Data from: Mild warming induces divergent plastic responses in gene expression among populations of a temperate butterfly
Data files
Mar 27, 2026 version files 14.88 MB
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README.md
5.06 KB
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smrExptOrg.rds
14.45 MB
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Verspagen2026_BlastResults.txt
400.22 KB
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Verspagen2026_DataMatrix.csv
6.90 KB
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Verspagen2026_FlowcelLane.xlsx
12.50 KB
Abstract
In response to potentially stressful conditions, for example, due to climate change, organisms can move, adjust through phenotypic plasticity, and evolve. Evolution can act on mean trait values, but also on plasticity itself. We performed a common garden experiment with two populations of Glanville fritillary butterflies originating from different latitudes in Europe, each tested at two temperature treatments. We investigated gene expression patterns using differential expression analysis as well as weighted gene co-expression network analysis (WGCNA) to disentangle genetic from plastic effects. We found that, regardless of population of origin, most differentially expressed genes were responsive to temperature. We also found strong evidence for variation in plasticity between populations (GxE), but no clear evidence for genetic assimilation or compensation. Patterns for gene co-expression modules were more complex, indicating the importance of considering coordinated, low-level changes across many genes. Biological processes overrepresented in differentially expressed genes and gene co-expression modules are generally related to cellular maintenance and growth. Our results highlight the importance of intraspecific differences in phenotypic plasticity in response to mild warming.
Dataset DOI: 10.5061/dryad.4xgxd25qj
Description of the data and file structure
This data was collected in a common garden experiment performed in 2022 with 2 populations and 2 temperature treatments.
Files and variables
File: Verspagen2026_DataMatrix.csv
Description: This file includes all information on the samples.
Variables
- ID: a unique identifier for each individual. It is made up of population, family, temperature, clutch, replicate and individual (all separately explained below)
- Population: codes for country of origin, with AF for Finland and CAT for Spain
- Family: indicates the experimental family, i.e. ID of the mother
- Temperature: experimental day temperature (25 or 34 degrees celsius). Night temperature was constant at 8 degrees celsius for all treatments.
- Clutch: egg clutch ID
- Replicate: further defines the experimental group the individual grew up in
- Individual: ID number to identify the individual
- Sex: sex of the individual as determined through SNPs on the Z chromosome
- Sampling day: day after starting the experiment that the individual was sampled
- Average group development time: average development time in days for each experimental group, determined from phenotypic data of the remaining larvae not sampled for RNA
- Proportion completed development: the proportion of completed development at the sampling time (sampling day / average group development time)
- Mass day 8: the group mass at day 8 of development (mg)
- Mass day 12: the group mass at day 12 of development (mg)
- Mass closest sampling day: the mass as measured closest to the sampling day (mg)
File: Verspagen2026_FlowcelLane.xlsx
Description: This file provides information on sequencing, such as library ID, flow cell name, and lane number. Sample name corresponds to the sample ID from the data matrix. Data matrix and sequencing info are combined and used for data exploration. Temperature and population identifiers are also used in further analysis.
Variables
- Sample name: an individual code for each sample consisting of a running number (only in this file), the population (AF = Finland, CAT = Spain), the experimental family (i.e. mother's ID), the temperature (34 or 25 degrees celcius), the egg clutch ID, and the individual ID (running number from 1-3).
- Library ID: a code to identify the library
- Flow cell name: name of the flow cell for this sample
- Lane number: lane number for this sample
File: Verspagen2026_BlastResults.txt
Description: The results of a blast of all genes against the Drosophila genome.
Variables
- subject_y: current gene name
- initial_alias: the Drosophila alias initially given to the gene
- converted_alias: the converted Drosophila alias
- name: the gene name in the Drosophila genome
- description: a description of the function of the gene
File: smrExptOrg.rds
Description: This is a file that contains all gene counts and metadata and can be used to run the analysis scripts.
Code/software
Code consists of four files:
- Verspagen2026_FamilySelection.R. This script is used to choose the families for the RNAseq experiment. It needs the IndividualData file from https://doi.org/10.5061/dryad.ngf1vhj14.
- Verspagen2026_DataExploration.R. This script performs the data exploration and quality check. It needs the raw sequencing data that are cleaned and aligned to the reference genome (https://doi.org/10.5524/100915) through https://nf-co.re/rnaseq/3.11.2. It also uses the data matrix, flowcel lane, and blast results data files stored in the current folder.
- Verspagen2026_WGCNA.R. This script does some more data exploration and performs WGCNA analysis. It needs output from Verspagen2026_DataExploration.R to run.
- Verspagen2026_GlmmSeqDE.R. This script performs differential expression analysis. It needs output from Verspagen2026_DataExploration.R to run.
- Verspagen2026_Overrepresentation.R. This script performs overrepresentation analysis. It needs outputs from Verspagen2026_WGCNA.R and Verspagen2026_GlmmSeqDE.R, as well as reference genome annotation files (https://doi.org/10.5524/100915).
Access information
Publicly accessible location of other data used in this publication, and to run the software
- Reference genome and annotations were downloaded from Smolander et al. (2021): https://doi.org/10.5524/100915
- The nf/core script used for alignment of sequencing data to the reference genome can be downloaded from here: https://nf-co.re/rnaseq/3.1
- Phenotype data on development can be downloaded from here: https://doi.org/10.5061/dryad.ngf1vhj14