DOI: 10.5061/dryad.hx3ffbgt1
title: Fitness trade-offs revealed by experimental evolution in <em>Drosophila melanogaster</em>

description: 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 sequencing reads used for the
 generation of allele frequencies for experiment 1, see NCBI PRJNA1031645
description: # 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.   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' data frame (e.g. allele frequency data for
 the sample described in the first row of the 'samps' data frame
 is provided in the first column of the 'afmat' data frame). 3.
 'eec' data frame: each row corresponds to a unique single
 nucleotide polymorphism (1.9 million in total), and values represent the
 estimated effective coverage for a particular sample (see
 [https://doi.org/10.1534/g3.119.400755](https://doi.org/10.1534/g3.119.400755) for the computation of the estimated effective coverage) . The columns then correspond to all samples listed in the 'samps' data frame, and are ordered by the corresponding row order of the 'samps' data frame (e.g. effective coverage data for the sample described in the first row of the 'samps' data frame is provided in the first column of the 'eec' data frame). 4. 'sites' data frame: SNP coordinate information (chromosomal arm and position) for each site in the afmat and eec data frames. This data frame has the same number of rows as the afmat and eec dataframes, whereby the SNP information for each row in the 'sites' data frame corresponds to the allele frequency and effective coverage values in the same row of the afmat and eec data frames. The coordinates in this file correspond the Drosophila melanogaster v5.39 reference genome ### Files and variables #### **File:** `Experiment1_PopulationExpansionTruncation.RData` **Description:**\ Allele frequency data from Experiment 1 of the study. A single genetically diverse, outbred *Drosophila melanogaster* population was used to seed four replicate cages. Each replicate underwent nine generations of population expansion followed by a single bout of population truncation. Pooled allele frequency estimates were generated at eight generations during the expansion phase and at seven time points during the truncation phase. --- #### **File:** `Experiment2_IndoorOutdoorMesocosmStudy.RData` **Description:**\ Allele frequency data from Experiment 2, which paired sampling from indoor mesocosms with sampling from an outdoor, semi-natural mesocosm. Indoor cages experienced sustained population expansion and were sampled at four time points (generations 1, 2, 8, and 11). The outdoor mesocosm was sampled across twelve time points in total. The data provided here include only the time points shared between the indoor and outdoor mesocosms (generations 1, 2, 8, and 11), as well as the final outdoor time point corresponding to population collapse (generation 12). The complete outdoor mesocosm time series was previously analyzed and reported by Bitter et al. (2024), *Nature* (doi: 10.1038/s41586-024-07834-x). #### **File:** indoor_cages_filteredx2.BiolReps.RData Allele frequency data derived from Experiment 1. These data contain those samples for which biological replicate sequencing data was generated (independent pools of 100 flies collected within the same experimental replicate and time point). These data were used in validation that Fst differentiation through time, exceeded that observed among biological replicates of Experiment 1. #### **File:** df.sig.OutdoorMesocosmExpansion.csv Data frame containing SNPs identified as significant during expansion in the outdoor mesocosm, as previously reported by Bitter et al. 2024 (doi: 10.1038/s41586-024-07834-x). **Description:**\ Allele frequency data from Experiment 2, which paired sampling from indoor mesocosms with sampling from an outdoor, semi-natural mesocosm. Indoor cages experienced sustained population expansion and were sampled at four time points (generations 1, 2, 8, and 11). The outdoor mesocosm was sampled across twelve time points in total. This table shows genetic divergence analysis results comparing two groups (labeled "1_11") at specific positions on chromosome 2L. Each row represents a genomic site with its position, effect size (coef.div), and statistical significance (p.div and FDR-adjusted values). The afShift column indicates the direction and magnitude of allele frequency changes between the groups. The sigLevel categorizes how strongly significant each result is, helping identify genomic regions with meaningful differences. ## Code/software The code analyzing the dataframes provided here are available at the following GitHub: [https://github.com/MarkCBitter/Drosophila-fitness-trade-offs/tree/main](https://github.com/MarkCBitter/Drosophila-fitness-trade-offs/tree/main)  ## Access information Other publicly accessible locations of the data and the data were derived from the following: * Raw sequencing reads for Experiment 1 are provided on NCBI: PRJNA1390176 * Raw sequencing reads for Experiment 2 are provided on NCBI: [PRJNA1031645](https://www.ncbi.nlm.nih.gov/bioproject/1031645) ­