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Published on: June 11, 2020
Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
Rasmus Nielsen1, Vanessa L Bauer DuMont, Melissa J Hubisz
1Institute of Biology and Centre for Bioinformatics, University of Copenhagen, Copenhagen, Denmark. rasmus@binf.ku.dk
Molecular Biology and Evolution
|October 17, 2006
Summary
We developed a new method to analyze codon usage bias and evolutionary rates in fruit fly lineages. This reveals changes in selection for optimal codons and mutation patterns in Drosophila melanogaster.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Codon usage bias influences protein evolution.
- Phylogenetic methods are crucial for understanding evolutionary dynamics.
- Estimating selection pressures and mutation rates requires sophisticated models.
Purpose of the Study:
- To develop a likelihood method for estimating codon usage bias parameters along phylogenetic lineages.
- To jointly estimate selection coefficients for optimal codon usage (S) and dN/dS ratios.
- To investigate evolutionary changes in Drosophila melanogaster, Drosophila simulans, and Drosophila yakuba.
Main Methods:
- Extension of classical codon-based models.
- Inclusion of a lineage-specific selection coefficient for optimal codon usage (S).
- Joint maximum likelihood estimation of S and dN/dS ratios.
Main Results:
- The Drosophila melanogaster lineage shows reduced selection for optimal codon usage.
- A shift in biological mutation rates was observed in D. melanogaster, with decreased A-to-G and increased C-to-T mutation rates.
- Neither reduced selection nor altered mutation patterns fully explain the observed data.
- Positive selection for unpreferred mutations at the Notch locus was confirmed.
Conclusions:
- Evolutionary dynamics in D. melanogaster are shaped by complex interactions between selection and mutation.
- The developed method provides a powerful tool for analyzing codon usage bias and evolutionary rates.
- Further research is needed to fully elucidate the interplay of factors driving molecular evolution.
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