Data from: Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study

Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.

由于大型植食性动物行踪难以捉摸，阐明热带雨林中大型植食动物与丰富植物多样性之间的营养关系乃是一项重大挑战。明晰此类植食动物在热带雨林生态系统运转中所扮演的角色，此项研究至关重要。本研究采用一种非侵入式研究手段，以环境样本高通量测序为基础，借助小型植物质体序列（trnL P6环，trnL P6 loop）与核糖体ITS1引物，该方法即DNA宏条形码（DNA metabarcoding），用于探究新热带界体型最大的植食动物——低地貘（lowland tapir）的食性。研究团队对采集自法属圭亚那保护区诺拉格站的貘粪便中提取的植物DNA完成了测序。尽管采样规模有限，本方法仍可靠地获取了该区域低地貘的食性相关数据。具体而言，通过trnL P6环鉴定得到的植物科与属中，分别有95.1%与74.4%的类群与已知貘类可取食的类群相吻合。借助该方法，本研究证实低地貘还可取食2个植物科与8个此前未被记录的属级类群。该方法的分类学分辨率仅可达到植物科与属水平。针对部分分类学疑难的植物科，可辅以ITS1基因小片段等条形码标记，将物种鉴定精度有效提升至种级水平。本研究将讨论该方法尚存的局限性，并探讨在当前研究阶段，该方法对于阐明行踪诡秘的热带雨林植食动物食性、深入理解其作为生态系统工程师所发挥的核心作用具有何种应用价值。