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Data from: Ecological and evolutionary significance of primates’ most consumed plant families

Citation

Lim, Jun Ying et al. (2021), Data from: Ecological and evolutionary significance of primates’ most consumed plant families, Dryad, Dataset, https://doi.org/10.5061/dryad.sbcc2fr40

Abstract

Angiosperms have been essential components of primate diet for millions of years, but the relative importance of different angiosperm families in primate diets and their influence on primate evolution and ecology remains unclear. Here, we assess the contribution and ecological and evolutionary significance of plant families to the diets of wild primates based on an unprecedented dietary dataset of over 8,000 dietary records, compiled from 140 primary sources encompassing 109 primate species. Out of the 204 angiosperm plant families recorded in primate diets, only ten families were consumed by >50% of primate species. Plants from the Moraceae and Fabaceae were the most widely and most frequently consumed and represent keystone resources of primates. Over three-quarters of primates in our dataset were recorded to feed on these two families, and combined, they make up close to 12% of primate diets on average. By analyzing the relative proportion of different plant parts consumed, we find that Moraceae was mainly consumed as fruit and Fabaceae as non-fruit parts, and consumption of these two families showed phylogenetic signal among primates. In particular, we also find that Moraceae consumption was associated with smaller home range sizes, even though frugivorous primates tend to have larger home ranges compared to folivores, possibly due to the year-round availability of Moraceae fruits and spatial asynchrony in their phenology. Our results suggest that primates may be intricately and subtly shaped by the plant families that they consume, and highlight the importance of dietary studies in understanding primate ecology and evolution.

Methods

Please refer to the Methods section and Electronic Supplementary Material of the published article, as well as the digitization notes provided in this repository

Usage Notes

Citation

If you use this dataset, please cite this Dryad repository and the following reference:

Lim, J.Y., Wasserman, M.D., Veen, J., Despres-Einspenner, M.-L. & Kissling, W.D. (2021) Ecological and evolutionary significance of primates' most consumed plant families. Proceedings of the Royal Society B, 288: 20210737. https://doi.org/10.1098/rspb.2021.0737

Contents

This data repository consists of the following files:

  1. Read me Word document containing more details on each file ("ReadMe.docx")
  2. R script for data processing, analysis and figure generation ("Primate_Diet_Script.R")
  3. Primate diet dataset ("Primate_Diet_v1-2_Data.xlsx")
  4. Full references and attributes of studies in the primate diet dataset ("Primate_Diet_v1-2_References.xlsx")
  5. Supplementary notes on how each study in the primate diet dataset was digitized ("Primate_Diet_v1-2_digitizationNotes.docx")
  6. Home range size and body size information of primates ("Primate_Traits.csv")
  7. Maximum clade credible phylogeny, derived from the posterior sample of trees provided by the Faurby et al 2018 dataset ("faurby_mcc_mean_heights.nex")
  8. Copy of EltonTraits dataset v1 ("EltonTraits_v1_MamFuncDat.txt")
  9. Copy of MammalDiet dataset v1 ("MammalDIET_v1.0.txt")

To run the R script on your local machine, you will first need to specify your local working directory by modifying the "main.dir" variable in the R script. Output will automatically be written into pre-defined folders (e.g., "results", "figures") in your defined working directory. If those pre-defined folders do not exist, they will automatically be created.

System Requirements

To run this code you will need an installation of R and some R packages. This includes both for the analysis of data and the plotting of the figures in the manuscript. Feel free to get in contact if you have trouble running the script.

Code was tested on R version 4.0.3 with the following packages attached (version number in parentheses): `piecewiseSEM` (v.2.1.0), `semPlot` (v1.1.2), `semTools` (v0.5-3), `lavaan` (v0.6-7), `ggrepel` (v0.8.1), `RColorBrewer` (v1.1-2), `ggtree` (v2.4.1), `reshape2` (v1.4.4), `wesanderson` (v0.3.6), `cowplot` (v1.1.0), `plyr` (v1.8.6), `caper` (v1.0.1), `mvtnorm` (v1.1-1), `MASS` (v7.3-53), `ggplot2` (v3.3.2), `phytools` (v0.7-70), `maps` (v3.3.0), `Matrix` (v1.2-18), `nlme` (v3.1-150), `ape` (v5.3), rnaturalearth (v0.1.0).

