm accurate parameter estimation and high statistical power for detecting variations in Ne and u.
• Analysis of Drosophila simulans data revealed rapid population expansion.
• Evidence suggests autosomes have a higher mutation rate than the X chromosome, with a likely female-biased sex ratio.

Conclusions:

• The developed methods effectively address biases caused by genomic heterogeneity in Ne and u.
• These tools enable robust demographic inference and facilitate studies on sex-biased evolution and the drivers of genetic variation.