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

AI Article Synopsis

  • - The study highlights the challenges of detecting sex-linked markers in genetic datasets, which can skew results related to genetic diversity and population structure due to their presence in neutral datasets.
  • - New R functions were developed to identify sex-linked loci in different sex determination systems and to determine the genetic sex of individuals, tested successfully on data from two bird and one mammal species.
  • - Results show that standard filtering methods miss a significant number of sex-linked loci, leading to inaccuracies in genetic analysis, such as overestimating population statistics and errors in parentage inference, emphasizing the importance of using the new functions for accurate biological conclusions.

Article 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-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population F by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).

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Source
http://dx.doi.org/10.1111/1755-0998.13844DOI Listing

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