DOI: 10.5061/dryad.5dv41nsgv
title: Data from: Are caiman nests microhabitats? Assessing their ecological role across different levels of anthropogenic disturbance

description: Wild vertebrates face increasing threats from human activities,
 particularly land-use changes, which disrupt ecological interactions and
 ecosystem structure. Crocodilian nests, viewed as microhabitats, are
 crucial for understanding these impacts and developing comprehensive
 conservation strategies. We aimed to assess vertebrate species richness,
 interactions, and visitation frequency at Caiman latirostris nests in
 Santa Fe, Argentina, across varying levels of habitat disturbance. Over
 four nesting seasons (2018-2022), we monitored 64 nests in forests,
 savannas, and marshes through camera traps, resulting in 9,062
 trap-nights. A total of 100 species were recorded, including 74 birds, 23
 mammals, and 3 reptiles, though some reptiles could not be identified due
 to nocturnal photos. Species richness correlated with nesting season and
 habitat type, peaking in the driest season and in forest environments.
 Despite expectations, no link was found between species richness and
 anthropization. Of the species observed, 62% interacted with the nests
 through commensalism, predation, or competition, while the rest were
 neutral. The Interaction Strength Index (ISI) effectively quantified these
 interactions, proving to be a reliable indicator of nesting area use and
 highlighting the role of caiman nests as microhabitats.
description: # Caiman nests as microhabitats \[Access this dataset on Dryad:
 DOI:10.5061/dryad.5dv41nsgv] This dataset compiles data collected through
 camera trap monitoring of 64 Caiman latirostris nests over four nesting
 seasons (2018–2022) in Santa Fe, Argentina. The study aimed to assess
 vertebrate species richness, interactions, and visitation frequency across
 different habitat types and levels of anthropogenic disturbance. The
 dataset includes metadata on species detections, derived measures of
 species richness, and interaction metrics such as the Interaction Strength
 Index (ISI). A total of 100 vertebrate species were recorded visiting
 caiman nests, of which 62 were found to interact effectively with them,
 providing insight into the ecological role of these animal-built
 structures. ## Description of the data and file structure The analyses
 were performed using RStudio software. First, metadata were extracted from
 the photos obtained through camera trapping, based on the information
 provided by the images (date and time) and the species labels previously
 assigned using Digikam software. The table "1.
 record_species_all" contains the metadata extracted from the photos
 obtained during the monitoring of caiman nests. Additionally, using the
 collected information, the table "2. species_richness" was
 created. This table contains the data analyzed using the script called
 "3. script_SpeciesRichness" to determine the importance of
 anthropization, nesting season, and nesting habitat type in shaping the
 vertebrate species richness at caiman nests. This table includes the
 following variables: Station, Season, Site, FLII (anthropization index),
 Nesting Environment Type (marsh, forest, savanna), and Species Richness
 (number of species). Third, using the table
 "record_species_all", a new table was created for each nest in
 the required format to determine independent records per species,
 following the methodology (script and structure) proposed by
 Camargo-Sanabria AA and Delgado-Martínez CM (2019): “Interacciones
 Fruto-Mamífero: data.table, tidyverse, reshape2, and dplyr” (Chapter 12,
 pp. 207–224, in Mandujano, S., & Pérez-Solano, L.A. [Eds.],
 Fototrampeo en R: organización y análisis de datos, Volume I. Instituto de
 Ecología A.C., Xalapa, Ver., Mexico. ISBN: 978-607-7579-90-8; digital
 version available at:
 [https://github.com/SMandujanoR/Foto-trampeo-R-Vol_I](https://github.com/SMandujanoR/Foto-trampeo-R-Vol_I)). The necessary tables to calculate the Interaction Strength Index (ISI) for each species at each nest, along with the resulting data, are included in the repository folder titled "ISI." This folder contains one subfolder for each camera trap station, and each subfolder includes the following files: base_analizada, base_trabajo, duration_result, EM_station, FC_result, IFI_mean_stand, Mode_indiv_result, and Species_time. To ensure compatibility with the functions developed by Camargo-Sanabria and Delgado-Martínez (2019), the variable names in the tables exactly match those used in their scripts. For instance, “SpeciesTree” actually refers to “SpeciesNest”, which in this study corresponds to "caiman". Below is a detailed description of the contents of each document included in this repository: The table “1._record_species_all.csv” (record_species_all) includes the following variables: * Station: Sampling station name (code used to identify each nest). * Species: Scientific name of the observed species (e.g., Hymenops perspicillatus). * DateTimeOriginal: Combined date and time. Format: dd/mm/yyyy hh:mm:ss. * Date (Date): Detection date. Format: dd/mm/yyyy. * Time (Time): Detection time. Format: hh:mm:ss. * metadata_NestEnviron: Nesting Environment Type (marsh, forest, savanna). * metadata_Site: Study areas (Alejandra, Cacique Ariacaiquín, Santurce, Huanqueros, Calchaquí). * metadata_FLII: Forest Landscape Integrity Index (FLII), an index used to classify the study sites according to their level of anthropogenic disturbance. Unit: integer. The table “2\_ species_richness.csv” (species richness) includes the following variables: * Station: Sampling station name (code used to identify each nest). * Season (Season): Monitoring season, usually covering two consecutive years. Format: “YYYY_YY” (e.g., 2018_19 indicates the season started in 2018 and ended in 2019). * Site: Study areas (Alejandra, Cacique Ariacaiquín, Santurce, Huanqueros, Calchaquí). * FLII: Forest Landscape Integrity Index (FLII), an index used to classify the study sites according to their level of anthropogenic disturbance. Unit: integer. * NestEnviron: Nesting Environment Type (marsh, forest, savanna). * SppRichness: Scientific name of the observed species (e.g., Hymenops perspicillatus). 