Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence‐capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence‐capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence‐capture recovered 80%–90% of the control sample species. DNA sequence‐capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low‐cost, whereas DNA‐sequence capture for biodiversity assessment is still in its infancy, is more time‐consuming but provides more taxonomic assignments.

中文翻译：

---

比较环境样本的多样性水平：使用 18S 和 COI 基因的 DNA 序列捕获和元条形码方法。

使用元条形码针对多个分类群的环境 DNA 研究提供了对任何栖息地物种多样性水平的非凡见解。主要缺点是存在引物偏差和难以识别稀有物种。我们测试了与元条形码方法并行的 DNA 序列捕获方法，以揭示一种方法相对于另一种方法的可能优势。两种方法均使用相同的 eDNA 样本和相同的 18S 和 COI 区域进行，然后进行高通量测序。使用来自 18S 和 COI 基因的一对引物对 Metabarcoded eDNA 文库进行 PCR 扩增。DNA 序列捕获文库富含 3,639 个靶向相同基因区域的诱饵。我们在计算机方法中针对标记和方法测试了扩增子序列变体 (ASV) 和操作分类单元 (OTU)，为此目的使用元条形码数据集。ASVs 方法为 COI 基因发现了更多物种，而 18S 基因则相反，这表明将读数聚类到 OTU 可能会偏向多样性丰富度，尤其是使用具有宽松阈值的 18S。此外，元条形码和 DNA 序列捕获恢复了 80%–90% 的对照样本物种。DNA 序列捕获的成本要高 8 倍，但与元条形码相比，它为 COI 识别的物种多 1.5 倍，为 18S 识别的属多 13 倍。两种方法都提供可靠的结果，共享大约。当核标记和线粒体标记结合时，40% 的物种和 72% 的科检索到更多的分类群。eDNA 元条形码已经非常成熟且成本低廉，而用于生物多样性评估的 DNA 序列捕获仍处于起步阶段，