Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs

Molecular Biology and Evolution
Xianming Wu, Laurence D Hurst

Abstract

The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more "bloated" than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis-exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis-splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observ...Continue Reading

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Citations

Nov 8, 2015·Molecular Biology and Evolution·XianMing Wu, Laurence D Hurst
Mar 6, 2016·Molecular Biology and Evolution·Emeric FiguetNicolas Galtier
Jan 24, 2016·Molecular Biology and Evolution·Rosina Savisaar, Laurence D Hurst
Dec 21, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Stephen J BushAraxi O Urrutia
Sep 30, 2017·Molecular Biology and Evolution·Liam Abrahams, Laurence D Hurst
May 3, 2015·Nucleic Acids Research·Ben SmithersJulian Gough
Nov 9, 2017·Genome Biology·Laurence D Hurst, Nizar N Batada
Jun 1, 2018·Wiley Interdisciplinary Reviews. RNA·Bernhard SchaefkeWei Chen
Aug 1, 2019·Molecular Genetics & Genomic Medicine·Martin de BoerDirk Roos
Apr 14, 2017·Human Genetics·Rosina Savisaar, Laurence D Hurst
Aug 17, 2020·Molecular Biology and Evolution·Alexander T Ho, Laurence D Hurst
Oct 13, 2020·Biochemistry. Biokhimii︠a︡·I V Poverennaya, M A Roytberg
May 5, 2021·Genome Biology and Evolution·Martijn CallensStéphanie Bedhomme

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Methods Mentioned

BETA
SMA

Software Mentioned

DnaSP
cens
PAML
MEGA
Nexus
R package “ lmodel2
BayesTraits
MUSCLE
Gblocks
pcor

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