Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared BLAST with the new program PROTAX, and we found that PROTAX improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera-trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by eight years of transect counts and camera-trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys, and has the potential to detect a broader range of species than more commonly used methods.

利用从尸食性蝇类（carrion flies）中提取的脊椎动物DNA开展的宏条形码（metabarcoding）分析，已被提议作为极具潜力的生物多样性监测手段。为评估其应用效能，我们在巴拿马巴罗科罗拉多岛（Barro Colorado Island, BCI）——该区域拥有研究较为充分的哺乳类动物群落——开展了尸食性蝇类的宏条形码调查，并将调查结果与日间样带计数及红外相机陷阱监测结果进行对比。我们在29个采样日内共收集到1084只蝇类，使用哺乳类特异性引物（16S）与脊椎动物特异性引物（12S）开展宏条形码实验，并依托Illumina MiSeq测序平台对扩增子进行测序。在分类学鉴定环节，我们将BLAST工具与新型程序PROTAX进行对比，结果显示PROTAX可提升物种鉴定的准确性。通过尸食性蝇类宏条形码分析，我们共检测到20种哺乳类、4种鸟类及1种蜥蜴类物种，其中除1种外其余均为巴罗科罗拉多岛的已知物种。尸食性蝇类宏条形码检测到的哺乳类物种数量，多于同期开展的日间样带计数（29个采样日，检出13种哺乳类）与红外相机陷阱监测（84个采样日，检出17种哺乳类）；同时，本方法检出的哺乳类物种数达到八年联合样带计数与相机监测记录物种总数的67%，不过该方法也遗漏了部分数量丰富的物种。本研究证实，尸食性蝇类宏条形码技术是开展哺乳类生物多样性调查的高效工具，其具备检出较常规监测方法更多物种类群的潜力。