Data and code from: Land use legacies shape wild boar (Sus scrofa) diet along a forest-urban gradient in Singapore
Data files
Jul 27, 2026 version files 3.88 MB
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analyse_dissimilarity.R
11.59 KB
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animal_loci_summary.R
8.77 KB
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asv_rarefaction.R
2.07 KB
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CO1D_ASVTable_Identified.csv
89.68 KB
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CO1D_Consensus_Assignments.csv
69.09 KB
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ITS2_ASVTable_Identified.csv
269.97 KB
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ITS2_Consensus_Assignments.csv
113.74 KB
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metadata.csv
3.59 KB
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plant_loci_summary.R
16.97 KB
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README.md
7.59 KB
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S16_ASVTable_NoNeg.csv
2.26 MB
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S16_Consensus_Assignments.csv
938.32 KB
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trnL_ASVTable_Identified.csv
61.90 KB
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trnL_Consensus_Assignments.csv
22.52 KB
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veg_model.R
6.95 KB
Abstract
Wild boars (Sus scrofa) are one of the most widespread mammals on the planet, but when overabundant, can cause negative impacts to ecosystems and people. In Singapore, native wild boars were extirpated in the mid-1900s amid rapid habitat loss and hunting, but have since re-established populations naturally and now sustain relatively high abundances in local forests where their natural predators remain absent, much of which is in close proximity to urban areas. Understanding the role that their dietary preferences play in their ecological success is thus crucial for managing their populations and human-wildlife conflict in the compact city state. Using DNA metabarcoding of faecal samples, we show that local wild boars exhibit a high degree of dietary flexibility. While there is a high prevalence of soil invertebrates and native plant foods in our samples, a wide variety of cultivated fruit tree species – common remnants of past land use in secondary forests – was also detected. DNA from native vertebrates such as mouse deer and leopard cats was also identified, suggesting that wild boar play important roles in local ecosystems. The extent of neighbouring vegetated areas explained plant and animal dietary composition, but was not strongly correlated with plant and animal dietary diversity. Our study suggests that food resources due to land use legacies may play a substantial role in subsidising local wild boar populations in Singapore. Management of cultivated tree species in secondary forests may thus be a potential strategy for regulating wild boar populations in the highly urban forests of Singapore.
Dataset DOI: 10.5061/dryad.qfttdz0x3
Description of the data and file structure
Data includes consensus BLAST assignments for amplicon-sequence variants (ASVs) obtained through metabarcoding of wild boar faecal samples, ASV tables (sample by ASV tables with sequencing read counts), and metadata associated with wild boar feacal samples.
Code to analyse ASV richness and dissimilarity between samples are also included.
Files and variables
Metadata
File: metadata.csv
Description:
Variables
- Sample: Sample ID
- Location: Subregion of Singapore sampling location is located.
- ForestCover: Percentage of land area within 1km of the sampling location covered in forest
- VegetationCover: Percentage of land area within 1km of sampling location covered by any vegetation type
- Latitude: Latitude of sampling location (in decimal degrees)
- Longitude: Longitude of sampling location (in decimal degrees)
Amplicon sequence variant (ASV) read count tables
File: trnL_ASVTable_Identified.csv
Description: Sample x amplicon sequence variant (ASV) table. Values represent read counts obtained through metabarcode sequencing of trnL amplicons.
Variables
- Sample: Sample ID
- ASVXX: Read counts for each amplicon sequence variant (ASV). Identities for each ASV are provided in the corresponding consensus assignments file ("trnL_Consensus_Assignments.csv").
File: ITS2_ASVTable_Identified.csv
Description: Sample x amplicon sequence variant (ASV) table. Values represent read counts obtained through metabarcode sequencing of ITS2 amplicons.
Variables
- Sample: Sample ID
- ASVXX: Read counts for each amplicon sequence variant (ASV). Identities for each ASV are provided in the corresponding consensus assignments file ("ITS2_Consensus_Assignments.csv").
File: CO1D_ASVTable_Identified.csv
Description: Sample x amplicon sequence variant (ASV) table. Values represent read counts obtained through metabarcode sequencing of CO1 amplicons. CO1 amplicons were enriched using bead-based and non-target blocking primer approaches before sequencing library preparation.
Variables
- Sample: Sample ID
- ASVXX: Read counts for each amplicon sequence variant (ASV). Identities for each ASV are provided in the corresponding consensus assignments file ("CO1D_Consensus_Assignments.csv").
File: S16_ASVTable_NoNeg.csv
Description: Sample x amplicon sequence variant (ASV) table. Values represent read counts obtained through metabarcode sequencing of S16 amplicons. ASVs that were amplified in the negative control have already been excluded.
