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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Effective population size does not predict codon usage bias in mammals.

Michael D Kessler¹, Matthew D Dean¹

¹Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089.

Ecology and Evolution

|December 16, 2014

Summary

This summary is machine-generated.

Effective population size (N e) does not strongly predict codon usage bias (CUB) across mammalian species. While selection shapes CUB within species, interspecific differences in N e do not consistently explain variations in CUB intensity.

Keywords:

Codon usage bias effective population size selection

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Area of Science:

Evolutionary biology
Genomics
Molecular evolution

Background:

Codon usage bias (CUB) describes the non-uniform usage of synonymous codons.
It is hypothesized that the intensity of CUB is influenced by effective population size (N e), with weaker selection in species with smaller N e.
Understanding the drivers of CUB variation is crucial for comprehending genome evolution.

Purpose of the Study:

To investigate the relationship between effective population size (N e) and codon usage bias (CUB) across mammalian species.
To determine if interspecific variation in N e predicts differences in CUB intensity in mammals.
To explore factors influencing CUB variation within and between mammalian species.

Main Methods:

Analysis of codon usage bias across 41 mammalian genomes using indirect proxies for N e (body mass, generation time).
Comparison of CUB between autosomal and X-linked genes, and genes with high versus low recombination rates.
Correlation analysis between genetic estimates of N e and CUB across six mammalian species (human, chimpanzee, rabbit, and three mouse species).

Main Results:

Codon usage bias was not correlated with body mass or generation time across 41 mammalian genomes.
Autosomal and high-recombination genes exhibited higher CUB than X-linked and low-recombination genes, respectively, suggesting intraspecific N e influences CUB.
Effective population size (N e) showed weak and inconsistent correlations with CUB across the six studied mammalian species.

Conclusions:

Interspecific divergence in effective population size (N e) does not strongly predict variation in codon usage bias (CUB) across mammals.
Intraspecific factors, such as recombination rate and gene location, appear to influence CUB more significantly than interspecific N e.
A unique distribution of selection coefficients across species may confound a direct link between N e and CUB.