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.
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.