An ecologist’s guide to the animal model

Abstract

Summary1. Efforts to understand the links between evolutionary and ecological dynamics hinge on our ability to measure and understand how genes influence phenotypes, fitness and population dynamics. Quantitative genetics provides a range of theoretical and empirical tools with which to achieve this when the relatedness between individuals within a population is known. 2. A number of recent studies have used a type of mixed-effects model, known as the animal model, to estimate the genetic component of phenotypic variation using data collected in the field. Here, we provide a practical guide for ecologists interested in exploring the potential to apply this quantitative genetic method in their research. 3. We begin by outlining, in simple terms, key concepts in quantitative genetics and how an animal model estimates relevant quantitative genetic parameters, such as heritabilities or genetic correlations. 4. We then provide three detailed example tutorials, for implementation in a variety of software packages, for some basic applications of the animal model. We discuss several important statistical issues relating to best practice when fitting different kinds of mixed models. 5. We conclude by briefly summarizing more complex applications of the animal model, and by highlighting key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.

Phylogenetic relatedness as a tool in restoration ecology: a meta-analysis

“…The proportion of remaining variance explained by each grouping factor (neighbour and target species identity) was estimated by calculating the 95% credible interval of its posterior distribution. It should be noted that this interval will never contain zero because variances are bounded to be positive [39]. Therefore, a wide credible interval with an extremely low bound suggests an insignificant effect of the grouping factor.…”

Heritable variation in maternally derived yolk androgens, thyroid hormones and immune factors

“…As complete broods were taken into the laboratory for this experiment, quantitative genetic parameters could have been estimated using full-sib analyses. Some parents of these broods were however related and to make use of this additional information we used so-called 'animal models', which utilize such pedigree information (Wilson et al, 2010). The animal model is a mixed model that allows partitioning the total phenotypic variance into several components, which are: the additive genetic variance (V A ), variance due to the non-genetic individual component (V ind ) and the residual variance (V res ).…”

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

“…The animal model is a form of mixed model incorporating pedigree information where the phenotype of each individual is modelled as the sum of its additive genetic value and other random and fixed effects. The method has a long history in animal breeding and is now commonly used for studies of free-living populations because of its ability to optimize the use of information in complex and incomplete pedigrees (Wilson et al, 2010).…”

“…Phenotypic variance (V p ) was therefore partitioned into five components after having taken fixed effects into account (described below): additive genetic (V a ), permanent environmental (V pe ), year of capture (V y ), year of birth (V yob ) and residual (V r ). All components were retained in final models even when not significant to prevent biasing V a upwardly (Wilson et al, 2010).…”