Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples

By E. E. Sigsgaard, H. Carl, P. Møller, P. F. Thomsen. 2015

375 citations recorded by the source corpus.

Abstract The European weather loach (Misgurnus fossilis) represents one of many European freshwater fishes in decline. Efficient monitoring is essential if conservation efforts are to be successful, but due to the species’ cryptic biology, traditional monitoring methods currently in use are inefficient, time consuming and likely prone to non-detection error. Here, we investigate the usefulness of environmental DNA (eDNA) monitoring as an alternative or supplementary method for surveying the Danish weather loach population, which is presumed to consist primarily of a single group of no more than 50 individuals. In 2008, the majority of historical Danish localities were surveyed, using traditional fishing techniques. We then applied eDNA methods to a number of these, as well as other potential localities. We successfully detected the weather loach at multiple sites in the single known remaining locality; a result that was later confirmed when local managers caught eight live specimens. Furthermore, the eDNA method indicated presence of the weather loach in another historical locality, where the species has not been observed since 1995. At the remaining localities, weather loach eDNA was not detected, providing further evidence for its absence. Importantly, the eDNA survey required less effort in person-hours and lower costs than the traditional fishing survey. This study confirms that eDNA monitoring is a valid supplement to traditional monitoring methods currently applied to monitor rare freshwater fishes. We propose that by providing reliable distribution data at lower cost and limited effort, the eDNA method can allow for increased management efficiency of endangered freshwater species such as the European weather loach.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8fb9b44724e27fd3c2ca57e2ac031cd4a6b166e7

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In Ecology

1. C. Turner
2. M. Miya
3. Toshifumi Minamoto
4. M. Barnes
5. Elise Furlan
6. P. F. Thomsen
7. Caren S. Goldberg
8. T. Sado

In Molecular Biology

1. C. Turner
2. M. Miya
3. Toshifumi Minamoto
4. M. Barnes
5. T. Sado
6. Elise Furlan
7. Caren S. Goldberg
8. P. F. Thomsen

Citations in the corpus

• Environmental DNA detects Critically Endangered largetooth sawfish in the wild (2016, methodology): “Its usefulness has been demonstrated in detecting rare, cryptic and threatened teleost fishes (e.g. Jerde et al. 2011, Janosik & Johnston 2015, Sigsgaard et al. 2015).”
• Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “…quantitative PCR inhibition in environmental DNA samples Wetlands Sample spiked with target amphibian dna Florida; Georgia; S. Carolina, USA Present Sigsgaard et al. (2015) Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples Streams Fish…”
• Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms (2015, background): “Sigsgaard et al. (2015) add the weather loach (Misgurnus fossilis), an endangered freshwater fish, to this list.”
• Assessing the cost‐efficiency of environmental DNA sampling (2016, methodology): “We assumed that eDNA samples were processed by a fully-equipped genetics laboratory; hence we did not include the costs of non-perishables or laboratory equipment (Sigsgaard et al. 2014).”
• The ecology of environmental DNA and implications for conservation genetics (2016, background): “Sigsgaard et al. (2015) reported that eDNA surveys for endangered fish in Denmark outperformed traditional methods.”
• Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, background): “, 1996) with speciesspecific primers and probes (e.g. Thomsen et al., 2012b; Wilcox et al., 2013; Sigsgaard et al., 2015) and 2) multispecies detection by NextGeneration Sequencing (NGS) after PCR amplification of eDNA using universal primers that target short mitochondrial DNA barcoding regions – e”
• Efficacy of Environmental DNA to Detect and Quantify Brook Trout Populations in Headwater Streams of the Adirondack Mountains, New York (2017, background): “, humic and fulvic acids) have in fact been reported to inhibit DNA amplification in environmental samples (Matheson et al. 2010; Sigsgaard et al. 2015).”
• An environmental DNA‐based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica) (2017, background): “The sensitivity of this technology can be used to improve presence/absence data for cryptic species (Dejean et al. 2012; Thomsen et al. 2012b; Sigsgaard et al. 2015) and accurately delineate the distribution of species (Jerde et al. 2011; Laramie, Pilliod & Goldberg 2014; Bylemans et al. 2016a).”
• Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods (2018, background): “…or sloughed skin cells has been 53 detected in various aquatic environments (Kelly et al., 2014a), including ponds (Takahara et 54 al., 2012, 2013; Sigsgaard et al., 2015), rivers (Jerde et al., 2013; Mahon et al., 2013; Wilcox 55 et al., 2013; Yamanaka & Minamoto, 2016), and marine waters…”