# Tempo and mode of genome evolution in a 50,000-generation experiment

## TL;DR

This study tracks genome changes in E. coli over 50,000 generations to understand how mutations contribute to adaptation.

## Contribution

The study reveals how beneficial and neutral mutations shape genome evolution during long-term adaptation.

## Key findings

- Most fixed mutations are beneficial, with fewer beneficial mutations as fitness increases.
- Nonsynonymous and intergenic mutations are overrepresented in adapting populations.
- Neutral mutations accumulate at a constant rate over time.

## Abstract

Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12 Escherichia coli populations to characterize their dynamics over 50,0 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation-accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.