Evolutionary Genetics Laboratory

Akashi Group

Population genetics and genome evolution

Faculty

AKASHI, Hiroshi
Professor

hiakashi@nig.ac.jp

researchmap

 Lab HP

Research Summary

Our group studies mechanisms of genome evolution with a focus on global adaptations and the dynamics of weak selection.
We integrate functional genomics data and evolutionary models to motivate our analyses. Current topics include:

  1. phenotypic bases and population genetics of selection on syn-onymous codon usage
  2. amino acid composition and biosynthetic constraints in protein evolution
  3. protein structure/function and modes of slightly deleterious and adaptive evolution.
Metabolic economics and microbrial proteome evolution. A) Chemical energy allocations for biosynthesis of a bacterial cell. About 75% of the budget is used for protein synthesis. Based on data from E. coli (Neidhardt et al. 1990). B) Protein adaptation for energetic efficiency. In Bacillus subtilis, abundant proteins employ less energetically costly amino acids.

Selected Publications

  • Matsumoto T, John A, Baeza-Centurion P, Li B, Akashi H. Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations. Mol Biol Evol. 2016 Jun;33(6):1580-9.
  • Matsumoto T, Akashi H, Yang Z. Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics. 2015 Jul;200(3):873-90.
  • Akashi H, Osada N, Ohta T. Weak selection and protein evolution. Genetics. 2012 Sep;192(1):15-31.
  • Matsumoto T, Akashi H. Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations. G3 (Bethesda). 2018 May 4;8(5):1755-1769.