Changing population size in McDonald-Kreitman style analyses: artifactual correlations and adaptive evolution between humans and chimpanzees

Soni, Vivak, Moutinho, Ana Filipa and Eyre-Walker, Adam (2022) Changing population size in McDonald-Kreitman style analyses: artifactual correlations and adaptive evolution between humans and chimpanzees. Genome biology and evolution, 14 (2). pp. 1-11. ISSN 1759-6653

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Abstract

It is known that methods to estimate the rate of adaptive evolution, which are based on the McDonald-Kreitman test, can be biased by changes in effective population size. Here, we demonstrate theoretically that changes in population size can also generate an artifactual correlation between the rate of adaptive evolution and any factor that is correlated to the strength of selection acting against deleterious mutations. In this context, we have investigated whether several site-level factors influence the rate of adaptive evolution in the divergence of humans and chimpanzees, two species that have been inferred to have undergone population size contraction since they diverged. We find that the rate of adaptive evolution, relative to the rate of mutation, is higher for more exposed amino acids, lower for amino acid pairs that are more dissimilar in terms of their polarity, volume, and lower for amino acid pairs that are subject to stronger purifying selection, as measured by the ratio of the numbers of nonsynonymous to synonymous polymorphisms (pN/pS). All of these correlations are opposite to the artifactual correlations expected under contracting population size. We therefore conclude that these correlations are genuine.

Item Type: Article
Keywords: McDonald–Kreitman, adaptive evolution, chimpanzee, human, Animals, Evolution, Molecular, Humans, Models, Genetic, Mutation, Pan troglodytes, Polymorphism, Genetic, Population Density, Selection, Genetic
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
SWORD Depositor: Mx Elements Account
Depositing User: Mx Elements Account
Date Deposited: 29 Apr 2022 16:32
Last Modified: 29 Apr 2022 16:45
URI: http://sro.sussex.ac.uk/id/eprint/105585

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