An R-based tool for identifying sex-linked markers from restriction site-associated DNA sequencing with applications to elasmobranch conservation

Abstract

Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function that can identify sex-linked markers in species with partially non-recombining sex chromosomes. We test the accuracy and speed of our function with an example dataset from a species of conservation concern, the White Shark, Carcharodon carcharias. We further compare our method against other approaches and find that our method detects more sex-linked markers that can be reliably mapped to reference genomes. Overall, we provide a conservation and fisheries-relevant tool that can reliably and efficiently assign sex from genetic data in species with a heterogametic sex and we demonstrate its utility by developing a sex-identification PCR test for White Sharks.