This README file was generated on [25/02/2024] by [Cooper Malanoski].

GENERAL INFORMATION

1. Title of Dataset: Climate change is an important predictor of extinction risk on macroevolutionary timescales

2. Author Information
   A. Principal Investigator Contact Information
   Name: [Cooper Malanoski]
   Institution: [Oxford University]
   Address: [Department of Earth Sciences, Oxford University, South
   Parks Road, Oxford, OX1 3AN, UK.]
   Email: [cooper.malanoski@earth.ox.ac.uk]

   B. Associate or Co-investigator Contact Information
   Name: [Dr. Erin Saupe]
   Institution: [Oxford University]
   Address: [1Department of Earth Sciences, Oxford University, South
   Parks Road, Oxford, OX1 3AN, UK.]
   Email: [erin.saupe@earth.ox.ac.uk]

3. Date of data collection: [NA]

4. Geographic location of data collection: [NA]

5. Information about funding sources: [National science research council (NERC), Award: NE/V011405/1

Leverhulme Prize

Chinese Academy of Sciences Visiting Professorship for Senior International Scientists, Award: 2021FSE0001]

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: [Copyright © 2024 the authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original US government works. https://www.sciencemag.org/about/science-licenses-journal-article- reuse]

2. Links to publications that cite or use the data: Malanoski et al. (2024). [Climate change is an important predictor of extinction risk on macroevolutionary timescales]. [Science].

3. Links to other publicly accessible locations of the data: [NA]

4. Links/relationships to ancillary data sets: [Monarrez et al. (2021) was used to source the Generic_bodysize_data_monarrezetal2021.csv file]

5. Was data derived from another source? [Yes]
   A. If yes, list source(s): [Monarrez et al. (2021) was used to source the Generic_bodysize_data_monarrezetal2021.csv file]

6. Recommended citation for this dataset:
   Malanoski et al. (2024). Data from: Climate change is an important predictor of extinction risk on macroevolutionary timescales. Dryad Digital Repository. [doi:10.5061/dryad.1ns1rn91g]

DATA & FILE OVERVIEW

1. File List:
   A) pbdbdata_code.Rmd
   B) Generic_bodysize_data_monarrezetal2021.csv
   C) raw_extracted_climatemodeldata.csv
   D) Geographic_range_code.Rmd
   E) Climate_based_variable_code.Rmd
   F) figures_code.Rmd
   G) intrinsic_and_extrinsic_variables.csv

2. Relationship between files: The utility of each dataset and code file is detailed below.

3. Additional related data collected that was not included in the current data package: [NA]

4. Are there multiple versions of the dataset? [No]
   A. If yes, name of file(s) that was updated: [NA]
   i. Why was the file updated? [NA]
   ii. When was the file updated? [NA]

DATA-SPECIFIC INFORMATION

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DATA-SPECIFIC INFORMATION FOR: Generic_bodysize_data_monarrezetal2021.csv

includes the genera, log body volume and log body size estimates provided in Monarrez et al. (2021). For our analyses we use logvol, but logsize is retained for future studies. We removed bony fish from the original dataset, and the reasoning is provided in the Supplementary methods and materials. We join the log volume with our data based on the genus level. Higher taxonomic ranking revisions which Monarrez et al. (2021) revised were applied to our data using code found in Geographic_range_code.Rmd.

1. Number of variables: 7

2. Number of cases/rows: 9,461

3. Variable List:

   • genus: all invertebrate genera with body size information in Monarrez et al. (2021), except for Bony fish genera.

   • class: Linnean Class

   • logsize: log body size data from Monarrez et al. (2021) calculated from the treatise images in mm-squared.

   • logvol: log body volume data from Monarrez et al. (2021) calculated from the treatise images in mm-cubed.

   • phylum: Linnean Phylum

   • order: Linnean Order

   • family: Linnean Family

4. Missing data: Some Na’s are present if a higher taxonomic ranking was not available for a genus.

5. Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: raw_extracted_climatemodeldata.csv

1. Number of variables: 12

2. Number of cases/rows: 462,855

3. Variable List:

   • collection_no: Collection number of occurrence in the PBDB

   • stage: Geologic stage

   • Age: Age in millions of years before present

   • phylum: Linnean phylum

   • class: Linnean class

   • order: linnean order

   • family: linnean family

   • genus: linnean genus

   • paleolng: Paleolatitude coordinates

   • paleolat: Paleolongitude coordinates

   • Localized temperature: The temperature extracted for each occurrence in degrees Celsius

   • Localized change in temperature: Change in temperature between stages for each occurrence in degrees Celsius.

