The capacity for adaptation to climate warming in a naturalized annual plant (Brassica rapa)
Data files
Oct 16, 2025 version files 2.33 MB
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01_Data_exploration.R
69.21 KB
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02_MCMC_dataprep.R
11.64 KB
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03_MCMC_ambient.R
106.95 KB
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04_MCMC_heated.R
106.64 KB
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05_MCMC_genetic_correlations.R
56.61 KB
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06_Climate_analysis.R
11.30 KB
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climate_combined_data.csv
516 B
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heatarrays_animal_pedigree.csv
105.53 KB
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heatarrays_brassica_2019_data.csv
1.65 MB
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README.md
12.82 KB
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S1_Frequentist_trait_mean_analysis.R
35.58 KB
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S2_Flowering_time_analysis.R
34.73 KB
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S3_MCMC_full_models.R
94.38 KB
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S4_lme4_Vg_broad.R
18.10 KB
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S5_MCMC_Vg_broad.R
21.67 KB
Abstract
The persistence of a declining population under environmental change may depend on how fast natural selection restores fitness, a process called “evolutionary rescue”. In turn, evolutionary rescue depends on a population’s adaptive capacity, which can be defined as the ratio between additive genetic variance for fitness (VA(W)) and mean fitness (W-), or represented by ΔevolW-. However, little is known about how both VA(W and (W-) change in wild populations during environmental change, including changes in dominance variance for fitness (VD(W)). We assessed the change in ΔevolW- and VD(W) for a Québec population of wild mustard (Brassica rapa) under climate warming. We also evaluated adaptive constraints that could arise from negative genetic correlations for fitness across environments. We grew a pedigreed population of 7000 plants under ambient and heated (+4°C) temperatures and estimated the change in mean survival and fecundity (W-), VA(W), and VD(W), plus cross-environment genetic correlations (rA). VA for fecundity non-significantly increased under heated conditions, mean fecundity (evolW-) increased significantly, and ΔevolW- was unchanged. We also detected no significant rA for survival and fecundity, suggesting little antagonistic constraint to adaptation. Overall, while this B. rapa population may feature some adaptive plasticity via fecundity, its adaptive capacity to warming seems limited.
Dataset DOI: 10.5061/dryad.k3j9kd5nb
Description of the data and file structure
Data files for "The capacity for adaptation to climate warming in a naturalized annual plant (Brassica rapa)"
Authors: Cameron P. So(1,2,3), Sydney Rotman(1), Karl Grieshop (1,4,5), Arthur E. Weis(1,6)
Affiliation: University of Toronto (1); McGill University (2); Quebec Centre for Biodiversity Science (3); Stockholm University (4); University of East Anglia (5); Koffler Scientific Reserve (6);
Corresponding Author: Cameron P. So (cameron.so@mail.mcgill.ca)
Submission Date: 2025-09-11
Short summary: Field experiment carried out at Koffler Scientific Reserve, testing the changes in adaptive capacities for a population of wild mustard when exposed to a warmer climate. All missing data represented as NA.
Files and variables
File: climate_combined_data.csv
Description: Climate data retrieved from the weather station (North York, ON) closest to the the experimental site at Koffler Scientific Reserve, and the weather station closest to the sampling site (St. Georges, QC).
Variables
- Month: Month of year (character)
- D_Month: Month of year (digit)
- Station: Weather station name
- Temp: Average daily air temperature (Celsius)
- Temp_StDev: Daily air temperature standard deviation (Celsius)
- Temp_Min: Average daily minimum temperature (Celsius)
- Temp_Max: Average daily maximum temperature (Celsius)
- Total_Precip: Total monthly precipitation (mm)
File: heatarrays_animal_pedigree.csv
Description: pedigree file for input to estimate quantitative genetic parameters, based on formating required for MCMCglmm.
Variables
- animal: unique plant ID out of the pedigreed population (animal is arbitrary and refers to the first quantitative genetic models used for animal husbandry)
- matID: unique maternal ID
- patID: unique paternal ID
File: heatarrays_brassica_2019_data.csv
Description: Cleaned but raw data prior to processing for MCMCglmm estimation of quantitative genetic parameters.
Variables
- posID: Unique identifier corresponding to the row and position of a given seed at a plot (ranges from 1-605; only plot 1 ranges from 1 to 615).
- individual: Unique identifier corresponding to the plant number within the entire experiment (1 through 7270).
- plot: Plot number (1 to 12)
- animal: Identity for relatedness in the animal model.
- packID: Unique identifier corresponding to the coin envelope containing the 10 seeds planted in a given plot. M stands for the maternal group, S stands for the sire group.
- mat_group: Unique identifier corresponding to the maternal group of the larger pedigree.
- matID: Unique identifier corresponding to the dam of the maternal group.
- patID: Unique identifier corresponding to the sire.
- famID: Unique identifier corresponding to the family group (1 to 62).
- treatment: Treatment applied: either 4 Celsius infrared heat (H) or ambient (A).
- germ_date: Germination date collected weekly (census 1-7) in the calendar year.
- germ_juln_date: Germination date using the Julian calendar.
