DOI: 10.5061/dryad.m905qfvg5
title: Stratified sampling enhances the understanding of bat–fruit networks in the southern Atlantic Forest

description: This repository brings together the datasets and scripts used to
 investigate bat-plant interactions along the vertical gradient of an
 Atlantic Forest in northern Paraná, Brazil. It includes raw and processed
 data, as well as R scripts for analyzing ecological interactions. This
 dataset was collected to investigate the dissimilarity of frugivorous bat
 assemblages, plant species, and their interactions across different forest
 strata in a conserved Atlantic Forest environment in southern Brazil. The
 data were generated to evaluate whether sampling focused on a single
 vertical stratum, such as the understory, provides an accurate or biased
 characterization of bat–fruit interaction patterns. Sampling was conducted
 monthly between September 2013 and August 2014 in the Salto Morato Natural
 Reserve, Paraná state, comprising 12 sampling campaigns and 61 sampling
 nights. Bats were captured using mist nets simultaneously deployed in
 three forest strata (understory, subcanopy, and canopy), allowing a
 stratified assessment of frugivorous bat assemblages, plant species, and
 their interactions along the forest vertical gradient. Fecal samples were
 collected from captured bats and analyzed to identify consumed plant
 species, generating records of bat–fruit interactions for each forest
 stratum. The dataset includes raw and processed data used to construct
 interaction matrices and quantify patterns of network structure, species
 specialization, and interaction dissimilarity among forest strata.
description: # Stratified sampling enhances the understanding of bat–fruit networks in
 the southern Atlantic Forest Dataset DOI:
 [10.5061/dryad.m905qfvg5](https://doi.org/10.5061/dryad.m905qfvg5) ##
 Description of the data and file structure This dataset was collected to
 investigate the dissimilarity of frugivorous bat assemblages, plant
 species, and their interactions across different forest strata in a
 conserved Atlantic Forest environment in southern Brazil. The data were
 generated to evaluate whether sampling focused on a single vertical
 stratum, such as the understory, provides an accurate or biased
 characterization of bat–fruit interaction patterns. Sampling was conducted
 monthly between September 2013 and August 2014 in the Salto Morato Natural
 Reserve, Paraná state, comprising 12 sampling campaigns and 61 sampling
 nights. Bats were captured using mist nets simultaneously deployed in
 three forest strata (understory, subcanopy, and canopy), allowing a
 stratified assessment of frugivorous bat assemblages, plant species, and
 their interactions along the forest vertical gradient. Fecal samples were
 collected from captured bats and analyzed to identify consumed plant
 species, generating records of bat–fruit interactions for each forest
 stratum. The dataset includes raw and processed data used to construct
 interaction matrices and quantify patterns of network structure, species
 specialization, and interaction dissimilarity among forest strata. ###
 Files and variables ### File name: **Main_script.R** **Description:** R
 script used to perform the majority of the analyses presented in the
 study. The script includes the construction and visualization of bat–fruit
 interaction networks; calculation of network-level metrics (connectance,
 specialization index (H2′), nestedness WNODF , and modularity); null model
 analyses; estimation of sampling completeness and interaction richness
 (Chao1); species-level metrics for bats and plants (normalized degree,
 specialization index d′ , and species strength); statistical comparisons
 among forest strata; and beta diversity of interactions among strata. The
 script reads the interaction matrices and species-level metric files
 provided in this dataset and reproduces all figures and numerical results
 reported in the manuscript. ### File name: **Three_strata_matrix.txt**
 **Description:** Interaction matrix representing bat–fruit interactions
 pooled across the three forest strata (understory, subcanopy, and canopy).
 Columns correspond to frugivorous bat species and rows correspond to plant
 species. Cell values represent the observed frequency of interactions,
 defined as the number of fecal samples containing at least one intact seed
 of a given plant species associated with a given bat species. This matrix
 was used to run interaction networks, calculate species-level and
 network-level metrics. Thus, if seeds of the same plant species were
 detected in four fecal samples from a given bat species, the interaction
 frequency was recorded as four. Zeros indicate the absence of recorded
 interactions between a given bat and plant species. **Variables:** *
 **Rows:** Plant species (identified to species level when possible;
 unidentified taxa labeled as *sp.*, *sp1*, *sp2*, etc.). * **Columns:**
 Bat species. * **Cell values:** Integer counts of observed bat–plant
 interactions based on fecal sample analyses. **Missing data:**\ No missing
 values. Absence of interactions is indicated by zeros. 
 
