DOI: 10.5061/dryad.pvmcvdnx1
title: Data from: Genetic variation for thermal adaptation in a cosmopolitan stored product pest

description: Ectotherms’ ability to adapt to climate warming depends on the
 availability of genetic variation. This is particularly important for
 insect pests because adaptation to warming could lead to greater crop
 damage and food shortages. We quantified genetic variation in the thermal
 reaction norms of life history traits in the bean beetle Callosobruchus
 maculatus, a stored product pest with a cosmopolitan distribution. We used
 these data to measure genetic variation in fitness, as quantified by the
 temperature response of the intrinsic growth rate. We find that the
 maturation rate, a trait subject to strong biochemical control, exhibits
 the least amount of genetic variation, while the birth rate, subject to
 regulatory feedback processes, exhibits the greatest amount. As a result,
 genetic variation in fitness is constrained by genetic variability in the
 thermal reaction norm for maturation, suggesting that maturation may be
 the key limiting factor in ectotherms' adaptation to climate warming.
description: # **Genetic variation for thermal adaptation in a cosmopolitan stored
 product pest** Data on temperature responses of life history traits of the
 beetle *Callosobruchus maculatus*. Includes experimental data and
 parameter estimations. ## Description of the data and file structure This
 data repository consists of 8 data files, 8 code scripts, and this README
 document, with the following data, code, filenames, and variables: **Data
 files:** 1. **exp_avg_rates.csv:** Contains average values of birth,
 maturation, and mortality rates at each experimental temperature,
 calculated as weighted means and weighted standard deviations (R package
 Hmisc) of the data in f1_avg_rates.csv. Note that absolute mean and SD
 were calculated for juvenile mortality. **Columns:** trial, temp_K
 (temperature in Kelvin), se_mat (standard error of the maturation rate),
 sd_mat (standard deviation of the maturation rate), mat_rate (mean
 maturation rate for all families at the corresponding temperature and
 trial, units: day ^-1^), se_adm (standard error of the adult mortality
 rate), sd_adm (standard deviation of the adult mortality rate),
 ad_mort_rate (mean adult mortality rate for all families at the
 corresponding temperature and trial, units: day ^-1^), se_jm (standard
 error of the juvenile mortality rate), sd_jm (standard deviation of the
 juvenile mortality rate), juv_mort (mean juvenile rate for all families at
 the corresponding temperature and trial, units: day ^-1^), se_birth
 (standard error of the birth rate), sd_birth (standard deviation of the
 birth rate), birth_rate (mean birth rate for all families at the
 corresponding temperature and trial, units: eggs/day). Note that the
 coldest temperature treatment in round 1 (15 °C or 288.15 K) failed to
 produce any adult beetles; therefore, rate values that were not measured
 are indicated as NA. 2. **f1_avg_params.csv:** Contains parameters from
 fits to the average experimental data (exp_avg_rates.csv). For
 descriptions of each column see Equation 1, Table 1, and Methods section
 in the original article. 3. **f1_params.csv:** Contains parameters from
 fits to individual family data. For descriptions of each column see
 Equation 1, Table 1, and Methods section in the original article. Note
 that birth rate was measured for all but 2 families; therefore, parameter
 values that were not estimated are indicated as NA. 4.
 **f1_avg_rates.csv:** Contains averages of experimental data for each
 genetic line (family) in the experiment. **Columns:** fam (family, genetic
 line), temp_K (temperature in Kelvin), mean_birth (mean birth rate, units:
 eggs/day), sd_birth (standard deviation of the birth rate), se_birth
 (standard error of the birth rate), n_birth (number of mating pairs used
 to quantify birth rate), mean_mat (mean maturation rate, units: day ^-1^),
 n_mat (number of individuals used to quantify maturation rate), mean_adm
 (mean adult mortality rate), n_adm (number of adult beetles used to
 quantify adult mortality rate, units: day ^-1^), juv_mortality (juvenile
 mortality rate, units: day ^-1^). Note that the coldest temperature
 treatment in round 1 (15 °C or 288.15 K) failed to produce any adult
 beetles and birth rate was measured for all but 2 families; therefore,
 rate values that were not measured are indicated as NA. 5.
