dictyNews

Electronic Edition

Volume 47, number 9

April 23, 2021



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Abstracts

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Inferring adaptive codon preference to understand sources of 

selection shaping codon usage bias



Janaina Lima de Oliveira1,2a, Atahualpa Castillo Morales2a, 

Laurence D. Hurst2, Araxi O. Urrutia2, Christopher R. L. 

Thompson3*, Jason B. Wolf2*



1. Instituto de Biologia, Universidade Federal da Bahia, Salvador, 

Bahia, 40170-115, Brazil

2. Milner Centre for Evolution and Department of Biology and 

Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK

3. Centre for Life’s Origins and Evolution, Department of Genetics, 

Evolution and Environment, University College London, Darwin 

Building, Gower Street, London, WC1E 6BT, UK



aThese authors contributed equally to this work

*Correspondence to: 

[log in to unmask] & [log in to unmask]





Molecular Biology and Evolution, in press



Alternative synonymous codons are often used at unequal 

frequencies. Classically, studies of such codon usage bias (CUB) 

attempted to separate the impact of neutral from selective forces by 

assuming that deviations from a predicted neutral equilibrium capture 

selection. However, GC biased gene conversion (gBGC) can also 

cause deviation from a neutral null. Alternatively, selection has been 

inferred from CUB in highly expressed genes, but the accuracy of 

this approach has not been extensively tested, and gBGC can 

interfere with such extrapolations (e.g. if expression and gene 

conversion rates covary). It is therefore critical to examine 

deviations from a mutational null in a species with no gBGC. To 

achieve this goal, we implement such an analysis in the highly AT 

rich genome of Dictyostelium discoideum, where we find no evidence 

of gBGC. We infer neutral CUB under mutational equilibrium to 

quantify ‘adaptive codon preference’, a nontautologous genome wide 

quantitative measure of the relative selection strength driving CUB. 

We observe signatures of purifying selection consistent with 

selection favouring adaptive codon preference. Preferred codons are 

not GC rich, underscoring the independence from gBGC. Expression-

associated ‘preference’ largely matches adaptive codon preference 

but does not wholly capture the influence of selection shaping 

patterns across all genes, suggesting selective constraints 

associated specifically with high expression. We observe patterns 

consistent with effects on mRNA translation and stability shaping 

adaptive codon preference. Thus, our approach to quantifying 

adaptive codon preference provides a framework for inferring the 

sources of selection that shape CUB across different contexts 

within the genome.





submitted by: Chris Thompson [[log in to unmask]]

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[End dictyNews, volume 47, number 9]