Identifying Single-Origin Rare Variants in Population Genomic Data.

ABSTRACT: Genomic analyses have shown that some mutations in large population genomic datasets may be the result of repeated, independent events at the same locus. However, the possibility of recurrent mutation is often ignored, even when it has the potential to introduce errors, such as when assuming co-ancestry for demographic analysis. Even rare variants such as doubletons, which should be particularly informative about recent demography, may have multiple origins despite arising relatively recently in the population. Here, we develop methods to (i) estimate the frequency of recurrent doubletons in a population genomic dataset from the occurrence of tri-allelic sites with two different singleton mutations and (ii) identify a subset of high confidence single-origin doubletons based on the presence

SUBMITTER: Reynolds JJ 

PROVIDER: S-EPMC12646071 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature