Data from: Order matters: Autocorrelation of temperatures dictates extinction risk in populations with nonlinear thermal performance
Data files
Dec 29, 2025 version files 2.64 GB
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AutocorrelationData.zip
2.64 GB
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README.md
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Abstract
Forecasting the risks caused by climate change often relies upon combining species' thermal performance curves with expected statistical distributions of experienced temperatures, without considering the order in which those temperatures occur. Such averaging approaches may obscure the disproportionate impacts that extreme events like heatwaves have on fitness and survival. In this study, we instead incorporate thermal performance curves with population dynamical modeling to elucidate the relationship between the sequence of temperature events -- driven by temporal autocorrelation -- and extinction risk. We show that the permutation of temperatures determines the extent of risk; as thermal regimes grow warmer, more variable, and more autocorrelated, the risk of extinction grows non-linearly and is driven by interactions between the thermal distribution and its temporal autocorrelation. Given that the mean, variance, and autocorrelation of temperatures are changing in nuanced ways across the globe, understanding these interactions is paramount for forecasting risk. Using empirical data from a benchmarked set of thermal performance curves, we demonstrate how extinction risk is impacted by interacting changes to temperature's distribution and autocorrelation level, while controlling for seasonal and diurnal cycling. Our results and modeling approach offer new tools for testing the robustness of thermal performance curves and emphasize the importance of looking beyond temporally-blind metrics, like mean population size or average thermal distributions, for forecasting impending extinction risks.
https://doi.org/10.5061/dryad.w0vt4b91q
This project utilized several models to test the impacts of varying the temporal autocorrelation of temperature time series on extinction risk, given a known organismal thermal tolerance. The first model (Model 1, 1.2) tests how varying different aspects of a thermal regime (mean, standard deviation, and autocorrelation of temperatures) alter different metrics of extinction risk for species with two idealized thermal performance curves (one generalist/temperate species and one specialist/tropical species); Model 1 examines how extinction risk and time to extinction vary across the full parameter space, while Model 1.2 examines the effects on population size across a narrower parameter set. Model 2 tests how varying the level of autocorrelation impacts more realistic scenarios by incorporating 38 empirical thermal performance curves with observed temperature data from the organisms' collection locations and varying the autocorrelation structure of the observed thermal regimes (while maintaining the observed seasonal and diurnal cycles).
1 Description of the data and file structure
The following is a list of files accessible after downloading and unzipping 'AutocorrelationData.zip', which contains two folders ('Model Input Files' and 'Model Output Files'), along with a brief description of their contents and how to work with them. The workflow for recreating the results of the related manuscript is further described in the GitHub repository referenced below.
All input data are provided as .csv files, spreadsheet files that can be viewed and manipulated in widely available programs like Microsoft Excel, Numbers, or Google Sheets. The .csv files alone are sufficient to recreate the results of this project. However, we additionally include some output files as .m file types, a binary code file best accessed using Wolfram Mathematica, for which they are the native export/import file type; code for reading and manipulating all such files is available in the Github repository. All .m files are made available for the convenience of recreating the exact plots generated in this project within Mathematica, but can be recreated (albeit with significant processing time) using the code provided in the Github repository. This description includes references to Mathematica code (.nb) files, all of which are not included in the Dryad repository but can be found in the GitHub repository (they are also available there as .pdf files for ease of reading for those without Mathematica access).
1.1 Model Input Files
1.1.1 'speciesparams.csv'
This .csv files contains all necessary input parameters for running and plotting Model 2 (using 'Model2.nb' and 'Model2_plotting.nb'). This file additional contains some of the output information from Model 2 for graphing purposes. Included variables are:
- species: Abbreviated species names (short-hand for genus and full species; e.g., A.pisum), which is used in the .nb files to call the rest of the data.
- CTmax, Topt, sigma_p: These are the thermal tolerance parameters for the fitted thermal performance curves (TPCs) of each species, provided by Deutsch et al. 2008 and Frazier et al. 2006. The curve parameterization follows Deutsch et al. 2008, such that CTmax is the critical thermal maximum (the right x-intercept), Topt is the thermal optimum (peak of the TPC), and sigma_p is a measure of breadth (such that sigma_p = (Topt - CTmin)/4).
- lat, long: These provide the collection latitude and longitude of each species.
- H gamma, P gamma: These denote the measured spectral exponent of the observed temperature time series in the historic (H) and recent (or present, P) time series.
- H P(Ext), P P(Ext): These columns are the proportion of simulations that went extinct (or the probability of extinction P(Ext) ) at the measured spectral exponent of the temperature time series in the historic (H) and recent (P) time series.
- H mean, H stdev, P mean, P stdev: These columns contain the measured mean and standard deviation (stdev) of the historic (H) and recent (P) temperature time series.
- Full species name: This is the complete scientific name of each species.
- Region: This is the broad region of the world the coordinates for the species fall into, as categorized by Duffy et al. 2022 (SHEX for Southern Hemisphere, NHEX for Northern Hemisphere, and TROP for the tropics).
1.1.2 'VisualCrossingData.zip'
Once unzipped, this file contains two .csv files per species. Each file is labeled by the shortened species name, the geographic coordinates, and the date range (either historic or recent) for which it contains the daily minimum and maximum temperatures (e.g., 'A.citricola_34.98,138.4_1994-01-01to2003-12-31.csv'). Each file contains four columns: 'datetime' is the collection date, 'tempmax' and 'tempmin' are the maximum and minimum temperatures observed that day, and 'source' indicates the type of data (options are 'obs' = observation historical weather station datapoints and 'stat' = statistically inferred datapoints). All temperatures are reported in Kelvin. Details of exactly how this data was retrieved from Visual Crossings Weather and processed are available in Appendix S4 (and see below). 'Model2.nb' will automatically retrieve the correct .csv files for any chosen species and time range from this folder.
1.2 Model Output Files
1.2.1 'Model1_outputs.zip'
Access this file by unzipping it. It contains two zipped .m files, which were generated (and can be recreated by) running 'Model1.nb'.
- extTime_tmax2000_dims21,7,7,1000.m.zip: Access this file by first unzipping it, then using code in 'Model1.nb'. This file contains the calculated extinction times generated for the generic generalist/temperate species for the range of mean, standard deviation, and autocorrelation temperature scenarios utilized in Model 1, and can be used to re-create Fig 4 by running 'Model1_plotting.nb'. This file can be recreated by running 'Model1.nb' but does require significant computing time and is thus included here for the convenience of the reader. The naming scheme is output variable (extTime), number of time steps (tmax = 2000), and dimensions of the output vector (21 autocorrelation levels, 7 mean temperate treatments, 7 standard deviation of temperature treatments, 1000 iterations).
- extTime_trop_tmax2000_dims21,7,7,1000.m.zip: Access this file by first unzipping it, then using code in 'Model1_plotting.nb'. This file contains the calculated extinction times generated for the generic specialist/tropical species for the range of mean, standard deviation, and autocorrelation temperature scenarios utilized and Model1, and can be used to re-create Fig 4 by running 'Model1_plotting.nb'. This file can be recreated by running 'Model1.nb' but does require significant computing time and is thus included here for the convenience of the reader. The naming scheme is output variable (extTime), TPC used (tropical), number of time steps (tmax = 2000), and dimensions of the output vector (21 autocorrelation levels, 7 mean temperate treatments, 7 standard deviation of temperature treatments, 1000 iterations).
1.2.2 'Model1.2_outputs.zip'
Access this file by unzipping it. It contains three .m files, which were generated (and can be recreated by) running 'Model1.2_abundance.nb'.
- extMetrics8_extTime_tmax2000_dims21,4,1,1000.m: The calculated extinction times for the generalist/temperate TPC across 1000 runs of 2000 time steps, tested across 21 autocorrelation levels, 4 mean temperature treatments, and 1 standard deviation of temperature treatment, using the file 'Model1.2_abundance.nb'. This file is plotted in Fig 3b using 'Model1.2_abundance_plotting.nb'.
- extMetrics8_popsize_tmax2000_dims21,4,1,1000.m: The calculated population sizes at each time step across the simulations for the generalist/temperate TPC across 1000 runs of 2000 time steps, tested across 21 autocorrelation levels, 4 mean temperature treatments, and 1 standard deviation of temperature treatment, using the file 'Model1.2_abundance.nb'. This file is plotted in Fig 3a using 'Model1.2_abundance_plotting.nb'.
- extMetrics8_trop_extTime_tmax2000_dims21,4,1,1000.m: The calculated extinction times for the specialist/tropical TPC across 1000 runs of 2000 time steps, tested across 21 autocorrelation levels, 4 mean temperature treatments, and 1 standard deviation of temperature treatment, using the file 'Model1.2_abundance.nb'. This file is plotted in Appendix S5 using 'Model1.2_abundance_plotting.nb'.
