Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

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...

Full description

Saved in:
Bibliographic Details
Published in:Molecular ecology resources 2022-10, Vol.22 (7), p.2599-2613
Main Authors: Pearman, William S., Urban, Lara, Alexander, Alana
Format: Article
Language:English
Subjects:
Best practice
Datasets
DNA sequencing
Empirical analysis
Filters
Filtration
Gene loci
Genetic diversity
Genomes
Genotyping
Hardy–Weinberg
Inference
Population
Population genetics
population genomics
Population structure
Population studies
RADseq
reduced representation sequencing
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.13646