Data from: Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

Ungulate browsing can have a strong effect on ecological processes by affecting plant community structure and composition, with cascading effects on nutrient cycling and animal communities. However, in the absence of direct observations of foraging, species-specific foraging behaviors are difficult to quantify. We therefore know relatively little about foraging competition and species specific browsing patterns in systems with several browsers. However, during browsing, a small amount of saliva containing buccal cells is deposited at the bite site, providing a source of environmental DNA (eDNA) that can be used for species identification. Here we describe extraction and PCR protocols for a browser species diagnostic kit. Species specific primers for mitochondrial DNA were optimized and validated using twigs browsed by captive animals. A time series showed that about 50% of the samples will amplify up to 12 weeks after the browsing event, and that some samples amplify up to 24 weeks after browsing (12.5%). Applied to samples of natural browsing from an area where moose (Alces alces), roe deer (Capreolus capreolus), fallow deer (Cervus dama), and red deer (Cervus elaphus) are sympatric, amplification success reached 75%. This method promises to greatly improve our understanding of multispecies browsing systems without the need for direct observations.

有蹄类动物取食可通过改变植物群落结构与组成，对生态过程产生显著影响，并进而对养分循环与动物群落产生级联效应。然而，若缺乏直接的取食观测数据，物种特异性取食行为难以量化，因此我们对多有蹄类共存生态系统中的取食竞争与物种特异性取食模式所知甚少。不过，在取食过程中，少量携带有颊细胞的唾液会沉积在啃食位点，由此可获得可用于物种鉴定的环境DNA（environmental DNA, eDNA）。本研究描述了一套啃食动物物种鉴定诊断试剂盒的提取与聚合酶链式反应（polymerase chain reaction, PCR）实验方案。研究针对线粒体DNA设计了物种特异性引物，并利用圈养动物啃食过的嫩枝对引物进行了优化与验证。时间序列实验结果显示，约50%的样本可在啃食事件发生后12周内完成扩增，部分样本甚至可在啃食后24周仍实现扩增（占比12.5%）。将该方法应用于同域分布驼鹿（Alces alces）、狍（Capreolus capreolus）、黇鹿（Cervus dama）与马鹿（Cervus elaphus）的自然啃食样本后，扩增成功率可达75%。该方法无需开展直接观测，即可大幅提升我们对多物种取食生态系统的认知水平。