DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer

Ruofei Li; Dandan Wang; Zhiming Cao; Yuqin Liu; Wenguo Wu; Wuhua Liu; Jianwen Zhan; Yongtao Xu

doi:10.7717/peerj.18665

DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer

PeerJ. 2024 Dec 23:12:e18665. doi: 10.7717/peerj.18665. eCollection 2024.

Authors

Ruofei Li^#¹, Dandan Wang^#¹, Zhiming Cao¹, Yuqin Liu¹, Wenguo Wu², Wuhua Liu², Jianwen Zhan², Yongtao Xu¹

Affiliations

¹ Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
² Taohongling Sika Deer National Nature Reserve Administration, Pengze, Jiangxi, China.

^# Contributed equally.

Abstract

Background: Food provides essential nutrients and energy necessary for animals to sustain life activities. Accordingly, dietary niche analysis facilitates the exploration of foraging strategies and interspecific relationships among wildlife. The vegetation succession has reduced understory forage resources (i.e., shrubs and herbs) available to sika deer (Cervus nippon kopschi). Little is known about the summer foraging strategies or the interspecific relationship between sika deer and Reeves' muntjac (Muntiacus reevesi).

Methods: The present study used high-throughput sequencing and DNA metabarcoding techniques to investigate the feeding habits and interspecific relationships between sika deer and Reeves' muntjac in our study.

Results: A total of 458 amplicon sequence variants (ASVs) were identified from fecal samples, with 88 ASVs (~19.21%) unique to sika deer and 52 ASVs (~11.35%) unique to Reeves' muntjac, suggesting the consumption and utilization of specific food items for the two species. The family Rosaceae was the most abundant for both species, especially Rubus spp. and Smilax china. Alpha diversity (local species richness) indicated that the dietary species richness of sika deer was higher than that of Reeves' muntjac, but the difference was not statistically significant. Sika deer also exhibited a higher evenness index (J' = 0.514) than Reeves' muntjac (J' = 0.442). Linear discriminant effect size analysis revealed significant differences in forage plants between the two herbivores. The niche breadths of sika deer and Reeves' muntjac were 11.36 and 14.06, respectively, and the dietary niche overlap index was 0.44. Our findings indicate the diet partitioning primarily manifested in the differentiation of food items and the proportion, which ultimately reduces the overlap of nutritional niches and helps avoid conflicts resulting from resource utilization. This study provides a deeper insight into the diversity of foraging strategies and the interspecific relationship of herbivores from the food dimension.

Keywords: DNA metabarcoding; Dietary partitioning; Herbivores; Niche overlap; Summer.

MeSH terms

Animals
China
DNA Barcoding, Taxonomic*
Deer* / genetics
Deer* / physiology
Diet* / veterinary
Feces / chemistry
Feeding Behavior / physiology
Herbivory*
High-Throughput Nucleotide Sequencing
Muntjacs / genetics
Rubus / genetics
Seasons*
Sympatry

Associated data

figshare/10.6084/m9.figshare.25026785.v5

Grants and funding

This work was supported by the National Natural Science Foundation of China (Project Nos. 32470552 and 31960118) and the Natural Science Foundation of Jiangxi Province of China (No. 20242BAB25349). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.