Pedigree metrics: What are they good for?

Estimating additive genetic variance (V_A) is key to understanding evolutionary potential in wild populations. V_A is commonly estimated using relatedness data from pedigrees in so-called `animal models'. The accuracy of these estimates depends strongly on information in the pedigree. Typically metrics describing pedigree structure (such as the number of individuals, maternities, pedigree depth etc.) are provided alongside V_A estimates. However, what these metrics represent is not well understood. Here, we first explored the evolution of metric reporting. Then, using 53 wild pedigrees, we demonstrated that precision of heritability (h^2; ratio of V_A to total phenotypic variance) estimates was strongly predicted by pedigree size, but other metrics provided little additional information about precision. An seldom-used analytical approximation almost exactly reproduced simulated standard errors for h^2 estimates from pedigrees and genomic relatedness matrices, offering an alternative to simulation-based power analysis for simple models. Although the utility of commonly reported metrics is limited for precision, they provide important information about risk of bias from confounding effects, which is valuable for planning future studies and assessing published ones. We demonstrated this using the example of unmodelled maternal effects. Future work on biases in h^2 estimation should explicitly take pedigree structure into account.

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Published
2026-10-30
DOI
https://doi.org/10.32942/x21q39
Primary Topic
Genetic and phenotypic traits in livestock
Type
preprint

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preprint

Pedigree metrics: What are they good for?

Kasha Strickland, Anne Charmantier, Céline Teplitsky, Julien Martin et al.
1 links
Genetic and phenotypic traits in livestock
preprint

Pedigree metrics: What are they good for?

Kasha Strickland, Anne Charmantier, Céline Teplitsky, Julien Martin, Denis J. F. Réale, Joel L. Pick, Niels Jeroen Dingemanse, Holger Schielzeth, Barbara Class, Jane Reid, Paul Acker, Ned Dochtermann, Yimen Araya Ajoy
preprint en

Abstract

Estimating additive genetic variance (V_A) is key to understanding evolutionary potential in wild populations. V_A is commonly estimated using relatedness data from pedigrees in so-called `animal models'. The accuracy of these estimates depends strongly on information in the pedigree. Typically metrics describing pedigree structure (such as the number of individuals, maternities, pedigree depth etc.) are provided alongside V_A estimates. However, what these metrics represent is not well understood. Here, we first explored the evolution of metric reporting. Then, using 53 wild pedigrees, we demonstrated that precision of heritability (h^2; ratio of V_A to total phenotypic variance) estimates was strongly predicted by pedigree size, but other metrics provided little additional information about precision. An seldom-used analytical approximation almost exactly reproduced simulated standard errors for h^2 estimates from pedigrees and genomic relatedness matrices, offering an alternative to simulation-based power analysis for simple models. Although the utility of commonly reported metrics is limited for precision, they provide important information about risk of bias from confounding effects, which is valuable for planning future studies and assessing published ones. We demonstrated this using the example of unmodelled maternal effects. Future work on biases in h^2 estimation should explicitly take pedigree structure into account.

Centre National de la Recherche Scientifique (FR), University of Ottawa (CA), Université du Québec à Montréal (CA), École Pratique des Hautes Études (FR), Norwegian University of Science and Technology (NO), Centre d'Écologie Fonctionnelle et Évolutive (FR), Urologische Klinik München (DE), Institut de Recherche pour le Développement (FR), North Dakota State University (US), Friedrich Schiller University Jena (DE), Ludwig-Maximilians-Universität München (DE), University of Edinburgh (GB)
National Science Foundation, Norges Forskningsråd
Genetic and phenotypic traits in livestock
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