Summary of study

A species thermal tolerance breadth (TTB) delineates the upper and lower temperatures (CTmax and CTmin for ectotherms and Tuc and Tlc for endotherms) that an organism can tolerate, thus TTB can be used as a correlate of extinction risk under climate change, as it reflects an organism’s ability to cope with temperature extremes. Theory suggests TTB evolves with the range of environmental temperatures. Classically, a relatively narrow TTB is observed in tropical vs temperate species. As a result, tropical ectotherms may feature increased extinction risk under climate change due to the proximity of their upper thermal limits (CTmax) and mean environmental temperatures.

In this study, we underscore that an organism’s lifestyle influences the extent of thermal fluctuation in its environment, and we predict that subterranean species have narrower TTBs than surface-dwelling species, as the former evolve under dampened thermal variance. We test this hypothesis in mammals, non-avian reptiles, and arthropods, using the existing data on thermal limits. We find that subterranean species featured reduced TTBs, and the difference was significant in mammals and non-avian reptiles, while subterranean arthropods had significantly lower CTmax and significantly higher CTmin than surface arthropods. Ultimately, our results suggest that classical theory extends past patterns of species geolocation to also encompass a species lifestyle.

Dataset description

The dataset contains data on the thermal tolerance limits (CTmax and CTmin for ectotherms or Tuc and Tlc for endotherms) for mammal, bird, non-avian reptile, amphibian and arthropod taxa modifed from the GlobTherm database by Bennett et al., 2018; 2021. In this database each species lifestyle has been classified as subterranean (belowground) or non-subterranean using a range of sources from species and natural history accounts, academic literature, textbooks, expert opinion and databases. The dataset also contains all R code used to run clean up the raw data, conduct the main and supplementary analyses, and visualize the results.

Description and list of files:

File: SubterraneanProject_DatabaseReferences.docx

Description:

Complete bibliography for all sources used to classify a species lifestyle (subterranean vs non-subterranean).

File: SubterraneanProject-DataOrganization.Rmd

Description:

R code to organize and clean up the data, using the rawdata.csv file to produce to finaldata.csv file.

File: SubterraneanProject-DataAnalysis.Rmd

Description:

R code to conduct the primary and supplementary analyses, uses the finaldata.csv file.

File: SubterraneanProject-Resamplinganalysis.Rmd

Description:

R code to conduct the supplementary bootstrapped PGLS analysis for non-avian reptiles and LMER analysis for arthropods.

File: SubterraneanProject-Graphing_Phylogenies.Rmd

Description:

R code used to visualize model results and develop supplementary figures.

File: mammal_phylogeny.txt

Description:

Phylogeny that was used to conduct the PGLS analysis for mammals from Bininda-Emonds et al., 2007 (doi:10.1038/nature05634).

File: TTOL_animals_unsmoothed.nwk

Description:

Phylogeny that was used to conduct the PGLS analysis for non-avian reptiles and amphibians from Hedges et al., 2015 (doi:10.1093/molbev/msv037).

File: SubterraneanProject_CleanData2025.csv

Description:

Final database that was used to conduct all analyses. In all columns, NA is used to indicate when data is not available.

Variables:

• Species: Genus & Species name.
• Tmax: The upper thermal limit in degrees Celcius.
• MaxMin: Range between Tmax and tmin (the thermal tolerance breadth).
• EnvMaxMin: Range of environmental air temperature for that species geolocation, calculated by taking the difference between temp.max and temp.min.
• max_metric: The metric associated with the upper thermal limit i.e. CTmax, CT50, LT50, LT100.
• lat_max: Latitude.
• long_max: Longitude.
• elevation_max: Elevation (m).
• REF_max: Reference of the thermal maximum.
• Tmin: The lower thermal limit in degrees celcius.
• min_metric: The metric associated with the lower thermal limit i.e. CTmin, LT50, LT100.
• lat_min: Latitude.
• long_min: Longitude.
• elevation_min: Elevation (m).
• REF_min: Reference for thermal minimum.
• Phylum: Taxonomic level as per NCBI.
• Class: Taxonomic level as per NCBI.
• Order: Taxonomic level as per NCBI.
• Family: Taxonomic level as per NCBI.
• Quality of TNZ:
  • 1: high quality estimate, conclusive evidence of an increase in metabolic rates, demonstrated by either multiple measurements beyond the (TNZ) or high intensity sampling,
  • 2: lower quality estimate - evidence of an increase in metabolic rate but insufficient data to fit a regression to estimate the UTNZ due to either a low sample size or low sampling intensity i.e. interval larger than 1 degrees celcius C between measurements,
  • 3: Data was excluded from the dataset when no evidence of an increase in metabolic rate was presented to support the UTNZ i.e. no measurements beyond the stated TNZ in text.
  • Only species with high quality estimates (1) were used in our analysis.
• temp.max: Environmental air temperature maximum based on species geolocation.
• temp.min: Environmental air temperature minimum based on species geolocation.
• burrow_user: Indicates whether a species uses burrows for various activities, such as nesting, sleeping etc. (Y = burrow user, N = not a burrow user, NA = no information available)
• burrow_digger: Indicates whether a species is known to create their own burrows. (Y = species creates its own burrows, N = species does not create burrows, NA = no information available).
• represented_more-than_once: indicates whether a species is represented more than once in the database, either due to a name change or due to changing species definitions in the literature. (Y = represented more than once, N = represented only once, NA = no information available).
• subterranean: Classification on whether a species is subterranean or not. (F = subterranean, N = non-subterranean, NA = no information available).
• data_order: Sequential order in the original database.
• ref_user: References for burrowing use behaviour.
• ref_digger: References for digging behaviour.
• ref_sub: References for subterranean lifestyle.
• Synonyms: Synonym to each species name.
• Family_Genus_info_used: Indicates whether genus level information was used to classify species lifestyle. (Y = genus information was used, N = genus information was not used, NA = no information available).
• Original_species_names: Original species name before modification to match phylogenetic tree.
• MaxMinMethod: Measurement metric combination (see Table S2 in main manuscript for complete description).
• adult_body_mass_g: Body mass in grams for mammals.
• body_mass_g: Body mass in grams for non-avian reptiles.