 ### File name: **Two_strata_matrix.txt** **Description:** This file
 contains a quantitative interaction matrix of bat–fruit interactions
 recorded in the subcanopy and canopy forest strata. The matrix was
 assembled from fecal sample analyses of frugivorous bats, including only
 interactions detected within these two strata. This matrix was used to run
 interaction networks, calculate species-level and network-level metrics.
 **Variables:** * **Rows:** Plant species (identified to species level when
 possible; unidentified taxa labeled as sp., sp1, sp2, etc.). *
 **Columns:** Bat species. * **Cell values:** Number of fecal samples in
 which seeds of a particular plant species were found for each bat species.
 **Missing data:**\ No missing values. Zero indicates that no interaction
 was detected between the corresponding bat and plant species in these
 strata. 
 
 ### File name: **Canopy_matrix.txt** **Description:** This file contains
 a quantitative interaction matrix of bat–fruit interactions recorded
 exclusively in the canopy forest stratum. The matrix was compiled from
 fecal sample analyses of frugivorous bats and includes only interactions
 observed in this stratum. This matrix was used to run interaction
 networks, calculate species-level and network-level metrics, and to
 analyze beta diversity of interactions. **Variables:** * **Rows:** Plant
 species (identified to species level when possible; unidentified taxa
 labeled as sp., sp1, sp2, etc.). * **Columns:** Bat species. * **Cell
 values:** Number of fecal samples in which seeds of a particular plant
 species were found for each bat species. **Missing data:**\ No missing
 values. Zero indicates that no interaction was detected between the
 corresponding bat and plant species in the canopy stratum. 
 
 ### File name: **Subcanopy_matrix.txt** \ **Description:** This file
 contains a quantitative interaction matrix of bat–fruit interactions
 recorded exclusively in the subcanopy forest stratum. The matrix was
 compiled from fecal sample analyses of frugivorous bats and includes only
 interactions observed in this stratum. This matrix was used to run
 interaction networks, calculate species-level and network-level metrics,
 and to analyze beta diversity of interactions. **Variables:** * **Rows:**
 Plant species (identified to species level when possible; unidentified
 taxa labeled as sp., sp1, sp2, etc.). * **Columns:** Bat species. * **Cell
 values:** Number of fecal samples in which seeds of a particular plant
 species were found for each bat species. **Missing data:**\ No missing
 values. Zero indicates that no interaction was detected between the
 corresponding bat and plant species in the subcanopy stratum. 
 
 ### File name: **Understory_matrix.txt** **Description:** This file
 contains a quantitative interaction matrix of bat–fruit interactions
 recorded exclusively in the understory forest stratum. The matrix was
 compiled from fecal sample analyses of frugivorous bats and includes only
 interactions observed in this stratum. This matrix was used to run
 interaction networks, calculate species-level and network-level metrics,
 and to analyze beta diversity of interactions. **Variables:** * **Rows:**
 Plant species (identified to species level when possible; unidentified
 taxa labeled as sp., sp1, sp2, etc.). * **Columns:** Bat species. * **Cell
 values:** Number of fecal samples in which seeds of a particular plant
 species were found for each bat species. **Missing data:**\ No missing
 values. Zero indicates that no interaction was detected between the
 corresponding bat and plant species in the understory stratum. 
 
