Testing for Hardy–Weinberg Proportions: Have We Lost the Plot?
2014/11/25 by Robin S. Waples · 430 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · #Allele #Artificial intelligence #Biology #Computational biology #Computer science #Disequilibrium #Evolution and Genetic Dynamics #Evolutionary biology #Genealogy #Genetic Mapping and Diversity in Plants and Animals #Genetic diversity and population structure #Genetics #History #Linkage (software) #Linkage disequilibrium #Mathematics #Perspective (graphical) #Plot (graphics) #Statistical hypothesis testing #Statistics
paper · pdf · doi:10.1093/jhered/esu062
published in Journal of Heredity 106(1), 1-19 (Oxford University Press)
openalex publication_date 2014/11/25 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/03
Abstract
Testing for Hardy-Weinberg proportions (HWP) is routine in almost all genetic studies of natural populations, but many researchers do not demonstrate a full understanding of the purposes of these tests or how to interpret the results. Common problems include a lack of understanding of statistical power and the difference between statistical significance and biological significance, how to interpret results of multiple tests, and how to distinguish between various factors that can cause statistically significant departures. In this perspective, which focuses on analysis of genetic data for nonmodel species, I 1) review factors that can cause departures from HWP at individual loci and linkage disequilibrium (LD) at pairs of loci; 2) discuss commonly used tests for HWP and LD, with an emphasis on multiple-testing issues; 3) show how to distinguish among possible causes of departures from HWP; and 4) outline some simple steps to follow when significant test results are found. Finally, I 5) identify some issues that merit particular attention as we move into an era in which analysis of genomics-scale datasets for nonmodel species is commonplace.
Citations
Cited by
- The Analysis of Polyploid Genetic Data
- Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses
- High inter-population connectivity and occasional gene flow between subspecies improves recovery potential for the endangered Least Bell’s Vireo
- ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data
- Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods
- Evidence of micro-evolution in Crocidura russula from two abandoned heavy metal mines: potential use of Cytb, CYP1A1, and p53 as gene biomarkers
- Genetic and mating system assessment of translocation success of the long‐lived perennial shrub Lambertia orbifolia (Proteaceae)
- Genetic diversity and spatial structures of snow leopards (Panthera uncia) reveal proxies of connectivity across Mongolia and northwestern China
- Gene flow prevents genetic diversity loss despite small effective population size in fragmented grizzly bear (Ursus arctos) populations
- Genome-wide evaluation of Scylla serrata (giant mud crab) population structure between and within two continental shelf regions of northern Australia
- Hybridisation rates, population structure, and dispersal of sambar deer (Cervus unicolor) and rusa deer (Cervus timorensis) in south-eastern Australia
- Describing a developing hybrid zone between red wolves and coyotes in eastern North Carolina, USA
- Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. [europepmc]
- Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis. [europepmc]
- Temporal Genetic Dynamics of an Experimental, Biparental Field Population of Phytophthora capsici . [europepmc]
- Population structure of an orchid mycorrhizal fungus with genus-wide specificity. [europepmc]
- Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits. [europepmc]
- rs2267531, a promoter SNP within glypican-3 gene in the X chromosome, is associated with hepatocellular carcinoma in Egyptians. [europepmc]
- Genetic analysis of African lions (Panthera leo) in Zambia support movement across anthropogenic and geographical barriers. [europepmc]
- Sex matters: Otolith shape and genomic variation in deacon rockfish ( Sebastes diaconus ). [europepmc]
- How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish. [europepmc]
- Inbreeding shapes the evolution of marine invertebrates. [europepmc]
- Classical homocystinuria: A common inborn error of metabolism? An epidemiological study based on genetic databases. [europepmc]
- Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream. [europepmc]
- Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles. [europepmc]
- Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis. [europepmc]
- Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus ) in Egypt. [europepmc]
- Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations. [europepmc]
- Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. [europepmc]
- Fitness costs of individual and combined pyrethroid resistance mechanisms, kdr and CYP-mediated detoxification, in Aedes aegypti. [europepmc]
- Drivers of population divergence and species differentiation in a recent group of indigenous orchids ( Vanilla spp.) in Madagascar. [europepmc]
- Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. [europepmc]
- Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. [europepmc]
- Occasional long-distance dispersal may not prevent inbreeding in a threatened butterfly. [europepmc]
- Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data. [europepmc]
- Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads. [europepmc]
- Are rabid raccoons ( Procyon lotor ) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes. [europepmc]
Related