DOI: 10.5061/dryad.n02v6wx8g
title: Data from: Dietary response of black-backed jackals (<em>Lupulella mesomelas</em>) to contrasted land use

description: This dataset contains prey species detections derived from DNA
 metabarcoding of black-backed jackal (Lupulella mesomelas) scats collected
 across three land-use types in the Eastern Cape, South Africa. The data
 provide species-level dietary occurrence information and associated sample
 metadata for use in studies of trophic ecology, dietary niche breadth, and
 predator–prey interactions. Raw sequence data were processed through a
 standardized bioinformatics pipeline, and the resulting operational
 taxonomic unit (OTU) table was taxonomically assigned and curated to
 produce the final dataset. To account for variation in sequencing depth
 among samples, detections are provided as presence–absence records at the
 species level. This data was used to investigate patterns of resource use
 across landscapes, compare dietary composition among sites and seasons,
 and support meta-analyses of carnivore diet based on metabarcoding
 approaches.
description: # Data from: Dietary response of black-backed jackals (*Lupulella
 mesomelas*) to contrasted land use Dataset DOI:
 [10.5061/dryad.n02v6wx8g](10.5061/dryad.n02v6wx8g) ## Description of the
 data and file structure **Bioinformatics Pipeline Summary** 1. **Quality
 Control** * Initial read quality assessed using *MultiQC* v1.14. * Reads
 with an average Q-score &lt; 30 were discarded. 2. **Trimming and
 Sorting** * Paired-end reads were trimmed and sorted into sample-specific
 FASTQ files using Illumina's default pipeline. * Primer sequences
 were removed using *Cutadapt* v3.5. * Unassigned reads were discarded. 3.
 **Merging and Filtering** * Forward and reverse reads were merged using
 *USEARCH* v11.0.667. * Merged reads were filtered to allow a maximum of
 one expected error per read. 4. **OTU Clustering and Taxonomic
 Assignment** * OTUs were clustered using the *UPARSE* algorithm (USEARCH),
 with a 97 % similarity threshold. * Chimeric and singleton reads were
 removed. * OTUs were assigned taxonomy using *BLAST* against the NCBI
 GenBank database: * OTUs with ≥ 95 % identity were assigned to species
 level (if unique match) or lowest common taxonomic level (if multiple
 matches). * OTUs with &lt; 95 % identity were classified as
 "undetermined" and excluded. 5. **Species-Level Aggregation and
 Taxonomic Corrections** * Read counts were aggregated per species across
 samples. * For taxonomically ambiguous groups (e.g., *Felidae*, *Bovidae*,
 *Rodentia*), manual correction was done by comparing co-occurrence
 patterns and adjusting assignments where necessary. 6. **Filtering
 Criteria** * OTUs identified as *Homo sapiens* or with read lengths &lt;
 70 bp ("None") were removed. * Samples with &lt; 1,000 total
 reads after filtering were excluded. * OTUs classified as *Canis spp.*
 were attributed to black-backed jackal. * Samples where jackal reads made
 up &lt; 1 % of total reads were excluded to avoid scat misidentification.
 7. **Final Data Transformation** * To account for variation in sequencing
 depth, data were converted to a **presence-absence format**. * A species
 was considered "present" if its read count was ≥ 10, based on
 background levels in negative controls. ### Files and variables ### File:
 `metadata_for_samara.csv` **Description**: Sample metadata used to
 describe each scat sample. **Variables**: * Sample name: Unique identifier
 for each scat sample * Sample_title (placement number and corresponding
 file name): This is the sample number without the “SAM” prefix. * Site:
 Land-use type where the scat was collected (Game farm, Livestock farm, or
 the Big 5 nature reserve Samara). * Scat collection: Date on which the
 sample was collected (format: DD-MM-YYYY). * DNA extraction date:
 Approximate date of DNA extraction (format: YYYY-MM-DD). * Season:
 Seasonal category assigned to each sample. * Sample description: Indicates
 whether the sample is a faecal sample or a DNA extraction control.
 Extraction controls contain no faecal material and consist only of
 extraction reagents. One control was included for every batch of 23
 samples to monitor contamination and extraction success. * Not applicable:
 refer to Sample description. ### Files:
 Steps_to_final_livestock_dataset.xlsx,
 Steps_to_final_game_farm_dataset.xlsx, and
 Steps_to_final_samara_Big5_dataset.xlsx **Description:** These files
 contain the final processed prey detection datasets used for statistical
 analyses. Each file corresponds to one of the three land use sites
 (Livestock farm, Game farm, and Samara Big 5 reserve) and documents the
 sequential filtering steps applied to the raw read data to produce the
 final presence–absence matrix. Each Excel file includes four worksheets
 representing the four processing steps described below. The final
 worksheet in each file contains the dataset used for downstream analyses.
 **Processing steps** **Step 1 – Minimum read threshold and initial
 filtering** OTU sequences identified as human contamination, shorter than
 70 bp, or labelled “None” were removed. Only samples with more than 1,000
 total reads after these exclusions were retained. Reads assigned to
 *Canis* spp. were classified as black-backed jackal. **Step 2 – Jackal
 read threshold** To exclude misidentified scats, only samples in which
 jackal reads comprised ≥ 1% of the total reads were retained. **Step 3 –
 Taxonomic cross-checking and manual curation** Closely related taxa that
 could not be reliably distinguished due to shared barcode polymorphisms
 were evaluated using correlation patterns among samples. Read counts were
 reassigned where necessary. This procedure was applied to selected
 members, for example Felidae, Bovidae, and Rodentia. **Step 4 – Conversion
 to presence–absence data** Species-level read counts were converted to
 binary detections to account for variation in sequencing depth. A species
 was recorded as present when ≥ 10 reads were detected in a sample. This
 threshold was based on observations from extraction and PCR blanks, which
 rarely exceeded 10 reads for any taxon other than *Homo sapiens*, *Canis*
 spp., or “None”. **Data structure (final worksheet)** **Sample** Sample
 identifier matching Sample_name in the metadata file. **Season** Season in
 which the sample was collected. **Species columns** Each column represents
 a prey species. **Cell values** 1 = species detected in the sample 0 =
 species not detected in the sample ### File: SAMARA_Raw_reads.7z
 **Description**: Raw reads after Miseq sequencing **Variables**: * Sample
 Matches the Sample_name from the metadata ### File: Usearch.sh
 **Description**: Shell Script for USEARCH Workflow