Evolutionary rescue of freshwater copepods during historical lake acidification

The persistence of populations facing severe environmental disturbance can be enabled by natural selection on heritable phenotypic variation - a process known as evolutionary rescue. Few studies have documented this process in complex natural settings and the long-term outcome of evolutionary rescue. Here, we used copepod resting eggs of Leptodiaptomus minutus from three time periods of lake ecological history, spanning ≈ 200 generations (100 years) in two populations impacted by historical acidification. Whole-genome sequencing of the resting eggs revealed significant allele-frequency shifts associated with acidification followed by pH recovery. We used a resurrection ecology approach to retrace adaptive shifts concomitant with environmental transitions. Copepods from the pre-acidification period were sensitive to acidity, whereas those from the acidification period were adapted to acidic pH. This tolerance was subsequently lost during pH recovery, implying an adaptive reversal. Demogr..., , , # Data from: Evolutionary rescue of freshwater copepods during historical lake acidification

#### Description of the data and file structure

We used copepod resting eggs of the freshwater species *Leptodiaptomus minutus* extracted from sediment cores dating from three time periods of lake ecological history, spanning ≈200 generations, in two populations impacted by historical acidification. Whole genome sequencing of the resting eggs was used to detect putative SNPs under selection from the acidification and follow allele frequency shifts associated with the environmental fluctuations. Demographic modelling was applied to the genomic data to retrace changes in genetic diversity related to the acidification. We used a resurrection ecology approach to retrace adaptive shifts concomitant with the environmental transitions.

### Files and variables

This repository contains several top-level files and folders, as well as subfolders:

1. **code_hpc:** This folder contains code written to b...,