4. Missing data codes: Some Na’s are present if a higher taxonomic ranking was not available for a genus.

5. Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: intrinsic_and_extrinsic_variables.csv

includes the climate model data for each occurrence in the PBDB data that can be sourced from pbdbdata_code.Rmd. This includes the localized temperatures and climate change estimates necessary to carry out future studies, and all analyses in Malanoski et al. (2024)

1. Number of variables: 17

2. Number of cases/rows: 22,222

3. Variable List:

   • ext: Binary extinction variable based on range through methods. A value of 0 indicates that the genus survived into subsequent stages and 1 indicates that the genus went extinct and is absent from subsequent stages.

   • Genus: Linnean genus

   • Stage: Geologic stage

   • Phylum: Linnean phylum

   • Class: Linnean class

   • Order: Linnean order

   • Family: Linnean family

   • Realized_thermal_niche_breadth: Realized thermal niche breadth calculated as the difference between the maximum and minimum occuppied temperatures for each genus. This variable is based on the median of all subsampled ranges for a genus.

   • Absolute_realized_thermal_preference: Realized thermal preference is calculated as the absolute value of the deviation in median occuppied temperature for a genus from the median for all occurrences within a stage. This variable is based on the median of all subsampled preferences for a genus.

   • Geographic_range_size: Geographic range size is calculated using the log convex hull area (km-squared). This variable is based on the median of all subsampled areas for a genus.

   • Body_size: Body size is calculated as the log body volume (mm-cubed) for each genus, derived from Monarrez et al. (2021).

   • Absolute_temperature_change: Change in temperature or climate change is calculated as the absolute change in temperature from stage n to n+1. This variable is based on the median of all subsampled ranges for a genus.

   • Realized_thermal_niche_breadth_std: Standardized realized thermal niche breadth

   • Realized_thermal_preference_std: Standardized realized thermal preference

   • Geographic_range_size_std: Standardized geographic range size

   • Body_size_std: Standardized body size

   • Absolute_temperature_change_std: Standardized absolute temperature change

4. Missing data codes: NA (data not applicable). Higher taxonomic levels may contain NA values if there are none applicable for a genus.

5. Specialized formats or other abbreviations used:

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DATA-SPECIFIC INFORMATION FOR: pbdbdata_code.Rmd

pbdbdata_code.Rmd is based on Kocsis et al. (2019) it can be used to download a dataset from the Paleobiology database (PBDB), and process and clean the data using the methods used in this manuscript.
The code filters out occurrences which cannot be assigned to a stage and assigns up to date stages, filters out taxa which are not included in Generic_bodysize_data_monarrezetal2021.csv, and vets the occurrences for spatial duplicates and data without coordinates.

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DATA-SPECIFIC INFORMATION FOR: Geographic_range_code.Rmd and Climate_based_variable_code.Rmd

Geographic_range_code.Rmd and Climate_based_variable_code.Rmd are used to calculate geographic range size, absolute realized thermal preference, realized thermal niche breadth, and absolute change in occupied temperature. These R-markdown files rely on the raw_extracted_climatemodeldata.csv file and We provide code to calculate these variables for both jackknife and bootstrap subsampling methods. The geographic range code is adapted from Casey et al. (2021). The output from these files is provided as intrinsic_and_extrinsic_variables.csv and is used as the input for our statistical models, which can be made using figures_code.Rmd.

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DATA-SPECIFIC INFORMATION FOR: figures_code.Rmd

figures_code.Rmd can be used and modified to reproduce the main text and supplementary tables and figures. The code initially runs all model combinations for our 5 predictors using a generalized linear mixed effect model. Then we use the output from the best model total.glmer2 to make the marginal effects plots seen in figure 2, the supplementary conditional mode plots, and the AIC tables seen in the supplemental materials and methods. Lastly, we provide the code to produce figure 1.

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