Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 7529
Title: Testing for Hardy-Weinberg and linkage equilibrium: Have we lost the plot?
Author: Robin S. Waples
Publication Year: 2014
Journal: Journal of Heredity
Keywords: hardy-weinberg,linkage disequilibrium,statistical power,multiple testing,population mixture,Wahlund effect

Testing for Hardy-Weinberg proportions (HWP) is routine in almost all genetic studies of natural populations, but few researchers 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 non-model 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 non-model species is commonplace.

Theme: Recovery and rebuilding of marine and coastal species
Foci: Characterize the population biology of species, and develop and improve methods for predicting the status of populations.
Develop methods to use physiological, biological and behavioral information to predict population-level processes.
Official Citation:

Waples, R.S.  2015.  Testing for Hardy-Weinberg proportions:  Have we lost the plot?  Journal of Heredity (invited Perspective) 106:1-19.