Dataset DOI: 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 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 

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 ­