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Nearly neutral evolution across the Drosophila melanogaster genome

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posted on 2023-06-09, 15:57 authored by David Castellano, Jennifer James, Adam Eyre-WalkerAdam Eyre-Walker
Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ~45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.

History

Publication status

  • Published

File Version

  • Accepted version

Journal

Molecular Biology and Evolution

ISSN

0737-4038

Publisher

Oxford University Press

Issue

11

Volume

35

Page range

2685-2694

Department affiliated with

  • Evolution, Behaviour and Environment Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Contributors

Ryan Hernandez

Legacy Posted Date

2018-11-20

First Open Access (FOA) Date

2019-08-24

First Compliant Deposit (FCD) Date

2018-11-19

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