Demographic feedbacks during evolutionary rescue can slow or speed adaptive evolution

Populations declining toward extinction can persist via genetic adaptation in a process called evolutionary rescue. Predicting evolutionary rescue has applications ranging from conservation biology to medicine, but requires understanding and integrating the multiple effects of a stressful environmental change on population processes. Here we derive a simple expression for how generation time, a key determinant of the rate of evolution, varies with population size during evolutionary rescue. Change in generation time is quantitatively predicted by comparing how intraspecific competition and the source of maladaptation each affect the rates of births and deaths in the population. Depending on the difference between two parameters quantifying these effects, the model predicts that populations may experience substantial changes in their rate of adaptation in both positive and negative directions, or adapt consistently despite severe stress. These predictions were then tested by comparison t..., , , # R code and simulation outputs

All results in this paper are based on simulation. This package includes the simulation code, outputs, and the scripts used in analyses and making figures.

## Description of the data and file structure

The basic algorithm is contained in the file QG_full_generalized.R. However, several variants were used throughout the paper. Below is a list of the files used in preparing each figure.

All scripts the analyze simulation data require a path set to the location of a directory include the archived outputs, which are each identified by name (azure, blue, cerulean, no_genes, selection_test, organic).

Each of these simulation data directories contains a table file which primarily serves to associate the initial random number seed with each replicate. For each replicate, a file is generated with the allele effects (e.g., azure_effects_0001.txt) and another file is produced with the complete genotype of each individual in the starting population (e.g., azu...