Metadata

Primate Diet dataset ("Primate_Diet_v1-2_Data.xlsx")

The dataset contains the following columns:

  • SpecName: Species name of primate used in the original paper. 
  • PrimateSpecies: Accepted species name, following taxonomy used by Galán-Acedo et al. (2019) Ecological traits of the world's primates, Scientific Data, 6, 55 (Version 4, updated August 2019).
  • Study_ID: Unique identifier for diet studies (i.e. different primate species, different groups/locations of same primate species, different seasons/years of data collection). Full reference information for each study can be found in the "Primate_Diet_v1_Reference.csv" file. 
  • Food: Food item as reported by original authors, including plant species names, animals, fungus, undetermined food items. If sum of diet percentages reported by study was lower than 100  (see "PercentageDietReported"), a placeholder "Unknown" food item was added. 
  • PlantFamily: Plant family belonging to the plant genus name reported. If we failed to match a plant family to a genus name, an "Unknown_plant" was assigned. For non-plant items (e.g. fungus, animal or unknown items), value is undefined (= N.A.)
  • PlantGenus: Genus names of plant species as reported by the original authors. 
  • PlantSpecies: Species names of plants as reported by original authors. 
  • PlantGenusAcc: Genus names of plant species after synonyms and spelling errors corrected
  • PlantSpeciesAcc: Genus names of plant species after synonyms and spelling errors corrected
  • Percentage_Paper: Percentage of specific food item as reported by original authors. Exception is when original authors reported feeding observations, after which the percentages were calculated manually based on the total feeding observations reported.
  • Percentages_Recalculated: Standardized percentage of food item (percentages scaled to sum to 100 if original paper percentages are above 100). If sum of diet percentages reported by study was lower than 100  (see "PercentageDietReported"), a placeholder "Unknown" food item was added with a percentage that ensure that the sum of percentages in the study up to 100.
  • TypeFood: Reports the type of the food item, including plants, animals, fungus, honey, dung, and unknown.  
  • PartPlant: Reported plant parts (e.g. young leaves, ripe fruits) consumed of a specific plant food item. If multiple plant parts were reported belonging to one percentage, they were reported in separately in PlantPart1, PlantPart2 etc. based on the order they reported in the original paper. All plant parts (+ synonyms) can be found in the second sheet.
  • Season: Reference number when a specific study studied a certain primate species in the same location in different periods, and reported the diet separately.
  • Group: Reference number when a specific study studied multiple groups of a certain primate species, and reported the diet separately.
  • Ref_ID:  Reference number for the different studies used. The notation is based on the first author and year of publication. 

Full reference and metadata for primate diet data ("Primate_Diet_v1-2_References.csv"):

  • StudyID: As above
  • Ref_ID: As above
  • SpecName: As above
  • Species: Accepted species name, following taxonomy used by Galán-Acedo et al. (2019) Ecological traits of the world's primates, Scientific Data, 6, 55 (Version 4, updated August 2019). Identical to PrimateSpecies column in data file.
  • Title: Title of reference for study.
  • Duration_months: Total number of months over which dietary data were collected.
  • SampleEffort_hours: Total amount of time (in hours) over which behaviour of primate species was observed.
  • Locality: Locality of study.
  • Country: Country where study was located.
  • DMS_Latitude: Latitude of study locality (in degree, minute, second format). This was manually georeferenced from locality information if not provided in the reference.
  • DMS_Longitude: Longitude of study locality (in degree, minute, second format). This was manually georeferenced from locality information if not provided in the reference.
  • Latitude: Latitude of study locality (in decimal degree format)
  • Longitude: Longitude of study locality (in decimal degree format)
  • SampleMethod: Method used to obtain dietary data of the primate species.
  • Group: See above
  • Season: See above
  • Citation: Citation of the papers used
  • Notes: Additional details about specific Study_IDs including the table(s) the data was extracted from, absence of plant parts, manually calculated percentages.

