https://doi.org/10.5061/dryad.80gb5mkxd

These are the scripts and data used for analysis in the manuscript 'Mosquito thermal tolerance is remarkably constrained across a large climatic range' by Lisa Couper, Johannah Farner, Kelsey Lyberger, Alexandra Lee, and Erin Mordecai. The manuscript investigates the evidence for mosquito thermal adaptation using Aedes sierrensis as a model system. We collected 10 populations of Aedes sierrensis from tree holes across western North America (spanning 1,200 km), then reared all individuals in the lab for one generation under common temperatures. We then separated F1 individuals into one of six temperature treatments ranging from 5-32℃ and tracked individuals daily to measure individual life history traits including larval and pupal survival and development rates, and adult lifespan. We then fit thermal performance curves to these experimental data to estimate upper and lower thermal limits and thermal optima for each population and trait. In our investigation of variation in mosquito thermal tolerance, we compared variation in these estimated upper thermal limits for each trait and population.

Description of the data and file structure

The following datasets were used in this experiment and analysis:

1. Nine climate .csv data files, each corresponding to a specific temperature variable, calculated from 2000 - 2020 for the area surrounding each tree hole. For each file, the climate variable is listed in the file name (e.g., 'Treehole_Exceed35_2000_end2021.csv'). The following variables are included in each file:
   1. Population: the tree hole at which the temperature variable is provided
   2. Year2000 - Year 2021: the year for which the temperature variable is provided. Units are either degrees C, or the number of days.
2. LifeHistoryData_PreProcessing.csv. This file contains the raw data from the experiment. Herein, each row denotes an individual mosquito used. The cleaning of this raw data file was conducted using the 'LifeHistoryTraitExp_Analysis_PreProcessing.R' script below. The following variables are included in this csv file:
   1. SampleID: the unique identifier for each mosquito
   2. Population: the tree hole from which the individual originated
   3. Temp.Treatment: "A" - "F", indicating whether the individual was held at 5, 13, 187, 24, 28, 32 degrees C.
   4. Date.Stated: the date at which that individual was placed at their designated temperature treatment, thus starting the experiment
   5. Date.Larval.Death: the date on which the individual died as a larvae, or 'NA' if the individual did not die at this life stage
   6. Larval.Diapause: y/n depending on whether the individual remained in diapause until the conclusion of the experiment. Note this is only relevant for individuals held at 5 or 13 degrees C.
   7. Date.Pupation: the date the individual pupated, or 'NA' if the individual died prior to this life stage transition
   8. Date.Pupal.Death: the date on which the individual died as a pupae, or 'NA' if the individual did not die at this life stage
   9. Date.Adult.Eclosion: the date on which the individual emerged as an adult, or 'NA' if the individual did not survive to this life stage transition
   10. Date.Adult.Death: the date on which the individual died as an adult, or 'NA' if the individual did not die at this life stage
   11. Sex: M/F, or 'NA' if the individual did not survive to adulthood
   12. Usage: a 'notes' column, used to indicate whether the individual should be used for sequencing (i.e., if there was any missing data in the prior columns, individuals were not kept for sequencing)
   13. Left.Wing.Length: the size (mm) of the individuals left wing
3. LifeHistoryTrait_Data_NAs.csv. This file contains the cleaned version of the above, raw data file, with cleaning performed in the R script: 'LifeHistoryTraitExp_Analysis_PreProcessing.R'. The same variables as above are included, with the addition of:
   1. Larval.Survival: 0/1 to indicate whether the individual died (0) or survived (1) the larval life stage
   2. Length.Larval.Dev: the length of the larval development period (in days)
   3. Length.Pupal. Dev: the length of the pupal development period (in days)
   4. Length.Juvenile.Dev: the length of the larval and pupal development period (in days)
   5. LarvalDevRate: the rate of larval development (1/days)
   6. PupalDevRate: the rate of pupal development (1/days)
   7. JuvenileDevRate: the rate of juvenile development (1/days)
   8. Juvenile.Survival: 0/1 to indicate whether the individual died (0) or survived (1) the larval and pupal life stage
   9. AdultLifepsan: the number of days from adult eclosion to death (or 'NA' if the individual did not reach adulthood)

Sharing/Access information

These same datasets and scripts are freely and publicly available at the following Github repository: https://github.com/lcouper/MosquitoThermalAdaptation/tree/main

Code/Software

Included here is:

1. EarthEngine_ClimateAnalysis_Script.rtf: an Earth Engine script used to calculate relevant temperature variables from PRISM data. This script was used to generate and compile the climate data provided in the nine climate .csv files above (e.g.,Treehole_Exceed35_2000_end2021.csv)
2. LifeHistoryExp_DataPreProcessing.R: The R script used to clean and re-shape the raw experiment data file (i.e., LifeHistoryData_PreProcessing.csv', the output of which becomes the file 'LifeHistoryTrait_Data_NAs.csv')
3. LifeHistoryTraitExp_DownstreamAnalysis.R: The R script used on the 'LifeHistoryTrait_Data_NAs.csv' data file to perform basic downstream analysis including the regression models and correlations described in the manuscript.
4. TraitFits_PDR.R, TraitFits_LDR.R, TraitFits_pLS.R, TraitFits_pPS.R, TraitFits_AL.R : The R scripts used to fit Bayesian thermal performance curve models for each trait. Here, each script conducts the fitting for a single trait. Abbreviations are as follows: PDR = pupal development rate, LDR = larval development rate, pLS = probability of larval survival, pPS = probability of pupal survival, AL = adult lifespan