3._script_SpeciesRichness.R: This is the script used to determine the importance of anthropization, nesting season, and nesting habitat type in shaping the vertebrate species richness at caiman nests. "ISI": This folder contains one subfolder for each camera trap station, and each subfolder includes the following files: base_analizada, base_trabajo, duration_result, EM_station, FC_result, IFI_mean_stand, Mode_indiv_result, and Species_time. The following is a description of the files mentioned. The table “base_trabajo” (working_dataset) includes the following variables: * CaptureID (Capture ID): Unique identifier for the capture or detection event. Unit: integer. * SpeciesTree (Species Tree): This field only contains “caiman”. It is not used in the analysis but remains in the table to support understanding of the dataset structure provided by Camargo-Sanabria and Delgado Martínez (2019). * StationID (Station ID): Sampling station name (code used to identify each nest). * Clase (Class): Taxonomic class of the organism (e.g., Birds). * Orden (Order): Taxonomic order of the organism (e.g., Passeriformes). * SpeciesID (Species ID): Scientific name of the observed species (e.g., Hymenops perspicillatus). * Individuals (Individuals): Number of individuals recorded in the event. Unit: integer. * Date (Date): Detection date. Format: dd/mm/yyyy. * Time (Time): Detection time. Format: hh:mm:ss. The table “species_times” includes the following variables: * Var1 (Structure type): Refers to the structure where the interaction was recorded. In this case, only “caiman” appears, indicating caiman nests. * Var2 (Species ID): Scientific name of the species observed (e.g., Hymenops perspicillatus, Salvator merianae). * TiempoIndep (Independence Time): Minimum time required between consecutive records of the same species for them to be considered independent events. Unit: minutes. The table “Duration_result” includes the following variables: * StationID (Station ID): Name of the sampling station (code used to identify each nest). Unit: integer * SpeciesID (Species ID): Scientific name of the observed species (e.g., Hymenops perspicillatus). * mean_duration (Mean duration): Average time the species remained at the station or nest. Unit: minutes. The table “EM_station” includes the following variables: * Season (Season): Monitoring season, usually covering two consecutive years. Format: “YYYY_YY” (e.g., 2018_19 indicates the season started in 2018 and ended in 2019). * Inicio (Start Date): Date when the monitoring period began at a station. Format: DD-MMM-YY (e.g., 23-dic-18 for December 23, 2018). Unit: date. * SpeciesTree (Species Tree): This field only contains “caiman”. It is not used in the analysis but remains in the table to support understanding of the dataset structure provided by Camargo-Sanabria and Delgado Martínez (2019). * StationID (Station ID): Sampling station name (code used to identify each nest). * Coord_X (X Coordinate): Easting coordinate of the station in a projected coordinate system (e.g., UTM Zone 17N). Unit: meters. * Coord_Y (Y Coordinate): Northing coordinate of the station in a projected coordinate system (e.g., UTM Zone 17N). Unit: meters. * Fin (End Date): Date when the monitoring period ended at a station. Format: DD-MMM-YY (e.g., 15-abr-19 for April 15, 2019). Unit: date. Dias (Days): Total number of days between the start date (Inicio) and end date (Fin) of monitoring. Unit: integer. The table “base_analizada” (analyzed_dataset) contains the same information as “base_trabajo” (working_dataset), with the addition of the following variables: * Time2 (DateTime combined): en * Independ (Independent Event): Indicates whether the event was considered independent (TRUE) or not (FALSE). The table “FC_result” includes the following variables: * StationID (Station ID): Sampling station name (code used to identify each nest). * SpeciesID (Species ID): Scientific name of the observed species (e.g., Hymenops perspicillatus). FC (Capture Frequency): A rate that expresses the number of independent events weighted by sampling effort (number of events / sampling effort in camera trap days * 100). These values are obtained using the code provided by Camargo-Sanabria and Delgado Martínez (2019). Unit: rate. The table “mode_indiv_result” includes the following variables: * StationID (Station ID): Sampling station name (code used to identify each nest). * SpeciesID (Species ID): Scientific name of the observed species (e.g., Hymenops perspicillatus). * mode_individuals (Mode): Mode of the number of individuals of each species observed at the nest. These values are obtained using the code provided by Camargo-Sanabria and Delgado Martínez (2019). Unit: integer. Additionally, access to photo sequences showing vertebrate activity at caiman nests is provided under the name "Supplementary Material 4." ## Sharing/Access information These data are available in this Dryad repository:DOI:10.5061/dryad.5dv41nsgv ## Code/Software The scripts used and the code based on Camargo-Sanabria and Delgado Martínez (2019) are described earlier in the "Description of the data and file structure" section.