Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.

ABSTRACT: We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using

SUBMITTER: Vaughn AH 

PROVIDER: S-EPMC11321360 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature