https://doi.org/10.5061/dryad.8kprr4xx1

Description of the data and file structure

1. Overview

This dataset contains species-level information on life-history trait space, anthropogenic threats, taxonomy, habitat, geographic distribution, and conservation status for 259 species of Testudines and Crocodilia.

The data were used to assess the loss of life-history trait diversity (LHTD) and phylogenetic diversity (PD) associated with individual anthropogenic threats and combinations of threats.

The dataset includes three data files and two R scripts. The data files contain complementary information used in the analyses, while the R scripts provide the code used to estimate loss of life-history trait diversity and loss of phylogenetic diversity.

All text files are tab-delimited files unless otherwise indicated.

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2. Files included in the dataset

2.1. final_dataset_FD.txt

This tab-delimited file contains the complete species-level dataset used for the analyses of life-history trait diversity. It contains information for 259 species, including their position in the two-dimensional functional spectrum (PC1 and PC2), anthropogenic threats, taxonomy, habitat, and conservation status.

2.2. threats.zip

This compressed archive contains the dataset used for the phylogenetic diversity analyses.

The archive contains the file threats.csv, a semicolon-delimited table containing species identity, anthropogenic threats, conservation status, and taxonomic information for 259 species.

2.3. data_interaction.txt

This tab-delimited file contains the dataset used to analyse the effects of combinations of anthropogenic threats on phylogenetic diversity. It contains the species' position in the functional spectrum (PC1 and PC2), six threat categories, and a binary variable indicating whether a species is considered threatened according to the criteria used in the analyses.

2.4. LHTD_code.R

R script used to estimate the loss of life-history trait diversity associated with individual threats and combinations of threats.

The script generates output files comparing the sum of the effects of individual threats with the combined effects of their interactions, for both the complete set of species and the subset of threatened species.

2.5. PD_code.R

R script used to estimate the loss of phylogenetic diversity associated with individual threats and combinations of threats.

The script generates output files for the complete set of species and for threatened species only. The resulting files can be used to assess whether the combined effects of threats are synergistic, additive, or antagonistic.

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3. Description of variables

3.1. Variables in final_dataset_FD.txt

PC1 and PC2 represent the position of each species in the two-dimensional functional spectrum used in the analyses. They are principal-component scores and therefore have no physical units.

Threat variables are binary indicators. A value of 1 indicates that the corresponding threat was identified for the species, whereas 0 indicates that the threat was not identified.

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3.2. Variables in threats.csv

The file threats.csv contains 259 species and the following variables:

The six threat variables are binary indicators, with 0 indicating that the threat was not identified and 1 indicating that the threat was identified.

Missing values (NA) occur in the threat variables and/or conservation status where information was not available.

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3.3. Variables in data_interaction.txt

The variables Trade, Local, Habitat, Disease, Climate, and Pollution correspond to the six main threat categories used in the analyses.

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4. Threat categories

The main anthropogenic threat categories included in the dataset are:

• Trade: threats associated with ilegal trade.
• Local consumption: threats associated with local overconsumption of species.
• Habitat disturbance: threats associated with disturbance or alteration of habitat.
• Disease: threats associated with disease and an alien species.
• Climate change: threats associated with climate change.
• Pollution: threats associated with pollution.

Additional threat information is retained in the Otros variable in final_dataset_FD.txt when it does not correspond to one of the six main threat categories.

Threat variables are coded as binary variables:

• 0 = threat not identified
• 1 = threat identified

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5. Conservation status

Conservation status is represented using the following categories:

• CE = Critically Endangered
• EN = Endangered
• VU = Vulnerable
• NT = Near Threatened
• LC = Least Concern
• DD = Data Deficient

The individual variables CE, EN, VU, NT, LC, and DD in final_dataset_FD.txt are binary indicators corresponding to these categories.

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6. Missing values

Missing information is represented as NA in the tabular datasets.

In final_dataset_FD.txt, the variable No data additionally indicates species for which no information was available for the corresponding threat information.

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7. File formats and software

final_dataset_FD.txt and data_interaction.txt are tab-delimited text files and can be opened using standard text editors, spreadsheet software, or statistical software.

threats.csv is a semicolon-delimited CSV file.

The analyses can be reproduced using R and the R scripts provided in this dataset (LHTD_code.R and PD_code.R).

The files can also be inspected and used independently of R using standard spreadsheet or statistical software.