Assessing the impact of pedigree quality on the validity of quantitative genetic parameter estimates

Abstract

AbstractInvestigating the evolutionary dynamics of complex traits in nature requires the accurate assessment of their genetic architecture. Using a quantitative genetic (QG) modeling approach (e.g., animal model), relatedness information from a pedigree combined with phenotypic measurements can be used to infer the amount of additive genetic variance in traits. However, pedigree information from natural systems is not perfect and might contain errors or be of low quality. Published sensitivity analyses revealed a limited impact of expected error rates on parameter estimates. However, natural systems will differ in many respects (e.g., mating system, data availability, pedigree structure), thus it can be inappropriate to generalize outcomes from one system to another. French-Canadian (FC) genealogies are extensive and deep-rooted (up to 9 generations in this study) making them ideal to study how the quality and properties (e.g., errors, completeness) of pedigrees affect QG estimates. We conducted simulation analyses to infer the reliability of QG estimates using FC pedigrees and how it is impacted by genealogical errors and variation in pedigree structure. Broadly, results show that pedigree size and depth are important determinants of precision but not of accuracy. While the mean genealogical entropy (based on missing links) seems to be a good indicator of accuracy. Including a shared familial component into the simulations led to on average a 46% overestimation of the additive genetic variance. This has crucial implications for evolutionary studies aiming to estimate QG parameters given that many traits of interest, such as life history, exhibit important non-genetic sources of variation.