- extMetrics8_trop_popsize_tmax2000_dims21,4,1,1000.m: The calculated population sizes at each time step across the simulations for the generalist/temperate TPC across 1000 runs of 2000 time steps, tested across 21 autocorrelation levels, 4 mean temperature treatments, and 1 standard deviation of temperature treatment, using the file 'Model1.2_abundance.nb'. This file is plotted in Appendix S5 using 'Model1.2_abundance_plotting.nb'.
1.2.3 'Model2_VCOutputs.zip'
Access this file by unzipping it; it contains all results generated from 'Model2.nb'. Each file contains the simulated extinction time for each species in either the historical (1994-01-01to2003-12-31) or recent (2014-01-01to2023-12-31) time period, using an extinction threshold of one individual, across all tested autocorrelation levels (e.g., 'model3.3.2_A.pisum_1994-01-01to2003-12-31_ext1.m'). There is an additional subfolder ('minpop') containing the simulated minimum population size observed in each time period for each species that never went extinct (e.g., 'model3.3.3_minPop_A.pisum_1994-01-01to2003-12-31_ext1.m'). These files are used to generate information in 'points.zip', as well as creating Fig 5 and extended figures with 'Model2_plotting.nb'.
This file also contains one subfolder named 'points', which contains 5 .csv files with plotting information for supplemental figures. Each file has five columns: Species (with the species name), H_gamma (the spectral exponent observed in the historical temperature time series), H_ExtTime (the average time to extinction across simulations at the historical spectral exponent), P_gamma (the spectral exponent observed in the recent temperature time series), and P__ExtTime (the average time to extinction across simulations at the recent spectral exponent). They are divvied up into separate files purely for plotting purposes; 'Model2_plotting.nb' automattically collects the appropriate data for each species and plot.
- allpoints.csv contains this information for every tested species.
- fullextinctpoints.csv contains this information for all species that went extinct 100% of the time.
- fullpersistpoints.csv contains this information for all species that went extinct 0% of the time.
- usefulpoints.csv contains this information for all species that went extinct some, but not all, of the time.
- uselesspoints.csv contains the complied information for species that went extinct either 0% or 100% of the time (i.e., fullextinctpoints and fullpersistpoints).
2 Sharing/Access information
The temperature time series data in VisualCrossingData.zip was downloaded from Visual Crossings Corporation using their Weather Query Builder. Files included in this dataset have been cleaned (checked for missing data, leap years removed), but raw data is accessible via their website by entering the coordinates and time range for each species (see Appendix S4).
Species data was derived from datasets compiled and analyzed by the following sources:
- Frazier, M. R., Huey, R., and Berrigan, D. (2006). Thermodynamics Constrains the Evolution of Insect Population Growth Rates: “Warmer Is Better.” The American Naturalist, 168(4): 512–520. Publisher: The University of Chicago Press.
- Deutsch, C. A., Tewksbury, J. J., Huey, R. B., Sheldon, K. S., Ghalambor, C. K., Haak, D. C., and Martin, P. R. (2008). Impacts of climate warming on terrestrial ectotherms across latitude. Proceedings of the National Academy of Sciences, 105(18):6668–6672. Publisher: National Acad Sciences
- Duffy, K., Gouhier, T. C., and Ganguly, A. R. (2022). Climate-mediated shifts in temperature fluctuations promote extinction risk. Nature Climate Change, 12(11):1037–1044. Publisher: Springer Science and Business Media LLC
3 Code/Software
All code is available at github.com/arobey63/autocorrelation (DOI: 10.5281/zenodo.17728683), including files for generating and plotting all outputs found in the paper. Each 'Model#' code must be run prior to each 'Model#_plotting' code, or the outputs required for plots must be downloaded from here. Most code requires no manual adjustments except for selecting the TPC or species on which to perform simulations and selecting the appropriate import and export locations, as noted in comments within code files.
All code was run using Mathematica V.13.0.1.
Included datasets (1) input data required to simulate extinction for 38 species with known thermal tolerances (arising from datasets compiled and used by Deutsch et al. 2008, Duffy et al. 2022, and Frazier et al. 2006) under two decades of observed climatic conditions at their collection locations (provided by Visual Crossings Corporation 2024); and (2) simulation outputs for several models which test extinction risk for species with different thermal tolerances, given variable thermal distributions and levels of autocorrelation, processed in Mathematica V.13.0.1 and as reported in the associated manuscript.
