Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.

ABSTRACT: Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linke

SUBMITTER: Robledo-Ruiz DA 

PROVIDER: S-EPMC12142712 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature