Akashi Group • Evolutionary Genetics Laboratory::National Institute of Genetics

Akashi Group • Evolutionary Genetics Laboratory

Population genetics and genome evolution

Faculty

AKASHI, Hiroshi

Professor

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Research Summary

We combine theoretical and laboratory studies to study mechanisms of genome evolution. Current interests include:

1 ) Phenotypic bases of weak selection: biosynthetic constraints or selection for efficient synthesis may be important global factors in genome and proteome evolution.
2 ) Modeling evolutionary processes: we employ computer simulations of weak selection and fitness interactions among mutations to determine statistical methods to detect subtle evolutionary forces.
3 ) lineage-specific genome evolution: we are trying to understand why nucleotide and amino acid composition vary strongly among closely related Drosophila.

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.