Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations

Microbial populations are often exposed to long-term abiotic disturbances, which can reduce population viability and cause local extinction. Eco-evolutionary theory suggests that spatial refuges can facilitate persistence and evolutionary rescue. However, one drawback of spatial refuges is reduced exposure to nutrients such as carbon and oxygen, suggesting the protective effect of refuges depends on the interplay between environmental conditions and the degree of stress. Here, we test this general idea using mathematical modelling, and experimental evolution of the model bacterium Pseudomonas fluorescens SBW25 under salinity stress. As our model predicted, we find that the ability of spatial refuges to rescue evolving populations from extinction crucially depends on nutrient availability. Populations evolving under salinity stress where nutrient-rich spatial refuges were available, harboured clones that displayed enhanced salt resistance, indicating that nutrient-rich spatial refuges ca..., , , # Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations

[https://doi.org/10.5061/dryad.05qfttfch](https://doi.org/10.5061/dryad.05qfttfch)

## Data and Code/software

Details: The datasets and code in this archive detail the requirements to replicate the statistical and genomics analysis outlined in the associated paper. The use of each section of code is outlined in their respective files.

Software: Analyses were performed using R v4.2.3. The code uses functions of dplyr, tidyverse, and ggplot2. The key packages used for the analyses are 'nlme' (linear models) and ‘vegan’ v 2.6-4 (MANOVA). Variant calling was performed using the breseq C++ computational pipeline (version 0.37.1) in a Linux environment and the SBW25 reference sequence (accession: AM181176).

Data/Code: The data and corresponding code are grouped accordingly:

#### **Measuring population density over time**

This data and analysis are used to determine...