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.

厘清大型草食动物与热带雨林极为丰富的植物多样性之间的营养关系是一项重大科研难题，原因在于这类动物行踪诡秘难寻。明确此类草食动物在热带雨林生态系统运转中所扮演的角色，对此类研究而言至关重要。我们采用了一种基于环境样本高通量测序的无创研究方案：通过靶向扩增小型植物质体序列（trnL P6环，trnL P6 loop）与核糖体ITS1引物，即DNA宏条形码（DNA metabarcoding）技术，来探究新热带区体型最大的草食动物——低地貘的食性。实验样本采集自法属圭亚那保护区内的努拉格站（Nouragues station），我们从所收集的貘粪便中提取植物DNA并完成测序。尽管本次研究的采样规模有限，但该方法仍可靠地获取了该站点低地貘的食性信息：通过trnL P6环鉴定出的植物科与属中，分别有95.1%与74.4%的类群与已知貘会取食的物种相匹配。借助该方法，我们还发现低地貘还会取食2个此前未被记录的植物科以及8个新的植物属。该方法的分类学分辨率仅能达到植物科与属级别；针对部分分类疑难类群，可辅以ITS1基因的小段序列作为补充条形码，从而将物种鉴定精度有效提升至种级别。我们将在后续讨论该方法尚存的局限性，以及在当前阶段，该方法对于解析行踪诡秘的热带雨林草食动物食性、进一步明确其作为生态系统工程师所发挥的作用具有多大的实用价值。