DOI: 10.5061/dryad.k3j9kd5nb
title: The capacity for adaptation to climate warming in a naturalized annual plant (<i>Brassica rapa</i>)

description: 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.
description: # The capacity for adaptation to climate warming in a naturalized annual
 plant (*Brassica rapa*) Dataset DOI:
 [10.5061/dryad.k3j9kd5nb](https://doi.org/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](mailto: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: *
 [https://github.com/socameron/Brassica-rapa-quant-gen](https://github.com/socameron/Brassica-rapa-quant-gen)