Bacterial evolution

See all publications from the lab

Lab members | Equal contribution

2025

Samhita L, Tamhankar S, Miranda J, Basu A, and Agashe D (2025). Cost of altered translation accuracy shapes adaptation to antibiotics in E. coli. Molecular Biology and Evolution 42(12):1-14 Open Access | MBE Highlight

Sane M, Parveen S and Agashe D (2025). Mutation bias alters the distribution of fitness effects of mutations. PLoS Biology 23(7):e3003282 Open Access

2024

M Sreepadmanabh, Ganesh M, Sanjenbam P, Kurzthaler C, Agashe D and Bhattacharjee T (2024). Cell shape affects bacterial colony growth under physical confinement. Nature Communications 15:9561 Online Access | NCBS news article

Garushyants SK, Sane M, Selifanova MV, Agashe D, Bazykin GA and Gelfand MS (2024). Mutational signatures in wild type Escherichia coli strains reveal dominance of DNA polymerase errors. Genome Biology and Evolution 16(4):evae035 Preprint | Online access

2023

Sane M, Diwan GD, Bhat BA, Wahl LM and Agashe D (2023). Shifts in mutation spectra enhance access to beneficial mutations. Proceedings of the National Academy of Science 120:e2207355120 Online access | NCBS news article | News feature in IndiaBioscience

Raval PK, Ngan WY, Gallie J and Agashe D (2023). The layered costs and benefits of translational redundancy. eLife 12:e81005 Open Access | eLife Digest | Press release

2022

Mahajan S and Agashe D (2022). Evolutionary jumps in bacterial GC content. G3|Genes|Genomes|Genetics 12:jkac108. Preprint | Online access | Research Matters article

Wahl LM and Agashe D (2022). Selection bias in mutation accumulation. Evolution 76: 528-540 Online Access | NCBS news article

2021

Samhita L, Raval PK, Stephenson G, Thutupalli S and Agashe D (2021). The impact of mistranslation on phenotypic variability and fitness. Evolution 75(5):1201-1217 Open Access | NCBS News article | Biopatrika interview

2020

Samhita L, Raval PK and Agashe D (2020). Global mistranslation increases cell survival under stress in E. coli. PLoS Genetics 16(3): e1008654 Open Access | NCBS news article | Recommended by Faculty of 1000

Sanjenbam P, Buddidathi R, Venkatesan R, Shivaprasad PV and Agashe D (2020). Phenotypic diversity of Methylobacterium associated with rice landraces in North-east India. PLoS One 15(2): e0228550 Open Access

2019

Kaminski Strauss S, …, Agashe D, …, Walunjkar N, …. and Yitzak Pilpel [total 63 authors] (2019). Evolthon: A community endeavor to evolve lab evolution. PLoS Biology 17(3): e3000182 Open access

2018

Sane M, Miranda JJ and Agashe D (2018). Antagonistic pleiotropy for carbon use is rare in new mutations. Evolution 72(10):2202-2213 Open access | NCBS News article

Diwan GD and Agashe D (2018). Wobbling forth and drifting back: The evolutionary history and impact of tRNA modifying enzymes. Molecular Biology and Evolution 35(8):2046-2059 Open access | NCBS News article

Mahajan S and Agashe D (2018). Translational selection for speed is not sufficient to explain variation in bacterial codon usage bias. Genome Biology and Evolution 10(2):562–576 Open access | GBE Special issue on synonymous mutations

2017

Agashe D (2017). The road not taken: Could stress-specific mutations lead to different evolutionary paths? PLoS Biology 15(6): e2002862 Open access

2016

Diwan GD and Agashe D (2016). The frequency of internal Shine-Dalgarno – like motifs in prokaryotes. Genome Biology and Evolution 8(6):1722-1733 Open access

Agashe D, Sane M, Phalnikar K, Diwan GD, Habibullah A, Martinez-Gomez NC, Sahasrabuddhe V, Polachek W, Wang J, Chubiz L and Marx CJ (2016). Large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium. Molecular Biology and Evolution 33: 1542-1553. Open access | MBE News

Nayak DD, Agashe D, Lee M-C and Marx CJ (2016). Selection maintains apparently degenerate metabolic pathways due to tradeoffs in using methylamine for carbon versus nitrogen. Current Biology 26:1416-1426 PDF

2015

Carroll SM, Chubiz LM, Agashe D and Marx CJ (2015). Parallel and divergent evolutionary solutions for the optimization of an engineered central metabolism in Methylobacterium extorquens AM1. Microorganisms 3:152-174 PDF

2014

Agashe D and Shankar N (2014). The evolution of bacterial DNA base composition. Journal of Experimental Zoology, series B 322 (7): 517-528 PDF

2009–2013

Agashe D, Martinez-Gomez NC, Drummond DA and Marx CJ (2013). Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Molecular Biology and Evolution 30(3): 549-560 PDF | SI | Recommended by Faculty of 1000