Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, non-invasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom designed group-specific primer set and next-generation sequencing for the detection of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada; the Grand River and the Sydenham River. Out of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns.

从水生环境样本中提取并鉴定DNA，为珍稀物种检测提供了一种非侵入式的替代方案。环境DNA（environmental DNA, eDNA）结合聚合酶链式反应（Polymerase Chain Reaction, PCR）与高通量测序（Next-Generation Sequencing, NGS，即元条形码技术metabarcoding），已被证实对珍稀水生物种的检测具有极高灵敏度。本研究采用定制的类群特异性引物组结合高通量测序技术，对三种受威胁物种（东方沙镖鲈 *Ammocrypta pellucida*、北方钝头鮠 *Noturus stigmosus* 以及闪光银𫚭 *Notropis photogenis*）、一种入侵物种（圆头鰕虎鱼 *Neogobius melanostomus*），以及加拿大安大略省南部两大五大湖支流——格兰德河与赛德姆河——内的另外78种本土鱼类进行了检测。在通过捕捞法与环境DNA法在两条河流中检出的82种鱼类中，本研究的环境DNA法分别在格兰德河与赛德姆河中检出了86.2%与72.0%的鱼类物种，其中包含本研究的四种目标物种。本研究的分析还揭示了目标物种与其他已检出物种之间存在显著的正、负物种共现模式。研究结果表明，相较于仅针对目标物种的检测手段，以鱼类群落及目标物种为靶标的环境DNA元条形码技术，能够更深入地解析生态系统中影响目标物种空间分布的各类因素。此外，环境DNA可便捷地作为初始调查工具，或与捕捞法结合使用，以更精准地绘制物种分布格局。