About: The impact of purifying and background selection on the inference of population history: problems and prospects

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	The impact of purifying and background selection on the inference of population history: problems and prospects
Creator	Jensen, Jeffrey Becher, Hannes Charlesworth, Brian Johri, Parul Riall, Kellen
source	BioRxiv
abstract	Current procedures for inferring population history are generally performed under the assumption of complete neutrality - that is, by neglecting both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects (DFE) and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection effects may result in the mis-inference of population growth under models of both constant population size as well as decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the DFE as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites may be used to infer demographic histories with reasonable accuracy.
has issue date	2020-07-06(xsd:dateTime)
bibo:doi	10.1101/2020.04.28.066365
has license	biorxiv
sha1sum (hex)	00fe44828602737ae06e2ab9dd8ffdfbd3ef640d
schema:url	https://doi.org/10.1101/2020.04.28.066365
resource representing a document's title	The impact of purifying and background selection on the inference of population history: problems and prospects
schema:publication	bioRxiv
resource representing a document's body	covid:00fe44828602737ae06e2ab9dd8ffdfbd3ef640d#body_text
is schema:about of	named entity 'complete' named entity 'demographic' named entity 'neutral' named entity 'selected' named entity 'distribution' »more»

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