A delay-deterministic model for inferring fitness effects from time-resolved genome sequence data

• Published in: bioRxiv
• Main Authors: Nene, Nuno R, Dunham, Alistair S, Illingworth, Christopher J R
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 07.12.2017
• Subjects: Demography; Evolution; Genetic diversity; Genetic drift; Genomes; Nucleotide sequence; Reproductive fitness
• DOI: 10.1101/229963

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the non-deterministic properties of mutation in a finite population. We propose an alternative approach which corrects for this error, which we denote the delay-deterministic model. Applying our model to a simple evolutionary system we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model.