ArticleMolecular ecology resources2025
Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.
Article in Molecular ecology resources, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genomic Tracking of Market-Derived Bull Shark Fins Back to Source Population of Origin.Molecular ecology · 2026Article
- The genomic footprint of myna invasion in Oman showcases desert isolation and urban connectivity.Scientific reports · 2026Article
- Investigating Sex-Biased Dispersal in a Vulnerable Marine Invertebrate, the European Spiny Lobster (Ecology and evolution · 2026Article
- Minor Allele Frequency Filtering Can Strongly Bias Uniqueness Estimates Within and Across Species.Ecology and evolution · 2026Article
- Population Structure and Genetic Diversity Analyses Reveal Isolation That May Imperil the Northernmost Colony of the Endangered Australian Sea Lion.Ecology and evolution · 2026Article
- A Shift to Metapopulation Genetic Management for Persistence of a Species Threatened by Fragmentation: The Case of an Endangered Australian Freshwater Fish.Molecular ecology · 2025Article
- Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.Molecular ecology resources · 2025Article
- Seascape Genomics of the Smooth Hammerhead SharkEcology and evolution · 2024Article
- Immediate Genetic Augmentation and Enhanced Habitat Connectivity Are Required to Secure the Future of an Iconic Endangered Freshwater Fish Population.Evolutionary applications · 2024Article
- Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii).Molecular ecology · 2024Article
- Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression.Evolutionary applications · 2024Article
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Authors and funding
8 authors.
Funding
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
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