 ### File name: **GN_bats.txt** **Description:** This file contains the
 normalized degree for each frugivorous bat species across different forest
 strata. The normalized degree is a species-level metric that quantifies
 the level of generalization, calculated as the proportion of available
 plant partners with which a bat species interacts. Maximum values of 1
 indicate species that interact with all available partners in the network.
 The dataset includes results for individual strata as well as pooled
 strata combinations. This file was used to generate graphs and compare
 species-level metrics across forest strata. **Variables:** * **Bats:**
 Species names of frugivorous bats. * **Normalized_degree:** Normalized
 degree of the bat species, representing its level of generalization. *
 **Strata:** Forest stratum or combination of strata where interactions
 were recorded. Codes are as follows: 1 = Understory  2 = Sub-canopy 3 =
 Canopy 4 = Sub-canopy + Canopy (two strata) 5 = Understory + Sub-canopy +
 Canopy (all three strata) **Missing data:**\ No missing values. 
 
 ### File name: **Bats_specialization.txt** **Description:** This file
 contains the species-level specialization index (d’) for frugivorous bats
 across different forest strata. The d’ index quantifies the deviation of
 interaction frequencies between partners relative to the abundance of
 interactions. Species with d’ values close to 1 tend to interact with
 their partners more frequently than expected based on interaction
 abundances, indicating high specialization. The dataset includes results
 for individual strata as well as pooled strata combinations. This file was
 used to generate graphs and compare species-level metrics across forest
 strata. **Variables:** * **Bats:** Species names of frugivorous bats. *
 **Specialization:** d’ index for each bat species, representing its level
 of specialization in the network. * **Strata:** Forest stratum or
 combination of strata where interactions were recorded. Codes are as
 follows: 1 = Understory 2 = Sub-canopy 3 = Canopy 4 = Sub-canopy + Canopy
 (two strata) 5 = Understory + Sub-canopy + Canopy (all three strata)
 **Missing data:**\ No missing values. 
 
 ### File name: **Strength_bats.txt** **Description:** This file contains
 species-level strength values for frugivorous bats across different forest
 strata. Species strength quantifies the importance of a species in the
 network based on the sum of dependencies of all other species with which
 it interacts. Dependency is calculated as the proportion of interactions
 that each species represents, considering the entire set of interactions
 of a focal species. This file was used to generate graphs and compare
 species-level metrics across forest strata. **Variables:** * **Bats:**
 Species names of frugivorous bats. * **Strength:** Species strength value
 for each bat species. * **Strata:** Forest stratum or combination of
 strata where interactions were recorded. Codes are as follows: 1 =
 Understory 2 = Sub-canopy 3 = Canopy 4 = Sub-canopy + Canopy (two strata)
 5 = Understory + Sub-canopy + Canopy (all three strata) **Missing data:**\
 No missing values. 
 
 ### File name: **GN_plants.txt** **Description:** This file contains
 species-level normalized degree values for plants across different forest
 strata. The normalized degree quantifies the level of generalization of a
 species, being calculated as the proportion of available partners with
 which the species interacts. Maximum values of 1 identify species that
 interact with all available partners in the network. This file was used to
 generate graphs and compare species-level metrics across forest strata.
 **Variables:** * **Plants:** Species names of plants. *
 **Normalized_degree:** Normalized degree value for each plant species. *
 **Strata:** Forest stratum or combination of strata where interactions
 were recorded. Codes are as follows:\ 1 = Understory\ 2 = Sub-canopy\ 3 =
 Canopy\ 4 = Sub-canopy + Canopy (two strata)\ 5 = Understory + Sub-canopy
 + Canopy (all three strata) **Missing data:**\ No missing values. 
 
