Fitness trade-offs revealed by experimental evolution in <em>Drosophila melanogaster</em>

This repository contains raw allele frequency data associated with the series of analyses presented in Bitter, Greenblum, Rajpurohit et al (2026) Ecology Letters.mThe study consisted of two experiments: An indoor experimental evolution study using four outbred, replicate populations of the DGRP whereby replicate populations underwent sustained reproduction selection for nine, non-overlapping generations and a single bout of stress-tolerance, truncations selection, and a paired indoor/outdoor mesocosm used to test whether SNPs identified via reproduction selection in an environmentally-controlled, lab setting displayed signals of selection and trade-offs in an outdoor mesocosm exposed to natural enviornmental fluctuations. Outdoor mesocosm data for this experiment were previously described and published by Bitter et al. For raw sequencing reads used for the generation of allele frequencies for experiment 1, see NCBI PRJNA1390176, and for raw&nbsp;sequencing reads used for the generation ..., , # Fitness trade-offs revealed by experimental evolution in *Drosophila melanogaster* Dataset DOI: [10.5061/dryad.hx3ffbgt1](https://doi.org/10.5061/dryad.hx3ffbgt1) ## Description of the data and file structure The two attached '.RData' files contain allele frequency data used in the analyses reported by Bitter, Greenblum, Rajpurohit et al. 2026 Ecology Letters. Â Loading each of the .RData files into R will then provide access to 4 distinct data frames : 1. 'samps' data frame: each row corresponds to a particular sample for which allele frequency data is available. The columns then correspond to sample information, notably replicate cage number and collection timepoint. 2. 'afmat' data frame: each row corresponds to a unique single nucleotide polymorphism (1.9 million in total), and values represent the allele frequency for a particular sample. The columns then correspond to all samples listed in the 'samps' data frame, and are ordered by the corresponding row order of the 'samps'...,