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

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posted on 2023-06-10, 03:18 authored by Vivak Soni, Ana Moutinho, Adam Eyre-WalkerAdam Eyre-Walker
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.

History

Publication status

  • Published

File Version

  • Published version

Journal

Genome biology and evolution

ISSN

1759-6653

Publisher

Oxford University Press (OUP)

Issue

2

Volume

14

Page range

1-11

Event location

England

Department affiliated with

  • Evolution, Behaviour and Environment Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2022-04-29

First Open Access (FOA) Date

2022-04-29

First Compliant Deposit (FCD) Date

2022-04-29

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