DOI: 10.5281/zenodo.18366923
title: Data from: Frugivore species richness influences dietary specialisation and network properties in Asian wet tropical forests

description: We examined how species richness in local plant-frugivore assemblages influences frugivore fruit choice behaviour, their dietary niche and the organisation of the plant-frugivore interaction network. 

Description of the data and file structure

Taxa Coverage: Fleshy-fruited woody plants and avian frugivores.

Geographic Coverage: Namdapha Tiger Reserve (27°23′–27°39′N and 96°15′–96°58′E), Pakke Tiger Reserve (26°54–27°16′N and 92°36′–93°09′E), Anamalai Tiger Reserve (10°12′–10°35′N and 76°49′–77°24′E), South Andaman (11°07′–12°15′N and 92°30′–92°50′E), Narcondam (13°30′N and 94°38′E) among the Indian sites, and Hala-Bala Wildlife Sanctuary (5°44′–5°57′N and 101°46′–101°51′E) in Thailand.

Temporal Coverage: 2016–2024.

Field data was collected for different sites by:1. Namdapha Tiger Reserve: Rintu Mandal, Himanshu Lad2. Pakke Tiger Reserve: Saniya Chaplod, Rohit Naniwadekar3. Anamalai Tiger Reserve: Rintu Mandal, Natasha Desai, Rasika Kadam, Vignesh Chandran4. South Andaman: Arpitha Jayanth, Aditya Gadkari, Vignesh Chandran5. Narcondam: Rohit Naniwadekar, Abhishek Gopal, Sartaj Ghuman, Navendu Page6. Hala-Bala Wildlife Sanctuary: Vatcharavee Sriprasertsil

More details about the data can be obtained from R. Naniwadekar from the Nature Conservation Foundation and from (Naniwadekar et al., 2019, 2021, 2025).

File Descriptions:

Data filesThere are 18 data files in this dataset:1. dat_sxy_anamalai.csv2. dat_tp_anamalai.csv3. dat_p_anamalai.nex4. dat_sxy_andaman.csv5. dat_tp_andaman.csv6. dat_p_andaman.nex7. dat_sxy_namdapha.csv8. dat_tp_namdapha.csv9. dat_p_namdapha.nex10. dat_sxy_narcondam.csv11. dat_tp_narcondam.csv12. dat_p_narcondam.nex13. dat_sxy_pakke.csv14. dat_tp_pakke.csv15. dat_p_pakke.nex16. dat_HMSC_variance_partitioning.csv17. dat_dPrime_NormalisedDegree_combined.csv18. dat_NetworkMetrics_original_and_rarefied.csv

The first 15 data files are data files required for running the Hierarchical Modelling of Species Communities (HMSC) for five of our study sites: Anamalai, Andaman, Namdapha, Narcondam, and Pakke. The SXY files contain species and environmental data, TP files contain species traits, and P files correspond to time-calibrated phylogenies of the species of interest. The details of the columns corresponding to these files are as follows:

SXY files (“dat_sxy_SiteName.csv”)1. tree_family - refers to the plant family the focal plants belonged to in our study 2. tree_code - unique code given to focal plants in each study site3. tree_sp - refers to the plant species the focal plants belonged to in our study4. seed_size - seed size of the focal plant (small, medium, or large)5. fruit_width - mean width of ripe fruits in mm of the focal plant6. pulp_lipid - lipid content in the pulp of ripe fruits of the focal plant (low, medium, or high)7. log_fcs - ripe fruit crop size of the focal plant (converted to natural log scale)The remaining columns in each SXY file correspond to the presence (1) or absence (0) of the avian frugivore species included in the analysis for a particular site.

TP files (“dat_tp_SiteName.csv”)1. bird_sp - avian frugivore species included in the analysis for a particular site2. degree_frugivory - degree of frugivory (percentage of fruits in diet)3. beak_width - beak width of avian frugivores in mm4. hwi - hand-wing index of each frugivore species

P files (“dat_p_SiteName.nex”)A time-calibrated phylogenetic tree of the avian frugivore species included in the analysis for a particular site.

The data set “dat_HMSC_variance_partitioning.csv” contains the outputs of the HMSC models, specifically, the percentage of variation explained by each fixed effect included in the model for five of our study sites. The details of the columns are as follows:1. Predictors - fixed effects included in the model2. Percentage_variation_explained - percentage of variation explained by each fixed effect3. Site - name of the study sites (five)4. Sp_richness - the total number of avian frugivore species recorded in each study  site during the entire study period (and not the number of frugivore species included in the model)

The data set “dat_dPrime_NormalisedDegree_combined.csv” contains the specialisation measures (Normalised Degree and Blüthgen’s d′) calculated for each avian frugivore species in our study using network analysis. The details of the columns are as follows:1. Frugivore_code - unique code given to each avian frugivore species2. Scientific_old - binomial names of avian frugivores as per https://www.birdtree.org/3. Scientific_updated - binomial names of avian frugivores as per Clement’s Checklist of Birds4. Normalised_Degree - Normalised Degree of each avian frugivore calculated using network analysis for each site5. D_prime - Blüthgen’s d′ of each avian frugivore calculated using network analysis for each site6. Site - name of the study sites (six)7. Sp_richness - the total number of avian frugivore species recorded in each study  site during the entire study period

The data set “dat_NetworkMetrics_original_and_rarefied.csv” contains the observed and rarefied values of four network-level metrics, namely, Connectance, Modularity, Specialisation, and weighted NODF for six plant-frugivore assemblages in our study. The details of the columns are as follows:1. Site - name of the study sites (six)2. Sp_Richness - the total number of avian frugivore species recorded in each study  site during the entire study period3. Metric - name of the network metric4. Original_Metric_Value         - the observed network metric values calculated using network analysis5. Rarefied_Mean - We randomly pulled 696 (the lowest number of interactions among our study sites) interactions from the original plant-frugivore interaction network for each study site to create the rarefied plant-frugivore interaction network, and calculated the aforementioned network metrics. We repeated the process 100 times for each site to calculate the mean network metric values.6. Rarefied_SD - Standard Deviation of the rarefied network metrics were calculated using the protocol mentioned above.

 

CodeThere are three R scripts (.R files) in this dataset:1. code_hmsc.R2. code_correlation_glmm_dPrime_NormalisedDegree_SpRichness.R3. code_correlation_network_metrics_SpRichness.R

The R script “code_hmsc.R” contains the R code to fit the model and run the HMSC analysis for each site (L1–L60), evaluate model convergence, compute variance partitioning, extract beta and gamma plots, and check for phylogenetic signal in the data (L65–L126), and finally plot the mean (and 95% CI) percentage variation explained by each predictor (L132–L162).

The R script “code_correlation_glmm_dPrime_NormalisedDegree_SpRichness.R” contains R code to check correlations between the species-level metrics Normalised Degree and Blüthgen’s d′ and the site-level frugivore species richness, GLMM codes to model those species-level metrics as a function of site-level frugivore species richness, and plot the outputs.

The R script “code_correlation_network_metrics_SpRichness.R” contains R code to check correlations between rarefied network metrics and site-level frugivore species richness, and plot the relationships.