DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species—even pairs of grazers matched in size, digestive physiology, and location—and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized.

生态位分化（niche partitioning）有助于在资源有限的环境中实现物种共存，进而提升生物多样性。数十年来，生物学家一直致力于解析大型哺乳动物食草动物（large mammalian herbivores, LMH）的多样类群如何划分食物资源。目前已发现多种互补性机制，包括对草本与非草本植物的选择性取食，以及对同一植株不同部位的时空利用分层。然而，由于传统方法难以开展全面的物种级鉴定，大型哺乳动物食草动物在食物植物物种层面的生态位分化程度仍鲜为人知。本研究利用DNA宏条形码技术（DNA metabarcoding），对非洲半干旱稀树草原中的7种优势大型哺乳动物食草动物（6种野生、1种家养）的食谱宽度、组成及重叠度进行了定量分析。这些物种的取食策略跨度极大，从几乎专食草本的类群到几乎专食木本植物的类群均有覆盖：基于平均相对读长丰度（relative read abundance, RRA）推断的青草摄入比例，从平原斑马的>99%到犬羚的<1%不等。青草的RRA值与青草摄入比例的同位素估算结果高度相关，表明RRA能够可靠反映取食量的定量信息。食谱重叠度在体型大小与青草摄入比例相近的物种间最高。尽管如此，所有物种的食谱组成均存在显著差异——即便是体型、消化生理与栖息环境均相似的食草动物类群亦是如此；有时不同取食功能群间的食谱相似性反而高于类群内部。这种分类学分辨率极高的食谱分化现象表明，采用粗略的营养级分类可能会对大型哺乳动物食草动物类群的种间竞争与共存关系得出误导性结论，而大型哺乳动物食草动物的多样性与植物多样性的关联可能比当前认知更为紧密。