We combine theoretical and laboratory studies to study mechanisms of genome evolution. Current interests include:
1 ) lineage-specific genome evolution: we are trying to
understand why nucleotide and amino acid composition
vary strongly among closely related Drosophila.
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 ) Phenotypic bases of weak selection: biosynthetic constraints or selection for efficient synthesis may be important global factors in genome and proteome 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.
Matsumoto, T., John, A., Baeza-Centurion, P., Li, B., and Akashi, H. (2016). Codon usage selection can bias estimation of the fraction of adaptive amino acid fixations. Mol Biol Evol 33, 1580-1589.
Akashi, H., Osada, N., and Ohta, T. (2012). Weak selection and protein evolution. Genetics 192, 15-31.
Osada, N., and Akashi, H. (2012). Mitochondrial-Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex. Mol Biol Evol 29, 337-346.