DOI: 10.5061/dryad.63tj806
title: Data from: Trophic ecology of large herbivores in a reassembling African ecosystem

description: 1. Diverse megafauna assemblages have declined or disappeared throughout
 much of the world, and many efforts are underway to restore them.
 Understanding the trophic ecology of such reassembling systems is
 necessary for predicting recovery dynamics, guiding management, and
 testing general theory. Yet there are few studies of recovering
 large-mammal communities, and fewer still that have characterized food-web
 structure with high taxonomic resolution. 2. In Gorongosa National Park,
 large herbivores have rebounded from near-extirpation following the
 Mozambican Civil War (1977-1992). However, contemporary community
 structure differs radically from the pre-war baseline: medium-sized
 ungulates now outnumber larger-bodied species, and several apex carnivores
 remain locally extinct. 3. We used DNA metabarcoding to quantify diet
 composition of Gorongosa’s 14 most abundant large-mammal populations. We
 tested five hypotheses: (i) the most abundant populations exhibit greatest
 individual-level dietary variability; (ii) these populations also have the
 greatest total niche width (dietary diversity); (iii) interspecific niche
 overlap is high, with the diets of less-abundant species nested within
 those of more-abundant species; (iv) partitioning of forage species is
 stronger in more structurally heterogeneous habitats; and (v) selectivity
 for plant taxa converges within guilds and digestive types, but diverges
 across them. 4. Abundant (and narrow-mouthed) populations exhibited higher
 among-individual dietary variation, but not necessarily the greatest
 dietary diversity. Interspecific dietary overlap was high, especially
 among grazers and in structurally homogenous habitat, whereas niche
 separation was more pronounced among browsers and in heterogeneous
 habitat. Patterns of selectivity were similar for ruminants—grazers and
 browsers alike—but differed between ruminants and non-ruminants. 5.
 Synthesis. The structure of this recovering food web was consistent with
 several hypotheses predicated on competition, habitat complexity, and
 herbivore traits, but it differed from patterns observed in more-intact
 assemblages. We propose that intraspecific competition in the
 fastest-recovering populations has promoted individual variation and a
 more nested food web, wherein rare species use subsets of foods eaten by
 abundant species, and that this scenario is reinforced by weak top-down
 control. Future work should test these conjectures and analyze how the
 taxonomic dietary niche axis studied here interacts with other mechanisms
 of diet partitioning to affect community reassembly following wildlife
 declines.
description: Raw diet
 dataThis fasta file contains
 unfiltered sequencing data (i.e. merged paired-end reads assigned to their
 original sample). The P6 loop of the chloroplast trnL (UAA) intron was
 amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and
 “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were
 obtained by a 2 x 150 bp paired-end sequencing on Illumina HiSeq 2500
 platform. First processing steps were performed using the OBITOOLS
 software (http://metabarcoding.org/obitools) as follows: (i) Direct and
 reverse reads corresponding to the same sequence were aligned and merged
 thanks to the ‘illuminapairedend’ program. Only merged sequences with a
 high alignment quality score were retained (&gt;=40). (ii) Each merged
 sequence was assigned to its original sample using the tags information
 previously added to primers using the ‘ngsfilter’ program. Only sequences
 containing both primers (with a maximum of 2 mismatches per primer) and
 exact tag sequences were selected. (iii) Strictly identical sequences were
 merged together while keeping information about the origin of
 sequences.Diet_GNP16_trnL_raw_data.fasta.gzFiltered diet dataThis table contains filtered sequences. Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 150 bp paired-end sequencing on Illumina HiSeq 2500 platform. Data were filtered according to the filtering procedure described in Pansu et al. (2018): ‘Trophic ecology of large herbivores in a reassembling ecosystem’. For each sequence, the number of reads reported per sample correspond to the average among replicates that passed filtering steps.Diet_GNP2016_trnL_filtered_data.txtMetadata fecal samplesThis file contains metadata associated to fecal samples analysed in this study.Metadata_GNP2016.txtGorongosa reference databaseThis fasta file contains the Gorongosa National Park DNA plant DNA (P6 loop of the trnL intron) reference database built for this studyGNP_gh_reference_database.fasta