DNA metabarcoding of corvid faecal samples

Establishing methods that allow for more focused management of wildlife under predator pressure may increase the efficiency of managing problematic predators. Non-invasive dietary analysis and identification of conservation-sensitive prey in the diet of 'culprit' predator individuals could help to facilitate this and is worthy of exploration. Recently on Phillip Island, Australia, Little Ravens Corvus mellori have emerged as a prominent predator on the clutches of burrow-nesting Little Penguins Eudyptula minor. We tested the feasibility of using non-invasive PCR approaches targeting the penguin mitochondrial 16S rRNA marker gene to establish whether penguin DNA could be detected in raven faecal samples, potentially enabling the identification of culprit ravens missed by extensive field observation. Using a metabarcoding approach, we examined the feasibility of non-invasively establishing other dietary items via high throughput amplicon sequencing. We documented components of raven diet using the universal mitochondrial 16S rRNA, insect-specific 'Chiar' 16S rRNA, and plant ITS2. The assemblage of dietary items did not differ with raven culprit status (i.e. a raven previously observed preying upon penguin), sex, or date. Penguin was detected in the diet of some individuals classified observationally as non-culprits. While some cases may conceivably have been false detections, other explanations include missed depredation events, consumption via scavenging, or consumption through secondary consumption (e.g. eating invertebrates that have consumed penguin). While this study found metabarcoding unreliable for unambiguous assigning of raven culprit status, at least as we implemented it, it may hold promise complementing observations if consumption via scavenging can be distinguished from direct depredation.建立针对捕食压力下野生动物的精细化管理方法，或可提升有害捕食者的管控效率。对"肇事"捕食者个体的膳食开展非侵入式分析，并鉴定其食谱中受保护的敏感猎物，或可助力上述目标的实现，值得深入探索。近期在澳大利亚菲利普岛（Phillip Island），细嘴渡鸦（Little Ravens, Corvus mellori）已成为穴居筑巢的小企鹅（Little Penguins, Eudyptula minor）卵的主要捕食者。本研究针对小企鹅线粒体16S rRNA（mitochondrial 16S rRNA）标记基因，采用非侵入式聚合酶链式反应（PCR, polymerase chain reaction）技术，检测渡鸦粪便样本中是否存在小企鹅DNA，以期识别野外大范围观测中遗漏的肇事渡鸦，验证该方法的可行性。同时，本研究采用元条形码（metabarcoding）技术，通过高通量扩增子测序（high throughput amplicon sequencing）非侵入式鉴定渡鸦的其他膳食组分，验证其可行性。本研究通过通用线粒体16S rRNA、昆虫特异性"Chiar" 16S rRNA及植物ITS2（internal transcribed spacer 2）标记，对渡鸦的膳食组成进行了记录。研究发现，渡鸦的膳食组成与肇事状态（即此前观测到捕食企鹅的渡鸦）、性别及采样日期均无显著差异。部分经野外观测归类为非肇事的渡鸦个体，其食谱中也检测到了小企鹅DNA。尽管部分检测结果可能为假阳性，但也存在其他合理解释：如野外观测遗漏的捕食事件、渡鸦通过食腐获取企鹅组织，或是通过次级捕食（例如捕食了已摄食企鹅的无脊椎动物）间接摄入企鹅DNA。尽管本研究发现，至少就本次研究的实施方式而言，元条形码技术无法精准判定渡鸦的肇事状态，但如果能够区分食腐与直接捕食两种摄入模式，该技术或可作为野外观测的有效补充手段，具备应用潜力。