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The consequences of not accounting for background selection in demographic inference

Jeffrey David Jensen, Gregory Bruce Ewing
2016
Journal paper
Abstract

Recently, there has been increased awareness of the role of background selection (BGS) in both data analysis and modelling advances. However, BGS is still difficult to take into account because of tractability issues with simulations and difficulty with nonequilibrium demographic models. Often, simple rescaling adjustments of effective population size are used. However, there has been neither a proper characterization of how BGS could bias or shift inference when not properly taken into account, nor a thorough analysis of whether rescaling is a sufficient solution. Here, we carry out extensive simulations with BGS to determine biases and behaviour of demographic inference using an approximate Bayesian approach. We find that results can be positively misleading with significant bias, and describe the parameter space in which BGS models replicate observed neutral nonequilibrium expectations.

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Related concepts (36)
Selection bias
Selection bias is the bias introduced by the selection of individuals, groups, or data for analysis in such a way that proper randomization is not achieved, thereby failing to ensure that the sample obtained is representative of the population intended to be analyzed. It is sometimes referred to as the selection effect. The phrase "selection bias" most often refers to the distortion of a statistical analysis, resulting from the method of collecting samples. If the selection bias is not taken into account, then some conclusions of the study may be false.
Bias
Bias is a disproportionate weight in favor of or against an idea or thing, usually in a way that is closed-minded, prejudicial, or unfair. Biases can be innate or learned. People may develop biases for or against an individual, a group, or a belief. In science and engineering, a bias is a systematic error. Statistical bias results from an unfair sampling of a population, or from an estimation process that does not give accurate results on average. The word appears to derive from Old Provençal into Old French biais, "sideways, askance, against the grain".
Effective population size
The effective population size (Ne) is a number that, in some simplified scenarios, corresponds to the number of breeding individuals in the population. More generally, Ne is the number of individuals that an idealised population would need to have in order for some specified quantity of interest (typically change of genetic diversity or inbreeding rates) to be the same as in the real population. Idealised populations are based on unrealistic but convenient simplifications such as random mating, simultaneous birth of each new generation, constant population size, and equal numbers of children per parent.
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