title: Quantitative genetic modeling and inference in the presence of nonignorable missing data.
abstract: Natural selection is typically exerted at some specific life stages. If natural selection takes place before a trait can be measured, using conventional models can cause wrong inference about population parameters. When the missing data process relates to the trait of interest, a valid inference requires explicit modeling of the missing process. We propose a joint modeling approach, a shared parameter model, to account for nonrandom missing data. It consists of an animal model for the phenotypic data and a logistic model for the missing process, linked by the additive genetic effects. A Bayesian approach is taken and inference is made using integrated nested Laplace approximations. From a simulation study we find that wrongly assuming that missing data are missing at random can result in severely biased estimates of additive genetic variance. Using real data from a wild population of Swiss barn owls Tyto alba, our model indicates that the missing individuals would display large black spots; and we conclude that genes affecting this trait are already under selection before it is expressed. Our model is a tool to correctly estimate the magnitude of both natural selection and additive genetic variance.
authors.affiliation: Department of Mathematical Sciences, NTNU, 7491 Trondheim, Norway. ingelins@math.ntnu.no.
authors.forename: Ingelin
authors.initials: I
authors.lastname: Steinsland
authors.forename: Camilla Thorrud
authors.initials: CT
authors.lastname: Larsen
authors.forename: Alexandre
authors.initials: A
authors.lastname: Roulin
authors.forename: Henrik
authors.initials: H
authors.lastname: Jensen
mesh_terms: D000818:Animals; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D011153:Population / Q000235:genetics; D019655:Quantitative Trait, Heritable; D018401:Sample Size; D012641:Selection, Genetic; D020305:Strigiformes / Q000235:genetics
keywords: Animal model; Tyto alba; missing not at random; sex-linked inheritance; shared parameter model