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Bayesian, Likelihood-Free Modelling of Phenotypic Plasticity and Variability in Individuals and Populations

Lookup NU author(s): Dr Joao Filipe, Professor Ilias Kyriazakis

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

There is a paradigm shift from the traditional focus on the “average” individual towards the definition and analysis of trait variation within individual life-history and among individuals in populations. This is a result of increasing availability of individual phenotypic data. The shift allows the use of genetic and environment-driven variations to assess robustness to challenge, gain greater understanding of organismal biological processes, or deliverindividual-targeted treatments or genetic selection. These consequences apply, in particular, to variation in ontogenetic growth. We propose an approach to parameterise mathematical models of individual traits (e.g., reaction norms, growth curves) that address two challenges: 1) Estimation of individual traits while making minimal assumptions about data distribution and correlation, addressed via Approximate Bayesian Computation (a form of nonparametric inference). We are motivated by the fact that available information on distribution of biological data is often less precise than assumed by conventional likelihood functions. 2) Scaling-up to population phenotype distributions while facilitating unbiased use of individual data; this is addressed via a probabilistic framework where population distributions build on separately-inferred individual distributions and individual-trait interpretability is preserved. The approach is tested against Bayesian likelihood-based inference, by fitting weight and energy intake growth models to animal data and normal- and skewed-distributed simulated data. i) Individual inferences were accurate and robust to changes in data distribution and sample size; in particular, median-based predictions were more robust than maximum likelihood-based curves. These results suggest that the approach gives reliable inferences using few observations and monitoring resources. ii) At the population level, each individual contributed via a specific data distribution, and population phenotype estimates were not disproportionally influenced by outlier individuals. Indices measuring population phenotype variation can be derived for study comparisons. The approach offers an alternative for estimating trait variability in biological systems that may be reliable for various applications,for example, in genetics, health, and individualised nutrition, while using fewer assumptions and fewer empirical observations. In livestock breeding, the potentially greater accuracy of trait estimation (without specification of multitrait variance-covariance parameters) could lead to improved selection and to more decisive estimates of trait heritability.


Publication metadata

Author(s): Filipe JAN, Kyriazakis I

Publication type: Article

Publication status: Published

Journal: Frontiers in Genetics

Year: 2019

Volume: 10

Online publication date: 20/09/2019

Acceptance date: 11/07/2019

Date deposited: 13/06/2019

ISSN (electronic): 1664-8021

Publisher: Frontiers Research Foundation

URL: https://doi.org/10.3389/fgene.2019.00727

DOI: 10.3389/fgene.2019.00727


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