COS 305-1 - Estimating invasive species abundance using advanced survey methods: a comparison of AUV imaging and eDNA assessments

Abstract: Accurate estimates of invasive species abundance are critical for evaluating their status, predicting their impacts, and developing management plans to combat their spread. However, assessing the abundance of aquatic species in large lakes remains challenging using conventional sampling gears such as trawls, traps, and nets. This may be particularly true for the round goby (Neogobius melanostomus), a Great Lakes invader with a preference for complex benthic habitats. Environmental DNA (eDNA) sampling offers an alternative approach to estimate species abundance using either the quantity of DNA or the amount of intraspecific genetic variation measured in an environmental sample, but the accuracy of these different abundance estimation frameworks has not yet been compared in natural environments. We test multiple eDNA approaches to determine if DNA marker type, sample volume, and quantification approach (DNA concentration or genetic diversity) influence the relationship between round goby abundance estimates derived from eDNA and visual observation from autonomous underwater vehicle (AUV) images from sites in the Great Lakes.

We found that DNA concentration assessed with qPCR of a mitochondrial marker from small-volume (0.5 L) eDNA samples is significantly associated with AUV-based abundance estimates, while the same approach using large-volume (100 L) samples shows no association with AUV images. Low levels of genetic diversity in the targeted gene regions prevented a robust assessment of genetic diversity-based abundance estimates from eDNA samples. We discuss critical considerations for using intraspecific genetic variation to estimate species-specific abundance, including potential limitations arising from different genetic markers, sampling protocols, and methodological approaches. This study provides support for the use of eDNA approaches to estimate species abundance using species-specific DNA concentrations and highlights the key advances required to harness the full potential of eDNA-based abundance estimates. Such advances to eDNA approaches will improve our ability to efficiently monitor invasive species presence and abundance, an essential step for minimizing their spread and impacts.