Abstract
AbstractThrough the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish‐U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish‐U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish‐U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish‐U in tropical and temperate freshwater environments, but that generally both teleo and MiFish‐U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.
Highlights
Biomonitoring tools are becoming increasingly necessary for monitoring the dynamics of biodiversity, especially in the light of global changes, which are causing a rapid species population decline (Kindsvater et al, 2014)
We propose a multicriteria comparative framework for assessing the performance of environmental DNA (eDNA) primer pairs, regarding (a) their capacity to bind and amplify a broad coverage of species using in silico polymerase chain reaction (PCR), (b) their capacity to discriminate among species, genera, and families, (c) their specificity and efficacy in situ across freshwater and marine environments as well as temperate and tropical environments
We evaluated the ability of a neural network to assign sequences amplified by the teleo and MiFish-U primer pairs to genus and family levels based on patterns within the sequences
Summary
Biomonitoring tools are becoming increasingly necessary for monitoring the dynamics of biodiversity, especially in the light of global changes, which are causing a rapid species population decline (Kindsvater et al, 2014). We propose a multicriteria comparative framework for assessing the performance of eDNA primer pairs, regarding (a) their capacity to bind and amplify a broad coverage of species using in silico PCR, (b) their capacity to discriminate among species, genera, and families, (c) their specificity and efficacy in situ across freshwater and marine environments as well as temperate and tropical environments We applied this framework to two widely used primer pairs of the 12S mtDNA marker designed to amplify fishes: teleo (Valentini et al, 2016) and MiFish-U (Miya et al, 2015). 4. We evaluated the performance of teleo and MiFish-U primer pairs to amplify DNA from fishes and recover species on eDNA samples in situ and whether this performance could vary across different ecosystems, from temperate to tropical and from marine to freshwater. We expect a higher performance of the teleo amplifying smaller fragments because DNA might be more degraded in tropical and marine environments
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