Variables
- Sample: Sample ID
- ASVXX: Read counts for each amplicon sequence variant (ASV). Identities for each ASV are provided in the corresponding consensus assignments file ("S16_Consensus_Assignments.csv").
Amplicon sequence variant (ASV) taxonomic assignment tables
File: trnL_Consensus_Assignments.csv
Description: Consensus BLAST taxonomic assignments for each amplicon sequence variant (ASV) obtained through trnL metabarcoding. Only plant ASVs identified to at least taxonomic order are included.
Variables
- ASV: Amplicon sequence variant ID
- Order: Putative taxonomic order of ASV
- Family: Putative taxonomic family of ASV ("NA" = family was not assigned)
- Genus: Putative taxonomic genus of ASV ("NA" = genus was not assigned)
- Species: Putative taxonomic species name of ASV ("NA" = species was not assigned)
- Database: Whether taxonomic reference came from GenBank databases ("Genbank") or if they were additionally corroborated by sequencing (unpublished) data from the Singapore Flora Genome Project ("Both")
File: ITS2_Consensus_Assignments.csv
Description: Consensus BLAST taxonomic assignments for each amplicon sequence variant (ASV) obtained through ITS2 metabarcoding. Only plant ASVs identified to at least taxonomic order are included.
Variables
- ASV: Amplicon sequence variant ID
- Order: Putative taxonomic order of ASV
- Family: Putative taxonomic family of ASV ("NA" = family was not assigned)
- Genus: Putative taxonomic genus of ASV ("NA" = genus was not assigned)
- Species: Putative taxonomic species name of ASV ("NA" = species was not assigned)
- Database: Whether taxonomic reference came from GenBank databases ("Genbank") or if they were additionally corroborated by sequencing (unpublished) data from the Singapore Flora Genome Project ("Both")
File: CO1D_Consensus_Assignments.csv
Description: Consensus BLAST taxonomic assignments for each amplicon sequence variant (ASV) obtained through CO1 metabarcoding. Only animal ASVs identified to at least taxonomic order are included. CO1 amplicons were enriched using bead-based and non-target blocking primer approaches before sequencing library preparation.
Variables
- ASV: Amplicon sequence variant ID
- Phylum: Putative taxonomic phylum of ASV
- Class: Putative taxonomic class of ASV
- Order: Putative taxonomic order of ASV
- Family: Putative taxonomic family of ASV ("NA" = family was not assigned)
- Genus: Putative taxonomic genus of ASV ("NA" = genus was not assigned)
- Species: Putative taxonomic species name of ASV ("NA" = species was not assigned)
File: S16_Consensus_Assignments.csv
Description: Consensus BLAST taxonomic assignments for each amplicon sequence variant (ASV) obtained through CO1 metabarcoding.
Variables
- ASV: Amplicon sequence variant ID
- Phylum: Putative taxonomic phylum of ASV ("NA" = phylum was not assigned)
- Class: Putative taxonomic class of ASV ("NA" = class was not assigned)
- Order: Putative taxonomic order of ASV ("NA" = order was not assigned)
- Family: Putative taxonomic family of ASV ("NA" = family was not assigned)
- Genus: Putative taxonomic genus of ASV ("NA" = genus was not assigned)
- Species: Putative taxonomic species name of ASV ("NA" = species was not assigned)
Code/software
All code was run on R v4.4.0. The following R packages (and associated dependencies) will be required: dplyr (v1.2.0), ggplot2 (v.4.0.0), plyr (v.1.8.9), reshape2 (v.1.4.4), sf (v.1.0-21), spdep (v.1.4-1), tibble (v.3.3.1), tidyr (v.1.3.2), vegan (v.2.6-6.1).
R scripts need to be run in the following order to generate the necessary intermediate files for each subsequent R script.
File: plant_loci_summary.R
Description: R code to calculate prevalence of taxonomic groups recovered though metabarcode sequencing of plant loci (trnL and ITS2)
File: animal_loci_summary.R
Description: R code to calculate prevalence of taxonomic groups recovered though metabarcode sequencing of animal loci (CO1)
File: asv_rarefaction.R
Description: R code to perform a sequencing read rarefaction approach to control for differences in sequencing depth across samples.
File: veg_model.R
Description: R code to run statistical linear models testing the relationship between vegetation cover and amplicon sequence variant richness across sites.
File: analyse_dissimilarity.R
Description: R code to run Mantel tests to examine the relationship between differences in vegetation cover and amplicon sequence variant composition across sites.
Access information
Other publicly accessible locations of the data:
- Raw sequence data is available on NCBI under BioProject number PRJNA1423465.
