living-up-to-thermal-potentials

Introduction

This repository contains the data and code used to produce results presented in Moore et al. 2023: Temperate species underfill their tropical thermal potentials on land. This study tests hypotheses about how the role of temperature in limiting species ranges might be overriden by antagonistic species interactions and other range-limiting factors. The study was designed to be reproducible, and running all scripts in order should successfully reproduce analyses and figures.

Data

A minimum dataset needed to reproduce all main analyses and large files that cannot be hosted on Github can be downloaded from the paper's Figshare repository, which is linked in the article Data Availability statement. For scripts to successfully run, the large files should be donwloaded into a folder titled 'large-files' in the repository's working directory.

Additional temperature, elevation, and depth data files used in analyses can be downloaded here:

• Berkeley Earth Daily Land (Experimental; 1880 – Recent) - Average High Temperature (TMAX) and Average High Temperature (TMAX)]
• NOAA OI SST V2 High Resolution Dataset - Mean Daily Sea Surface Temperature
• General Bathymetric Chart of the Oceans - TID Grid
• EarthEnv Global 10-km topography - Maximum and Minimum, GMTED2010

Realized range polygons needed to run analysis can be downloaded here:

• IUCN Spaial Files - AMPHIBIANS, BLENNIES, CLUPEIFORMES, FILTERED, FW_FISH, MAMMALS, MARINEFISH, PUFFERFISH, REPTILES, SEABREAMS_PORGIES_PICARELS, SHARKS_RAYS_CHIMAERAS, WRASSES_PARROTFISHES
• GARD Version 1.1

Code

The following are all of the R scripts contained in this repository and a short description of what each accomplishes:

01_creating-temperature-depth-elev-data.R

• prepares global air and sea surface temperature, depth, and elevation data for use in analyses

02_collating-realized-range-maps.R

• extracts and organizes realized range polygons

03_trait-wrangling.R

• collates and cleans trait data for species incldued in the analysis

04_acclimatisation-analysis.R

• collates and cleans pre-existing acclimation response ratio databases for use in the acclimatisation analysis

05_modelling-operative-temperatures.R

• models operative temperatures in different microhabitat for terrestrial species

06_creating-potential-ranges.R

• creates potential thermal ranges

07_quantifying-niche-filling.R

• measures potential thermal niche filling in thermal space

08_quantifying-range-filling.R

• measures potential thermal range filling in geographic space

09_model-selection_niche.R

• fits models to warm and cool niche filling and plots predictions

10_model-selection_range.R

• fits models to range filling and asymmetry in underfilling and plots predictions

11_sensitivity_model-selection_niche.R

• checks sensitivity of warm and cool niche filling results to behaviour and acclimatisation

12_sensitivity_model-selection_range.R

• checks sensitivity of range filling and asymmetry in underfilling results to acclimatisation

13_sensitivity_model-selection_niche_no-dormancy.R

• checks sensitivity of warma and cool niche filling results to exclusion of dormant species

14_sensitivity_model-selection_range_no-dormancy.R

• checks sensitivity of range filling and asymmetry in underfilling results to exclusion of dormant species

15_sensitivity_range-source.R

• checks sensitivity of warm and cool niche filling results to realized range source

16_niche-filling-figures.R

• creates warm and cool niche filling figures

17_range-filling-figures.R

• creates range filling figures

18_sensitivity_NicheMapR.R

• tests sensitivity of results on land to parameters used in operative temperature models

19_phylo-gls-sensitivity-analysis.R

• tests sensitivity of results to choice of method used to control for evolutionary relatedness

20_create-minimum-dataset.R

• creates a minimum dataset needed to reproduce main analyses

Ownership

This reposity is owned by Nikki A. Moore and Jennifer M. Sunday. All data, scripts, and figures may be used by others with proper acknowledgement.