ArticleMolecular ecology resources2022
Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data.
Article in Molecular ecology resources, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed.
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- Effects of Different SNP Calling and Sequence Mapping Choices on the Inference of Genetic Architecture Underlying Migration Tendency.Ecology and evolution · 2026Article
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- Minor Allele Frequency Filtering Can Strongly Bias Uniqueness Estimates Within and Across Species.Ecology and evolution · 2026Article
- Detecting local adaptation under weak genetic structure in an endemic damselfly: an integrative eco-evolutionary approach.BMC ecology and evolution · 2026Article
- Population Genomic Structure and Demographic History of Black Guillemots Breeding Across the North Atlantic.Ecology and evolution · 2026Article
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- Genotyping-by-Sequencing Reveals Low Genetic Diversity and Pronounced Geographic Structuring in the Endangered Medicinal PlantPlants (Basel, Switzerland) · 2026Article
- Hardy-Weinberg Equilibrium Filtering in Population Genomics: Empirical Review and Decision Framework for Improved Practice.Ecology and evolution · 2026Review
- A Logratio Approach to the Analysis of Autosomal Genotype Frequencies Across Multiple Samples.Molecular ecology resources · 2026Article
- Missing or Mis-Telling the Story? Trade-Offs for Restriction-Site Associated Compared to Whole Genome Sequencing.Molecular ecology · 2026Article
- To Migrate or not to Migrate? Exploring the Genomic Basis of Partial Migratory Behavior in Bats.Genome biology and evolution · 2025Article
- A Fragile Stronghold: Genomics Reveal Angelshark Population Vulnerability in Corsica, a Key Mediterranean Refuge.Ecology and evolution · 2025Article
- Opinion: Why Sex-Based Genomic Differentiation Should Not Be Overlooked in Population Genetics.Molecular ecology · 2025Article
- Exploring genetic diversity and population structure of Myanmar indigenous chickens using double digest restriction site-associated DNA sequencing.Animal genetics · 2025Article
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Abstract
Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across the genome of an organism. The dominant class of RRS approaches assay loci associated with restriction sites within the genome (restriction site associated DNA sequencing, or RADseq). RADseq is frequently applied to non-model organisms since it enables population genetic studies without relying on well-characterized reference genomes. However, RADseq requires the use of many bioinformatic filters to ensure the quality of genotyping calls. These filters can have direct impacts on population genetic inference, and therefore require careful consideration. One widely used filtering approach is the removal of loci that do not conform to expectations of Hardy-Weinberg equilibrium (HWE). Despite being widely used, we show that this filtering approach is rarely described in sufficient detail to enable replication. Furthermore, through analyses of in silico and empirical data sets we show that some of the most widely used HWE filtering approaches dramatically impact inference of population structure. In particular, the removal of loci exhibiting departures from HWE after pooling across samples significantly reduces the degree of inferred population structure within a data set (despite this approach being widely used). Based on these results, we provide recommendations for best practice regarding the implementation of HWE filtering for RADseq data sets.
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