 ### File name: **Specia_plants.txt** **Description:** This file contains
 species-level specialization (d’) values for plants across different
 forest strata. The specialization index (d’) quantifies the deviation of
 interaction frequencies between partners in relation to the abundances of
 interactions. Species with d’ values close to 1 tend to interact with
 their partners more frequently than expected based on abundance, showing
 high specialization. This file was used to generate graphs and compare
 species-level metrics across forest strata. **Variables:** *
 **Morphotype:** Species names of plants. * **Specialization:**
 Specialization (d’) value for each plant species. * **Strata:** Forest
 stratum or combination of strata where interactions were recorded. Codes
 are as follows:\ 1 = Understory\ 2 = Sub-canopy\ 3 = Canopy\ 4 =
 Sub-canopy + Canopy (two strata)\ 5 = Understory + Sub-canopy + Canopy
 (all three strata) **Missing data:**\ No missing values. 
 
 ### File name: **Stren_plants.txt** **Description:** This file contains
 species-level strength values for plants across different forest strata.
 Species strength quantifies the importance of a species in the network
 based on the sum of dependencies of all other species with which it
 interacts. Dependency is calculated as the proportion of interactions that
 each species represents, considering the entire set of interactions of a
 focal species. This file was used to generate graphs and compare
 species-level metrics across forest strata. **Variables:** *
 **Morphotype:** Species names of plants. * **Strength:** Species strength
 value for each plant species. * **Strata:** Forest stratum or combination
 of strata where interactions were recorded. Codes are as follows:\ 1 =
 Understory\ 2 = Sub-canopy\ 3 = Canopy\ 4 = Sub-canopy + Canopy (two
 strata)\ 5 = Understory + Sub-canopy + Canopy (all three strata) **Missing
 data:**\ No missing values. 
 
 ### File name: Venn_D.R **Description:** This R script was used to
 generate Venn diagrams to visualize the presence, exclusivity, and overlap
 of species across different forest strata, as well as their interactions.
 The script uses interaction matrices, which are described below. 
 
 ### File name: Bats_by_stratum.txt **Description:** This file lists bat
 species recorded in each forest stratum. It was used to generate Venn
 diagrams showing species presence, exclusivity, and overlap across strata.
 **Variables:** * Species: Bat species name. * Strata: Forest stratum where
 the species was recorded (canopy, subcanopy and understory). **Missing
 data:**\ No missing values. 
 
 ### File name: Binary_canopy.txt **Description:** This file contains a
 binary interaction matrix of bat–fruit interactions recorded exclusively
 in the canopy forest stratum. This matrix was used to generate Venn
 diagrams showing species presence, exclusivity, and overlap, as well as to
 visualize differences in interactions between strata. **Variables:** *
 Rows: Plant species. * Columns: Bat species. * Values: 1 = interaction
 observed; 0 = no interaction observed. **Missing data:**\ No missing
 values. 
 
 ### File name: Binary_subcanopy.txt **Description:** This file contains a
 binary interaction matrix of bat–fruit interactions recorded exclusively
 in the sub-canopy forest stratum. This matrix was used to generate Venn
 diagrams showing species presence, exclusivity, and overlap, as well as to
 visualize differences in interactions between strata. **Variables:** *
 Rows: Plant species. * Columns: Bat species. * Values: 1 = interaction
 observed; 0 = no interaction observed. **Missing data:**\ No missing
 values. 
 
 ### File name: Binary_understory.txt **Description:** This file contains
 a binary interaction matrix of bat–fruit interactions recorded exclusively
 in the understory forest stratum. This matrix was used to generate Venn
 diagrams showing species presence, exclusivity, and overlap, as well as to
 visualize differences in interactions between strata. **Variables:** *
 Rows: Plant species. * Columns: Bat species. * Values: 1 = interaction
 observed; 0 = no interaction observed. **Missing data:**\ No missing
 values. 
 
