DOI: 10.5061/dryad.x69p8czx4
title: Data from: On the correlated evolution of ecological lifestyle and thermal tolerance

description: The breadth of thermal tolerance delineates the upper (CTmax/Tuc) and
 lower (CTmin/Tlc) temperatures relevant to survival and/or persistence of
 organisms, and it is a correlate of extinction risk under climate change.
 Theory suggests that tolerance breadth evolves with the range of
 environmental temperatures. For instance, a narrow tolerance breadth is
 classically observed in tropical vs temperate species, and tropical
 ectotherms may feature increased extinction risk under climate change due
 to the proximity of CTmax and mean environmental temperatures. Here, we
 underscore that an organism’s lifestyle influences the extent of thermal
 fluctuation in its environment. We predict that subterranean species
 feature a narrower thermal tolerance breadth than surface-dwelling
 species, as the former evolve under dampened thermal variance. Using
 thermal limits data, we test this hypothesis in reptiles, mammals, and
 arthropods. Subterranean species (n = 5 – 37 per taxon) featured reduced
 tolerance breadths compared to surface-dwelling species, and the
 difference was significant in reptiles and mammals; additionally,
 subterranean arthropods featured a significantly lower CTmax and
 significantly higher CTmin than surface species. Thus, classical theory on
 thermal tolerance extends beyond patterns of geolocation to species
 lifestyle, where evolution under dampened thermal variance can reduce
 thermal tolerance breadth and influence other thermal traits.
description: # Data from: On the correlated evolution of ecological lifestyle and
 thermal tolerance #### 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.