Data from: Selection for early reproduction leads to accelerated aging and extensive metabolic remodeling in Drosophila melanogaster
Data files
May 02, 2025 version files 1.08 MB
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A-C_Normalized_Metabolomics_Time_Series_Data.csv
311.99 KB
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Metabolomics_Raw_Data.xlsx
519.23 KB
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README.md
5.36 KB
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Winter_2023_Mortality.csv
240.72 KB
Abstract
Experimental evolution studies that feature selection on life-history characters are a proven approach for studying the evolution of aging and variation in rates of senescence. Recently, the incorporation of genomic and transcriptomic approaches into this framework has led to the identification of hundreds of genes associated with different aging patterns. However, our understanding of the specific molecular mechanisms underlying these aging patterns remains limited. Here, we incorporated extensive metabolomic profiling into this framework to generate mechanistic insights into aging patterns in Drosophila melanogaster. Specifically, we characterized metabolomic change over adult lifespan in populations of D. melanogaster where selection for early reproduction has led to an accelerated aging phenotype relative to their controls. Using these data we: i) evaluated evolutionary repeatability across the metabolome; ii) assessed the value of the metabolome as a predictor of “biological age” in this system; and iii) identified specific metabolites associated with accelerated aging. Generally, our findings suggest that selection for early reproduction resulted in highly repeatable alterations to the metabolome and the metabolome itself is a reliable predictor of “biological age”. Specifically, we find clusters of metabolites that are associated with the different rates of senescence observed between our accelerated aging population and their controls, adding new insights into the metabolites that may be driving the accelerated aging phenotype.
https://doi.org/10.5061/dryad.1ns1rn92x
The Datasets consist of three files containing data from Drosophila melanogaster populations under selection for early reproduction (A-type), their controls (C-type), and their sub-populations AO (A-type derived from O-type), ACO (A-type derived from C-type derived from O-type), CO (C-type derived from O-type), and nCO (new C-type derived from O-type).
- The full LC-MS metabolomics data set for 80 pooled samples from adult females at four age classes (Metabolomics_Raw_Data.xlsx)
- The normalized, mean-centered version of the same metabolomics data (A-C_Normalized_Metabolomics_Time_Series_Data.csv)
- Mortality data for the same populations (Winter_2023_Mortality.csv)
Description of the data and file structure
The full LC-MS metabolomics data (Metabolomics_Raw_Data.xlsx) is structured in six tables with the following information
- Key: A key to the rest of the tables
- Sample ID: This sheet provides sample numbers that were used for LC-MS analysis (NWMRC ID) and the corresponding sample ID. The order of sample numbers shows the order in which the samples were analyzed. QC(I)#1, QC(I)#2, etc. indicate the same instrument quality control sample analyzed repeatedly, every 10 samples. A pooled commercial human plasma sample was used as the instrument quality control to monitor the instrument stability during the analysis. QC(S)#1, QC(S)#2, etc. indicate the same sample quality control sample analyzed repeatedly, every 10 samples. A pooled sample made using a small portion from each of the samples was used as the sample quality control.
- Data Reproducibility: This sheet provides metabolite data for the instrument quality control samples [QC(I)'s] and sample quality control samples [QC(S)'s] used in the analysis as indicated in the Sample ID sheet. Coefficient of variation (CV) for each metabolite, average CV and median CV are also provided for both QC(I) and QC(S) samples to assess the instrument performance during the analysis. Any metabolite not detected is indicated as N/A.
- Relative Quant Data: This sheet provides the full list of metabolites targeted in the analysis and their relative concentration. HMDB ID and KEGG ID are also provided for each metabolite in columns 2 and 3, respectively, to help with further analysis of the data such as pathway analysis, if needed. Sample IDs shown in the first row are the numbers we have given (NWMRC IDs). Please refer to the Sample ID sheet for the corresponding ID for the samples. When isotope labeled internal standards are used for absolute quantitation or additional quality check, they are listed towards the end of the sheet. Any metabolite not detected in the sample is indicated as N/A. Please note, the data is not normalized either with reference to the protein amount or quality control data [QC(I) or QC(S)].
- Sample Info: This sheet contains information for each sample including: sample run ID (NWMRC ID), serial number, sample ID, sample size (number of flies), sample type, population (A-type sub-populations of AO or ACO, and C-type sub-populations of CO or nCO), and day (from egg).
- Metabolite Information: This sheet provides some important information on the metabolites targeted in the analysis. Information provided includes HMDB ID, KEGG ID, molecular formula, CAS number and typical pathway each metabolite represents.
The Normalized, mean centered metabolomics data (A-C_Normalized_Metabolomics_Time_Series_Data.csv) is structured in a single table, with sample information provided in the first seven columns, including:
- Pop - selection regime sub-population replicate (repicate 1-5 for sub-populations AO, ACO, CO, and nCO)
- Day - age from egg in days
- Sel - selection regime sub-population (either AO, ACO, CO, and nCO)
- SimpleSel - selection regime (either A-type or C-type)
- RunOrder - the LC-MS run order
- Batch - the LC-MS batch (either 1 or 2)
- NumberOfFliesInSample - the pooled sample size (typically 50 flies)
- Remaining columns provide normalized, mean-centered abundance values for each sample (row) by specific metabolite (column).
The mortality data is structured in a single table (Winter_2023_Mortality.csv), with sample information in the first five columns, including:
- Selection - selection regime sub-population (either AO, ACO, CO, or nCO)
- Population - population replicate number (1-5)
- Age - days since start of assay (assay starts with flies aged 14 days since egg)
- Alive - total number of live flies in the population
- Sex - indicates the which sex for which the count is relevant (males (M) and females (F) are accounted for separately)
- AlivePerc - the percent of files alive relative to previous time point
- AgeSpecificMort - calculated age specific mortality
- SimpleSel - selection regime (A-type (A) or C-type (C))
- DeadPerDay - number of dead flies counted for that day
Code/Software
R-code for data normalization and subsequent analysis associated with this dataset can be found at https://github.com/mphillips67/A-and-C-Metabolomic-Trajectory-Project
Data sets include full LC-MS data for 80 pooled metabolomic samples of adult female Drosophila melanogaster collected from 10 replicate populations under selection for early reproduction (A-type) and their controls (C-type) at four timepoints spanning adulthood. Normalized metabolomic data is also provided for this same data set.
Additionally, mortality data for both males and females are presented for these same populations.