Abstract
In this paper, we demonstrate how simulation studies can be used to answer questions about identifiability and consequences of omitting effects from a model. The methodology is presented through a case study where identifiability of genetic and/or individual (environmental) maternal effects is explored. Our study system is a wild house sparrow (Passer domesticus) population with known pedigree. We fit pedigree‐based (generalized) linear mixed models (animal models), with and without additive genetic and individual maternal effects, and use deviance information criterion (DIC) for choosing between these models. Pedigree and R‐code for simulations are available. For this study system, the simulation studies show that only large maternal effects can be identified. The genetic maternal effect (and similar for individual maternal effect) has to be at least half of the total genetic variance to be identified. The consequences of omitting a maternal effect when it is present are explored. Our results indicate that the total (genetic and individual) variance are accounted for. When an individual (environmental) maternal effect is omitted from the model, this only influences the estimated (direct) individual (environmental) variance. When a genetic maternal effect is omitted from the model, both (direct) genetic and (direct) individual variance estimates are overestimated.
Highlights
I have a biological hypothesis I want to test for my favorite study system
We provide guidelines on how to set up a relevant simulation study for pedigree-based models for a case study based on a study system of a natural insular population of house sparrows (Passer domesticus)
If the difference is above a critical value CDDIC we conclude that the H1 is true, and we have identified a maternal effect
Summary
I have a biological hypothesis I want to test for my favorite study system. Is my data set large enough and does it have enough structure to verify my hypothesis? Is the test I use appropriate? And if I leave out important terms in my models what happens with the estimates of the other parameters?Most quantitative biologists working with natural populations are in this situation of doubt regularly. I have a biological hypothesis I want to test for my favorite study system. We provide guidelines on how to set up a relevant simulation study for pedigree-based models for a case study based on a study system of a natural insular population of house sparrows (Passer domesticus) (see Ringsby et al 2002; Jensen et al 2008; P€arn et al 2009; Hagen et al 2013; Baalsrud et al 2014; Holand et al 2015; Nossen et al 2016, and references therein). This case study is based on the same data set as in Holand et al (2013) and the pedigree is available. We want explore the consequences when maternal effects are present, but left out of the model
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