- germ_bin: Successful germination recorded throughout censuses (1=yes, 0=no).
- notes1: Notes taken during census 1 through 3 for germination only (2019-04-29, 2019-05-09, and 2019-05-14).
- double: Multiple plants (2+) detected within the plot position. Data later omitted in analysis.
- damage: Plants removed from the study since accidentally damaged during a census.
- leaf1: Number of leaves at least partially unfolding on plant during census 3
- notes2: Notes taken during census 3 (2019-05-16).
- leaf2: Number of leaves at least partially unfolding on plant during census 4.
- notes3: Notes taken during census 4 (2019-05-21).
- leaf3: Number of leaves at least partially unfolding on plant during census 5.
- notes4: Notes taken during census 5 (2019-05-27 [P1-8] AND 2019-05-28 [P1-12] AND 2019-05-29 [P1-12]).
- leaf4: Number of leaves at least partially unfolding on plant during census 6.
- notes5: Notes taken during census 6 (2019-06-03 [P1-4] AND 2019-06-04 [P5-6,10-12] AND 2019-06-05 [P7-9]]).
- leaf5: Number of leaves at least partially unfolding on plant during census 7.
- notes6: Notes taken during census 7 (2019-06-11 [P1-4] AND 2019-06-12 [P5-6, 8, 11-12] AND 2019-06-14 [P7, P9-10]).
- leaf6: Number of leaves at least partially unfolding on plant during census 8.
- notes7: Notes taken during census 8 (2019-06-18 [P1-2] AND 2019-06-19 [P3-6, 11-12] AND 2019-06-20 [P8, 10] AND 2019-06-21 [P7, P9]).
- leaf7: Number of leaves at least partially unfolding on plant during census 9.
- notes8: Notes taken during census 9 (2019-06-24 [P1-2] AND 2019-06-25 [P3-6, 12] AND 2019-06-26 [P7-11]).
- leaf8: Number of leaves at least partially unfolding on plant during census 10.
- notes9: Notes taken during census 10 (2019-07-02 [P1-3] AND 2019-07-03 [P4-6, 12] AND 2019-07-04 [P7-11]).
- leaf9: Number of leaves at least partially unfolding on plant during census 11.
- notes10: Notes taken during census 11 (2019-07-08 [P1-2] AND 2019-07-09 [P3-6, 12] AND 2019-07-10 [P7-11]).
- flwr_date: First flowering date (census 7-13).
- flwr_juln_date: Germination date using the Julian calendar.
- flwr_bin: Successful flowering (opened flowers) throughout censuses (1=yes, 0=no).
- flwr_clstr1: Number of flowered clusters (must be open) observed during census 5.
- bud_clstr1: Number of branches with buds (must be green and big) observed during census 5.
- notes11: Notes taken during census 5 (2019-05-27 [P1-8] AND 2019-05-28 [P1-12] AND 2019-05-29 [P1-12]).
- flwr_clstr2: Number of flowering clusters (must be open) observed during census 6.
- bud_clstr2: Number of branches with buds (must be green and big) observed during census 6.
- notes12: Notes taken during census 6 (2019-06-03 [P1-4] AND 2019-06-04 [P5-6,10-12] AND 2019-06-05 [P7-9]]).
- flwr_clstr3: Number of flowering clusters (must be open) observed during census 7.
- bud_clstr3: Number of branches with buds (must be green and big) observed during census 7.
- notes13: Notes taken during census 7 (2019-06-11 [P1-4] AND 2019-06-12 [P5-6, 8, 11-12] AND 2019-06-14 [P7, P9-10]).
- flwr_clstr4: Number of flowering clusters (must be open) observed during census 8.
- bud_clstr4: Number of branches with buds (must be green and big) observed during census 8.
- notes14: Notes taken during census 8 (2019-06-18 [P1-2] AND 2019-06-19 [P3-6, 11-12] AND 2019-06-20 [P8, 10] AND 2019-06-21 [P7, P9]).
- flwr_clstr5: Number of flowering clusters (must be open) observed during census 9.
- bud_clstr5: Number of branches with buds (must be green and big) observed during census 9.
- notes15: Notes taken during census 9 (2019-06-24 [P1-2] AND 2019-06-25 [P3-6, 12] AND 2019-06-26 [P7-11]).
- flwr_clstr6: Number of flowering clusters (must be open) observed during census 10.
- bud_clstr6: Number of branches with buds (must be green and big) observed during census 10.
- notes16: Notes taken during census 10 (2019-07-02 [P1-3] AND 2019-07-03 [P4-6, 12] AND 2019-07-04 [P7-11]).
- flwr_clstr7: Number of flowering clusters (must be open) observed during census 11.
- bud_clstr7: Number of branches with buds (must be green and big) observed during census 11.
- notes17: Notes taken during census 11 (2019-07-08 [P1-2] AND 2019-07-09 [P3-6, 12] AND 2019-07-10 [P7-11]).
- flwr_clstr8: Number of flowering clusters (must be open) observed during census 12.
- bud_clstr8: Number of branches with buds (must be green and big) observed during census 12.