File: SubterraneanProject_RawData2025.csv

Description:

Raw data that has not been processed, and was adapted from the Bennett et al, 2018 (doi:10.1038/sdata.2018.22), and Bennett et al., 2021 (doi:10.1038/s41467-021-21263-8) GlobTherm Database. In all columns, NA is used to indicate when data is not available.

Variables

• Genus: Genus
• Species: Species
• N_Tmax: Total number of individuals used in the experiment.
• Tmax: The upper thermal limit in degrees celcius.
• MaxMin: Range between Tmax and tmin (the thermal tolerance breadth).
• EnvMaxMin: Range of environmental air temperature for that species geolocation, calculated by taking the difference between temp.max and temp.min.
• max_metric: The metric associated with the upper thermal limit i.e. CTmax, CT50, LT50, LT100.
• error: Error of the thermal maximum.
• error.measure: Measure of error (SD = standard deviation, SE = standard error).
• Multiple.measures: If both critical and lethal measures of thermal tolerance are available for the species it is indicted by Y otherwise N when not available.
• max_pretreatment: Pre-treatment temperature if species were acclimatized before experimentation (F = field fresh).
• max_ramp: The rate of temperature change that individuals were warmed at in degrees celcius per minute.
• lat_max: Latitude.
• long_max: Longitude.
• elevation_max: Elevation (m).
• REF_max: Reference for the thermal maximum.
• N_Tmin: Total number of individuals used in the experiment.
• tmin: The lower thermal limit in degrees Celcius.
• min_metric: The metric associated with the lower thermal limit i.e. CTmin, LT50, LT100.
• min_pretreatment: Pre-treatment temperature if species were acclimatized before experimentation (F = field fresh).
• ramp_min: The rate of temperature change that individuals were cooled at in degrees celcius per minute.
• lat_min: Latitude.
• long_min: Longitude.
• elevation_min: Elevation (m).
• REF_min: Reference for the thermal minimum.
• Phylum: Taxonomic level as per NCBI.
• Class: Taxonomic level as per NCBI.
• Order: Taxonomic level as per NCBI.
• Family: Taxonomic level as per NCBI.
• Quality.of.UTNZ:
  • 1: high quality estimate, conclusive evidence of an increase in metabolic rates, demonstrated by either multiple measurements beyond the (TNZ) or high intensity sampling
  • 2: lower quality estimate - evidence of an increase in metabolic rate but insufficient data to fit a regression to estimate the UTNZ due to either a low sample size or low sampling intensity i.e. interval larger than 1 degrees celcius between measurements
  • 3: Data was excluded from the dataset when no evidence of an increase in metabolic rate was presented to support the UTNZ i.e. no measurements beyond the stated TNZ in text.
  • Only species with high quality estimates (1) were used in our analysis.
• temp.max: Environmental air temperature maximum based on species geolocation.
• temp.min: Environmental air temperature minimum based on species geolocation.
• burrow_user: Indicates whether a species uses burrows for various activities, such as nesting, sleeping etc. (Y = burrow user, N = not a burrow user, NA = no information available).
• burrow_digger: Indicates whether a species is known to create their own burrows. (Y = species creates its own burrows, N = species does not create burrows, NA = no information available).
• hibernates: indicates whether a species is known to hibernate/brumate based on the geographical coordinates given in the database. (Y = species hibernates/brumates, N = species does not hibernate, NA = no information available).
• aestivates: Indicates whether a species is known to aestivate based on the geographical coordinates given in the database. (Y = species aestivates, N = species does not aestivate, NA = information on the species was searched for but there was no information available, X = information on the species was not searched for).
• represented.more.than.once: Indicates whether a species is represented more than once in the database, either due to a name change or due to changing species definitions in the literature. (Y = represented more than once, N = represented only once, NA = no information available).
• subterranean: Classification on whether a species is subterranean or not. (F = subterranean, N = non-subterranean, NA = no information available).
• data_order: Sequential order in the original database.
• ref_user: References for burrowing use behaviour.
• ref_digger: References for digging behaviour.
• ref.hib: References for hibernation.
• ref.aestivates: References for aestivation.
• ref_sub: References for subterranean lifestyle.
• ref.body.mass: References for body mass.
• Synonyms: Synonym to each species name.
• Family_Genus_info_used: Indicates whether genus level information was used to classify species lifestyle. (Y = genus information was used, N = genus information was not used, NA = no information available)
• Notes: Notes based on what was found during the literature search.

Instructions to run the code and analysis:

All files can be run in Rstudio, each file sequentially relies on the file before it (i.e. SubterraneanProject-Graphing&Phylogenies relies on the global variables created in SubterraneanProject-DataAnalysis, which relies on the DataOrganization.rmd file). All analyses and visualization code use the CleanData2025.csv file, while the data organization file uses the RawData2025.csv file.

All analyses for the main manuscript were conducted with R version 4.1.3, and the packages: ape v. 5.5, geiger v. 2.0.7, ggeffects v. 1.3.2, lme4 v. 1.1.27.1, lmerTest v. 3.1.3, nlme v. 3.1-153, phytools v. 0.7.80, and car v. 3.1-2.