Diet DNA reveals novel African Forest elephant ecology on the grasslands of the Congo Basin

Abstract

Elephants are essential ecological engineers, creating and maintaining landscape structure and ecosystem function. The recently distinguished and critically endangered forest elephant is currently classified as a selective, non‐destructive frugivorous browser that maintains forest diversity, while the savanna elephant is a mixed feeder, often pushing over trees while maintaining grasslands. The presence and diets of forest elephants on grasslands and the potential maintenance of these systems remain largely unexplored. In the ecotone between the Guinea‐Congolian forest and Sudanian‐Guinean savanna ecosystems in Garamba National Park, DRC, we investigated forest elephant diet selection as a function of sex, age, and habitat using diet DNA (dDNA) metabarcoding of non‐invasively collected dung. GPS collar data were used to determine annual habitat use. Dietary niche partitioning was assessed among megaherbivores in the grasslands. Fecal samples represented the diet of individuals within each habitat, providing valuable insight into the plant biodiversity. Ecological patterns of diet were also revealed using a taxonomically free exact sequence variance approach, highlighting useability in a poorly characterized region. In the early wet season, these typically frugivorous forest elephants were consuming mostly grasses in both the woodland and grassland habitats and showing no sexual dimorphism in diet selection when in the same habitats. However, males were greater risk‐takers, entering the human‐altered landscape to forage on fruit. The forest elephants play a distinctive role within this tropical grassland when compared to other megaherbivores and utilize the unique ecosystem throughout the year. This elephant population is exhibiting behavioral plasticity and shifting their gardening efforts to a novel resource in the grasslands as opposed to their standard role in the forests, which is key to understanding their impact as ecosystem drivers within this landscape. This shift in behavior may result in this recovering elephant population playing a functional role in the restoration and maintenance of these grasslands.

Browsers or Grazers? New Insights into Feral Burro Diet Using a Non-Invasive Sampling and Plant DNA Metabarcoding Approach

“…We standardized the relative abundance of each sample so the sum of all reads of the top 170 and 220 ESVs (at Lake Pleasant and Sinbad HMAs, respectively) totaled 100%. To describe the taxonomic composition of the diet, we matched ESVs to the representative taxa, using a match criteria threshold of >90% similarity to the reference sequences [ 54 , 55 ]. If the representative species assigned to each ESV did not exist in our study areas, we assigned another species of the same genus to the ESV based on the list of plant species in each area (Lake Pleasant [ 56 ]; Sinbad [ 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 ]).…”

“…To describe the taxonomic composition of the diet, we matched ESVs to the representative taxa, using a match criteria threshold of >90% similarity to the reference sequences [ 54 , 55 ]. If the representative species assigned to each ESV did not exist in our study areas, we assigned another species of the same genus to the ESV based on the list of plant species in each area (Lake Pleasant [ 56 ]; Sinbad [ 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 ]). Exact sequence variants that were identified at only the family level or their identified genera were not present in the study area and were only included in family-level analyses.…”

“…Exact sequence variants that were identified at only the family level or their identified genera were not present in the study area and were only included in family-level analyses. If the representative family did not exist in the study area or the ESV was not identified at the family level, we removed it from analysis and standardized the relative abundances of remaining ESVs so the sum of all reads totaled 100% [ 48 , 55 ]. ESVs that matched similar genera were combined and labeled as operational taxonomic units (OTUs).…”

“…ESVs that matched similar genera were combined and labeled as operational taxonomic units (OTUs). For example, multiple ESVs that matched “ Poa spp.” were combined into one unique OTU for this genus at each study area [ 22 , 55 ].…”

“…For example, multiple ESVs that matched "Poa spp." were combined into one unique OTU for this genus at each study area [22,55].…”