 **f1_b_rates.csv:** Contains birth rate data. **Columns:** fam (family,
 genetic line), trial, temp_K (temperature in Kelvin), mating_pair (mating
 pair ID), avg_lifespan (average female lifespan in that mating pair),
 tot_egg (total number of eggs laid by a female beetle during its
 lifespan), birth_rate (birth rate, calculated by dividing
 tot_egg/avg_lifespan, units: eggs/day). 6. **f1_m_rates.csv:** Contains
 maturation rate data. **Columns:** fam (family, genetic line), trial,
 temp_K (temperature in Kelvin), start_date (date the egg was laid and
 placed in its respective temperature treatment), egg_ID, avg_dev (average
 development time of the emerged adult beetle, unit: days), mat_rate
 (maturation rate, calculated by taking the inverse of avg_dev, unit:
 day ^-1^). Note that average development time at 15 °C (288.15 K) is
 indicated as NA since this temperature failed to produce any adult
 beetles. 7. **f1_ad_mort.csv:** Contains adult mortality data.
 **Columns:** fam (family, genetic line), trial, temp_K (temperature in
 Kelvin), start_date (date the egg was laid and placed in its respective
 temperature treatment), egg_ID, avg_lifespan (average lifespan of the
 adult beetle, in days), ad_mort_rate (adult mortality rate, calculated by
 taking the inverse of avg_lifespan, units: day ^-1^). 8.
 **f1_juv_mort.csv:** Contains juvenile mortality data. **Columns:** fam
 (family, genetic line), trial, temp_K (temperature in Kelvin), j (number
 of eggs that did not develop into adults), a (number of adults emerged
 from that family at their respective experimental temperature), trial,
 mean_mat (average maturation rate of the emerged adults, units: day ^-1^),
 sd_mat (standard deviation of the maturation rate), se_mat (standard error
 of the maturation rate), n_mat (number of adults used to calculate the
 average maturation rate), dev_time (average development time, calculated
 as the inverse of mean_mat, unit = days), tot_eggs (total number of eggs,
 after adding columns j and a), juv_mort (juvenile mortality, calculated as
 abs(log(a/tot_eggs)/dev_time). **Code scripts and workflow:** use the
 scripts in the order they are listed 1.
 **parameter_estimation.R:** Produces the parameter estimations for
 temperature responses of life history traits (birth, maturation, adult and
 juvenile mortality) on the averages of experimental data
 (exp_avg_rates.csv). Parameters were saved on file f1_avg_params.csv and
 are also used in Table 1. 2. **family_curves.R:** Script to build family
 level curves for all traits and *r(T)*. Produces the file fam_rates.csv
 which contains family level curves for Figs 2 and 3 and files rt_avg1.csv
 and rt_avg2.csv used in Fig. 3. 3. **fig2.R:** Script to reproduce Fig. 2,
 average experimental values, predicted average responses, and family level
 curves for all traits. 4. **fig3.R:** Reproduces Fig.3, predicted response
 of *r(T)*, using previously derived data files. 5. **fig4.R:** Calculates
 coefficient of variation (CV) values using experimental data for all
 traits and reproduces Fig. 4. 6. **Table2.R:** Calculates the proportion
 of variation due to genetic (G), environmental (E), interaction (G × E)
 and residual effects for each trait, shown in Table 2. 7. **Fig_S1S4.R:**
 Script to reproduce supplementary figures S1-S4 (trait comparisons between
 the two trials at all temperatures). 8. **FigS5.R:** Script to reproduce
 supplementary figure S5 (individual family values of *r(T)*). ##
 Code/Software All analyses were performed using R version 4.5.0
 (2025-04-11)"How About a Twenty-Six" in RStudio Version RStudio
 2025.05.0+496 "Mariposa Orchid" Release
 (f0b76cc00df96fe7f0ee687d4bed0423bc3de1f8, 2025-05-04) for macOS