Supplementary notes on how each study in the primate diet dataset was digitized ("Primate_Diet_v1-2_digitizationNotes.docx")

This supplement is a record of how we digitized food items reported in each study in our dataset, as well as the added interpretation that was necessary to ensure that all the diets are accounted for (e.g., diet percentages for each study sum up to 100%)("Primate_Diet_v1-2_Data.xlsx"). Multiple studies that come from the same reference are treated together for ease of reference. For each reference, a summary of the relevant data and notes on digitization is provided. The former is a description of all salient information reported in the reference on the primate diet. This may range from a breakdown of diet into different categories to more detailed food item lists, and may be textual (in the main text or in tables) or graphical (e.g., pie charts or other figures). The latter is a description of how we inputted this information into the dataset (i.e., "Primate_Diet_v1-2_Data.xlsx")

Body size and home range size of primate species ("Primate_Traits.csv")

Data is derived from the primate trait dataset by Galán-Acedo et al. (2019) Ecological traits of the world's primates, Scientific Data, 6, 55 (Version 4, updated August 2019). The dataset is available via the following link: https://zenodo.org/record/2600338

  • Family: Taxonomic family
  • Species: Species name of primate
  • BodyMass_kg: Body mass (in kilograms) of primate. If multiple estimates were in the database, we calculated the average.
  • HomeRange_ha: Home range size (in hectares) of primate. If multiple estimates were in the database, we calculated the average (regardless of methodology).

Maximum clade credible phylogeny ("faurby_mcc_mean_heights.nex")

We used the posterior distribution of trees ("Complete_phylogeny.nex" file) provided as part of the PHYLACINE dataset, Faurby et al. (2018) Phylacine 1.2: The Phylogenetic Atlas of Mammal Macroecology, Ecology, 99, 2626. Maximum clade credibility phylogeny was generated using TreeAnnotator, and node ages were simply the average of node heights of the corresponding clade across the posterior sample of trees that contained that clade. This was performed by selecting the "Mean heights" option.

Copy of EltonTraits dataset v1 ("EltonTraits_v1_MamFuncDat.txt")

The EltonTraits database was used to cross-validate estimates of frugivory and folivory (Wilman et al. 2014 Elton Traits 1.0: Species-level foraging attributes of the world's birds and mammals, Ecology, 95, 2027.). No modifications were made. The same file, as well as the metadata for this dataset can be obtained from http://www.esapubs.org/archive/ecol/E095/178/

Copy of MammalDiet dataset v1 ("MammalDIET_v1.0.txt")

The MammalDiet database v1 was used to cross-validate estimates of frugivory and folivory (Kissling et al. 2014 Establishing amcroecological trait datasets: digitization, extrapolation, and validation of diet preferences in terrrestrial mammals worldwide, Ecology and Evolution, 4, 2913 - 2930.). No modifications were made. The same file as well as the metadata for this dataset can be obtained from http://datadryad.org/stash/dataset/doi:10.5061/dryad.6cd0v. 

Output

The R script will generate a list of outputs in a "results" folder. Description of each file are as follows:

  • Filtered dataset ("diet_subset.csv"), wherein studies for which (i) the sampling period was shorter than six months in duration, (ii) the majority of the diet (greater than 50%) was not known or reported or (iii) the plant family for the majority of the plant portion of the diet (greater than 50%) was either not identified by the author(s) of the study or could not be taxonomically verified by us during collation, were omitted. 
  • Phylogenetic signal results ("phylosig_res.csv")
  • Relative proportion of different plant part category in consumption of different plant families ("plantfamily_dietcategories.csv")
  • Relative proportion of different diet category ("fruit", "leaf", "others", "unknown", "animal") in diet of primate species ("primate_dietcategories.csv")
  • Percentage of the ten most consumed plant families in the diets of primate species ("topten_familyprop.csv")
  • Percentage of the ten most consumed plant families in the diets of primate species in matrix format, where species are represented by the rows and the plant families by the columns ("topten_familyprop_matrix.csv"). A derived file where percentages have been rounded to the closest 0.1 percent is also provided ("topten_familyprop_matrix_clean.csv "). Values less than 0.1 are listed as "<0.1".

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Award: 824.15.007