 ### File name: Canopy_interactions.txt **Description:** This file lists
 all bat–fruit interactions recorded exclusively in the canopy forest
 stratum. It was used to generate Venn diagrams showing species and
 interaction presence, exclusivity, and overlap across forest strata.
 **Variables:** * Interactions: Unique identifier for each bat–plant
 interaction, combining the bat and plant species names (e.g.,
 *Sturnira_lilium_Solanum_*sp4). **Missing data:**\ No missing values. 
 
 ### File name: Subcanopy_interactions.txt **Description:** This file
 lists all bat–fruit interactions recorded exclusively in the sub-canopy
 forest stratum. It was used to generate Venn diagrams showing species and
 interaction presence, exclusivity, and overlap across forest strata.
 **Variables:** * Interactions: Unique identifier for each bat–plant
 interaction, combining the bat and plant species names (e.g.,
 *Sturnira_lilium_Piper_hispidum*). **Missing data:**\ No missing values.
 ### File name: Understory_interactions.txt **Description:** This file
 lists all bat–fruit interactions recorded exclusively in the understory
 forest stratum. It was used to generate Venn diagrams showing species and
 interaction presence, exclusivity, and overlap across forest strata.
 **Variables:** * Interactions: Unique identifier for each bat–plant
 interaction, combining the bat and plant species names (e.g.,
 *Sturnira_lilium_Piper_hispidum*). **Missing data:**\ No missing values.
 ## Code/software **Software/Code and Workflow** All analyses and
 visualizations were performed using R
 ([www.r-project.org](http://www.r-project.org)), a free and open-source
 environment for statistical computing and graphics. The following R
 packages were used for data processing, network analyses, and plotting:
 **bipartite (v2.18)** – to calculate network- and species-level metrics,
 including network size, number of interactions, asymmetry, connectance
 (C), specialization (H2’), weighted nestedness (WNODF), weighted
 modularity (Qw), normalized degree, species-level specialization (d’), and
 species strength. Null models for network metrics were generated using the
 r2dtable. **iNEXT (v3.0.1)** – to estimate sampling completeness of
 interaction networks using the Chao1 estimator. **stats (v3.6.2)** – for
 statistical analyses, including ANOVA, Kruskal–Wallis, and post hoc tests
 (Tukey or Dunn) to evaluate differences in species-level metrics among
 strata. \**ggplot2  **– to generate visualizations of species-level
 metrics and comparisons across strata. **betalink (v2.2.1)** – to
 calculate beta diversity of interactions, including dissimilarity due to
 species turnover (βST), interactions among shared species (βOS), and total
 dissimilarity (βWN). **VennDiagram** (v1.7.3) – to plot Venn diagrams
 illustrating the sharing and exclusivity of species and interactions
 across forest strata. 
 
 **Workflow:** Interaction data were compiled into weighted matrices for
 each forest stratum (understory, subcanopy, and canopy), with plant
 species in rows and bat species in columns. Each cell represents the
 observed frequency of interactions, defined as the number of fecal samples
 containing seeds of a given plant species associated with a particular bat
 species. Analyses were first conducted separately for each stratum and
 subsequently for combinations of two and three strata to evaluate gradual
 effects across the vertical gradient. Network-level metrics, including
 null models and sampling completeness, were calculated first, followed by
 species-level metrics, which were then used to generate graphs and perform
 comparisons across strata. Interaction dissimilarity between strata was
 assessed using beta diversity metrics. Species and interaction exclusivity
 and overlap across strata were visualized using Venn diagrams. **Included
 scripts:** R scripts for data import, calculation of network- and
 species-level metrics, null model testing, beta diversity calculation, and
 Venn diagram plotting. Tab-delimited input files containing species
 occurrences and interactions for each stratum. ## Access information Other
 publicly accessible locations of the data: * The dataset and R scripts
 supporting this study are publicly available at:
 [https://github.com/karolportosupi/Bat-fruit-interaction.git](https://github.com/karolportosupi/Bat-fruit-interaction.git) Data was derived from the following sources: * No external datasets were used; all data were generated by the authors.