DOI: 10.5061/dryad.wdbrv160k
title: Data from: Cross-continental analysis shows that disturbance effects on reptile body condition do not predict abundance responses

description: Ecological disturbances are discrete events that alter or transform the
 physical, chemical, or biological characteristics of ecosystems. Animal
 populations are vulnerable to disturbance, and the risk-disturbance
 hypothesis and population collapse framework propose that population
 declines can be predicted by declines in animal body condition. However,
 no research has empirically examined the general relationship between body
 condition and abundance, nor their relationship in response to
 disturbance. We used a combined dataset representing 33 studies and
 &gt;42,000 observations of 75 species from Australia, New Zealand,
 Spain, and the United States to test predictions relating to the
 relationship between reptile body condition and abundance. We first
 investigated the relationship at the site level and then used
 meta-analytical models to test whether populations showed linked changes
 in abundance and body condition in response to disturbance. We further
 tested whether key environmental and species traits influenced this
 relationship and whether there was a time-lagged effect of body condition
 responses on abundance. Our results provided no strong support for the
 risk-disturbance hypothesis or population collapse framework. We found a
 positive relationship between mean reptile body condition and abundance at
 the site level. However, the relationship was largely lost when
 investigating population responses to disturbance. We provide a new
 conceptual framework that shows how disturbances can modify or uncouple
 the relationship between abundance and body condition by influencing
 underlying drivers, such as predation, competition, and resource
 availability. As such, the impacts of disturbance on reptile body
 condition cannot be assumed to reflect or predict abundance responses.
 Monitoring programs that infer population impacts based on changes in body
 condition should confirm the relationship between these two variables in
 the relevant study system.
description: Between October and December 2023, datasets suitable for analyses
 were identified through three main methods: (1) reviewing the data sources
 of a recent global meta-analysis investigating reptile body condition
 responses to disturbance (Macdonald et al. 2023), (2) using ‘Scopus’ to
 identify prominent authors publishing in the field of reptile abundance
 responses to disturbance, and (3) asking existing networks and research
 collaborators for recommendations. Adopting a formal systematic review
 approach was not suitable for this study because we needed to obtain raw,
 unpublished data from data custodians (the author group) and consult with
 them regarding data cleaning and interpretation. We compiled 33 author
 datasets that investigated reptile responses to disturbance. Each
 underlying dataset contained (1) field data collected at sites with and
 without disturbance, (2) reptile capture data at each site, and (3)
 individual reptile snout-vent length and weight measurements at each
 site.
description: # Data from: Cross-continental analysis shows that disturbance effects on
 reptile body condition do not predict abundance responses
 [https://doi.org/10.5061/dryad.wdbrv160k](https://doi.org/10.5061/dryad.wdbrv160k) ## **Description of the data and file structure** These datasets and R code support our published research. R Studio is required to run the R script and analysis. **Primary datasets** used in this analysis are: 'Site_survey_dataset.csv', 'Population_dataset.csv', and 'Population_time_lagged_dataset.csv'. See the manuscript for details on data processing and analysis.  **Secondary datasets** that were used to create primary datasets are found in the file 'Secondary_datasets.xlsx'. See Table S1, S2 (supplementary document) and 'Data Sources' (manuscript) for more details about the secondary datasets, or contact the relevant co-authors (found within 'Secondary_datasets.xlsx).  ### **File descriptions** | **File name** | **Description** | | :------------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Site\_survey\_dataset.csv  | Dataset used for models investigating the site-survey level relationship between reptile body condition and capture rates. See site-survey variables for details. | | Population\_dataset.csv | Dataset for models investigating the relationship between body condition and abundance responses to disturbance. See population variables for details.  | | Population\_time\_lagged\_dataset.csv | Dataset for models investigating the time-lagged relationship between body condition and abundance responses to disturbance. See population variables for details.  | | Output.nex | Data to create a phylogenetic matrix for population-level analysis. | | output2.nex | Data to create a phylogenetic matrix for site-survey level analysis.   | | Secondary\_datasets.xlsx | Secondary capture ('dataset code \_ C ') and body condition ('dataset code \_ SMI ') data for each underlying dataset. See the secondary summary for details. | ### **Site-survey data variables** | **Column header** | **Description** | | :----------------- | :---------------------------------------------------------------------------------------- | | study\_ID | Unique ID for the underlying dataset. | | survey\_period | Code to differentiate between distinct surveys. | | site\_name | Code for different distinct sites. | | site\_survey\_code | Combined 'site name'\_'survey\_period'. | | species\_orig | Species name as per the underlying dataset. | | species | Updated species name. | | genus | Updated genus name. | | family | Taxonomic family.  | | order | Taxonomic order. | | disturbance\_type | Disturbance type at site. Multiple = more than one disturbance. Control = no disturbance. | | disturbance.s. | Disturbance type in more detail.  | | disturbed | Binary value -  (0 = not disturbed, 1 = disturbed). | | mean\_SMI | Mean scaled mass index at the site. | | SMI\_sd | Standard deviation for the mean scaled mass index at the site. | | SMI\_se | Standard error for the mean scaled mass index at the site. | | study\_species | Combined 'study\_ID'\_'species'. | | CR\_C | Scaled capture rates at the site. | | phylo | Species names matched to the phylogenetic matrix created for analysis. | ### **Population data variables** | Column header | Description | | :------------------ | :------------------------------------------------------------------------------------------------------------------------------------------- | | study\_ID | Unique ID for the underlying dataset. | | location | Country where the data were collected. | | species\_orig | Species name as per the underlying dataset. | | species | Updated species name. | | genus | Updated genus name. | | family | Taxonomic family.  | | order | Taxonomic order. | | reproduction\_mode | Reproductive strategy of species. | | SVL\_size | Mean snout-to-vent length of species (mm). | | SVL\_ref | Citation for snout-to-vent length source. | | survey\_methods | Broad methods are used for catching reptiles. | | disturbance\_detail | Disturbance type in detail. Often differentiates between rows for different annual surveys or important variables within secondary datasets. | | dist\_type2 | Disturbance group (levels: pulse, press). Population dataset only. | | TSD | Time since disturbance (if applicable) | | dist\_notes | Relevant notes for disturbance type. | | disturbance\_type | Disturbance type | | control\_detail | Relevant notes or details about the control sites | | LRR\_SMI | Log response ratio for the Scaled Mass Index. Population dataset only. | | LRR\_SMI\_se | Variance of the log response ratio for the Scaled Mass Index. Population dataset only. | | LRR\_SMI\_P | Log response ratio for the Scaled Mass Index from the previous year. Population\_time\_lagged dataset only. | | LRR\_SMI\_P\_se | Variance of the log response ratio for the Scaled Mass Index from the previous year. Population\_time\_lagged dataset only. | | LRR\_AB | Log response ratio for capture rates | | LRR\_AB\_se | Variance of the log response ratio for capture rates | | controlled | Additional variables from the secondary datasets were controlled for during log response ratio calculations | | phylo | Species names matched to the phylogenetic matrix created for analysis | ### **Secondary dataset summary** Contains: * Summary sheet: Provides dataset codes, corresponding authors, and email addresses.  * 'dataset code' \_ C = capture data for species and site-surveys used to calculate capture rates and log response ratios for the primary datasets (site-survey dataset and population datasets). * 'dataset code' \_ SMI = body condition data of species and individuals used to calculate log response ratios for the primary datasets (site-survey dataset and population datasets).  #### **Capture data variables**  | **Column header** | **Description** | | | :------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------- | | **site** | Code for different distinct sites | **treatment ** | | **'#'** - Multiple columns are used if the secondary dataset examined multiple disturbance types. | Differentiates between disturbed and control sites. Some secondary datasets have more than one level of disturbance. | | | **variable'#'** - Multiple columns are used if more than one variable was used in the data processing or log response ratio calculations. | Levels of the key variable that were used in data processing and/or log response ratio calculations.  See population datasets (columns "disturbance detail" and "controlled" to understand how these variables were used in log response ratio calculations.  | | | **survey\_period** - There can be more than one survey period column (e.g., based on month and season or year). | Distinct survey periods of secondary datasets that were used in the analysis for this research. These columns were used to create the site-survey dataset, calculate log response ratios for different survey periods, and create the time-lagged population dataset. | | | **survey\_effort** | Numerical value for variation in field survey effort (e.g., number of traps, number of trap nights, or period of search time). This data was used to standardise count data to capture rates during data processing. | | | **'genus'\_'species'** - Most secondary datasets contain values for multiple species and therefore contain multiple columns for different species. | Numerical value for the number of individuals caught at each site. These numbers are converted to capture rates and used in the analysis. | | #### **Body condition data variables** | **Column header** | **Description** | | :----------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | site | Code for different distinct sites | | **treatment'#'** - Multiple columns are used if the secondary dataset examined multiple disturbance types. | Differentiates between individuals caught at disturbed and control sites. Some secondary datasets have more than one level of disturbance. | | **variable'#'** - Multiple columns are used if more than one variable was used in the data processing or log response ratio calculations. | Levels of key variable that were used in data processing and/or log response ratio calculations.  See populations datasets (columns "disturbance detail" and "controlled" to understand how these variables were used in log response ratio calculations.  | | **survey\_period** - There can be more than one survey period column (e.g. based on month and season or year). | Distinct survey periods of secondary datasets that were used in the analysis for this research. These columns were used to create the site-survey dataset, calculate log response ratios for different survey periods, and create the time-lagged population dataset. | | **species**   | Scientific name of the individual measured.  | | **mass** | Weight of individuals (g), except for TJ\_02 (units: kg) | | **svl** | Snout-to-vent length of individuals (mm), except for TJ\_02 (unit: cm) | | **SMI** | Scaled mass index of an animal.  |