Estimating linkage disequilibrium and selection from allele frequency trajectories.

ABSTRACT: Genetic sequences collected over time provide an exciting opportunity to study natural selection. In such studies, it is important to account for linkage disequilibrium to accurately measure selection and to distinguish between selection and other effects that can cause changes in allele frequencies, such as genetic hitchhiking or clonal interference. However, most high-throughput sequencing methods cannot directly measure linkage due to short-read lengths. Here we develop a simple method to estimate linkage disequilibrium from time-series allele frequencies. This reconstructed linkage information can then be combined with other inference methods to infer the fitness effects of individual mutations. Simulations show that our approach reliably outperforms inference that ignores linkage dise

SUBMITTER: Li Y 

PROVIDER: S-EPMC9991507 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature