Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a non-invasive method for analyzing animal diets. Currently, metabarcoding, a PCR-based method, is the method of choice for analyzing such data. However, this method has limitations, specifically PCR bias, which can result in the overestimation of the importance of certain taxa and the failure to detect other taxa because they do not amplify. The present study compared metabarcoding with metagenomics, a marker-free method, to assess the diversity of prey items in the feces of a critically endangered South African estuarine pipefish, Syngnathus watermeyeri, and its widely distributed congener (S. temminckii) to investigate the potential dietary competition. Our results showed a distinct difference between the diets of S. watermeyeri and S. temminckii, with the former mainly consuming calanoid copepods and the latter preferring caridean shrimp. Metagenomics produced more species identifications than metabarcoding; however, most of the species identified are not present in South Africa. The identifications made by both methods mostly belonged to the same families, but some prey items were identified only by either method. Both methods would benefit from a complete reference database of South African estuarine macroinvertebrates.

中文翻译：

---

eDNA 元条形码与宏基因组学：两种河口尖嘴鱼饮食竞争的评估

了解濒危物种的饮食偏好有助于实施保护策略，包括栖息地恢复、迁移和圈养繁殖。来自粪便的环境 DNA (eDNA) 为分析动物饮食提供了一种非侵入性方法。目前，基于 PCR 的元条形码方法是分析此类数据的首选方法。然而，这种方法有局限性，特别是 PCR 偏差，这可能导致高估某些分类群的重要性以及无法检测其他分类群，因为它们不会放大。本研究将元条形码与宏基因组学（一种无标记方法）进行了比较，以评估极度濒危的南非河口尖嘴鱼 Syngnathus watermeyeri 及其广泛分布的同类物（S. watermeyeri）粪便中猎物的多样性。temminckii) 来调查潜在的饮食竞争。我们的结果显示 S. watermeyeri 和 S. temminckii 的饮食之间存在明显差异，前者主要食用 calanoid 桡足类，而后者更喜欢 caridean 虾。宏基因组学比元条形码产生了更多的物种鉴定；然而，大多数已确定的物种并不存在于南非。两种方法进行的鉴定大多属于同一科，但部分猎物只能通过两种方法进行鉴定。这两种方法都将受益于南非河口大型无脊椎动物的完整参考数据库。前者主要吃 calanoid 桡足类动物，而后者则更喜欢 caridean 虾。宏基因组学比元条形码产生了更多的物种鉴定；然而，大多数已确定的物种并不存在于南非。两种方法进行的鉴定大多属于同一科，但部分猎物只能通过两种方法进行鉴定。这两种方法都将受益于南非河口大型无脊椎动物的完整参考数据库。前者主要吃 calanoid 桡足类动物，而后者则更喜欢 caridean 虾。宏基因组学比元条形码产生了更多的物种鉴定；然而，大多数已确定的物种并不存在于南非。两种方法进行的鉴定大多属于同一科，但部分猎物只能通过两种方法进行鉴定。这两种方法都将受益于南非河口大型无脊椎动物的完整参考数据库。