- notes18: Notes taken during census 12 (2019-07-17 [P1-2] AND 2019-07-18 [P3-5] AND 2019-07-19 [P6-9] AND 2019-07-20 [P12] AND 2019-07-22 [P10-11] AND 2019-07-23 [ADDITIONAL]).
- flwr_cmpl_date: Date of flowering completion (census 9-13).
- flwr_compl_juln: Germination date using the Julian calendar.
- seed_bin: Successful production of seed pods by the end of the season.
- seed_dmg: Number of seed pods attacked by birds and other herbivores.
- seed_undmg: Number of seed pods undamaged by herbivory.
- seed_pods: Total number of seed pods produced over the season (seed_dmg + seed_undmg).
- notes19: Notes taken during census 12 (2019-07-17 [P1-2] AND 2019-07-18 [P3-5] AND 2019-07-19 [P6-9] AND 2019-07-20 [P12] AND 2019-07-22 [P10-11] AND 2019-07-23 [ADDITIONAL]).
- height: Plant height measured from the soil to the heighest point in metres during census 13.
- notes20: Notes taken during census 12 (2019-07-17 [P1-2] AND 2019-07-18 [P3-5] AND 2019-07-19 [P6-9] AND 2019-07-20 [P12] AND 2019-07-22 [P10-11] AND 2019-07-23 [ADDITIONAL]).
- stem_diam: Stem diameter measured at the base of the plant in mm during census 13.
- notes21: Notes taken during census 12 (2019-07-17 [P1-2] AND 2019-07-18 [P3-5] AND 2019-07-19 [P6-9] AND 2019-07-20 [P12] AND 2019-07-22 [P10-11] AND 2019-07-23 [ADDITIONAL]).
- seed_num: Number of seeds collected (for plots 1,2,10, and 11. Note plots 4,6,8 and 10 were random sampled to estimate bird damage). See supplementary materials for methods. Data collected 2019-2020 school year.
- posX: The x coordinate associated with posID in the 20x30 grid.
- posY: The y coordinate associated with posID in the 20x30 grid.
- germ_raster: Number of germinated neighbours using the Queen's rule in a 3x3 grid INCLUDING the plant itself if germinated. (NOT RAW - CALCULATED)
- germ_neigh: Number of germinated neighbours FINAL using the Queen's rule in a 3x3 grid subtracting the plant itself if germinated. (NOT RAW - CALCULATED)
- cone_vol: Volume of the stem up to the flowering point (V=pi(r^2)h/3). (NOT RAW - CALCULATED)
- cone_vol_raster: Cumulative sum of stem volume of neighbouring plants in a 3x3 grid INCLUDING the plant itself if germinated. (NOT RAW - CALCULATED)
- cone_vol_neigh: Cumulative sum of stem volume of neighbourhing plants in a 3x3 grid subtracting the plant volume itself if germinated. (NOT RAW - CALCULATED)
- NOTE: Any 'NA's denote unavailable, as data/notes were not collected/written at that census.
File: 01_Data_exploration.R
Description: Data processing and exploratory graphs
File: 02_MCMC_dataprep.R
Description: Full data processing step, with overlaps from 01_Dataexploration.R Produces MCMC_cleaned.csv for MCMCglmm estimation of quantitative genetic parameters.
File: 03_MCMC_ambient.R
Description: Estimates quantitative genetic parameters (Va, Vd, Vm, h2) and trait means for plants in the ambient treatment. Imported data files can be produced from 02_MCMC_dataprep.R
File: 04_MCMC_heated.R
Description: Estimates quantitative genetic parameters (Va, Vd, Vm, h2) and trait meansfor plants in the heated treatment. Imported data files can be produced from 02_MCMC_dataprep.R
File: 05_MCMC_genetic_correlations.R
Description: Estimates additive genetic variance for plasticity and additive genetic correlations. Imported data files can be produced from 02_MCMC_dataprep.R
File: 06_Climate_analysis.R
Description: Extracts and plots climatic data from climate_combined_data.csv
File: S1_Frequentist_trait_mean_analysis.R
Description: Estimates trait means and treatment effects under Frequentist framework
File: S2_Flowering_time_analysis.R
Description: Estimates flowering times and treatment effects
File: S3_MCMC_full_models.R
Description: Attempts to estimate quantitative genetic parameters in full model, including ambient and heated data. Imported data files can be produced from 02_MCMC_dataprep.R
File: S4_lme4_Vg_broad.R
Description: Estimates broad sense genetic variance under Frequentist framework.
File: S5_MCMC_Vg_broad.R
Description: Estimates broad sense genetic variance under Bayesisan framework
Code/software
All analyses were completed in R with the following package versions:
- MCMCglmm v2.29
- nadiv 2.16.2.0
- QGglmm 0.7.4
Additional analyses and their package versions are provided in the Supplementary Materials.
Additional information
All data files that are imported for analysis, such as those in MCMC_heated or MCMC_ambient scripts, can be produced from the original data file from heatarrays_brassica_2019.csv using the parameters provided. If you require the actual data file due to personal computational limits, please contact the corresponding author.
Access information
Other publicly accessible locations of the data:
