Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

McElroy, Mary E.; Dressler, T.; Titcomb, Georgia; Wilson, Emily A.; Deiner, Kristy; Dudley, Tom L.; Eliason, Erika J.; Evans, Nathan T.; Gaines, Steven D.; Lafferty, Kevin D.; Lamberti, Gary A.; Li, Yiyuan; Lodge, David M.; Love, Milton S.; Mahon, Andrew R.; Pfrender, Michael E.; Renshaw, Mark A.; Selkoe, Kimberly A.; Jerde, Christopher L.

doi:10.3389/fevo.2020.00276

Cited by 96 publications

(103 citation statements)

References 88 publications

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“…These sources of eDNA are easily caught on a filter or pelleted from a water sample, from which DNA can be extracted and analyzed. Thus, from a water sample, it is possible to detect specific species or even whole communities (Deiner et al, 2017;Bylemans et al, 2019;McElroy et al, 2020). Quantitative real-time PCR (qPCR) or digital droplet PCR (ddPCR) are commonly used for species-specific detection (Rusch et al, 2018;Capo et al, 2019;Mauvisseau et al, 2019a;, and for relative or absolute quantification of target DNA, respectively (Demeke and Dobnik, 2018;Quan et al, 2018), while high-throughput sequencing and metagenomics is used to study whole communities (Thomsen et al, 2012;Hänfling et al, 2016;McElroy et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, from a water sample, it is possible to detect specific species or even whole communities (Deiner et al, 2017;Bylemans et al, 2019;McElroy et al, 2020). Quantitative real-time PCR (qPCR) or digital droplet PCR (ddPCR) are commonly used for species-specific detection (Rusch et al, 2018;Capo et al, 2019;Mauvisseau et al, 2019a;, and for relative or absolute quantification of target DNA, respectively (Demeke and Dobnik, 2018;Quan et al, 2018), while high-throughput sequencing and metagenomics is used to study whole communities (Thomsen et al, 2012;Hänfling et al, 2016;McElroy et al, 2020). While qPCR is currently the most common platform to analyze eDNA samples using species-specific assays, recent studies suggest that the detection rate of eDNA in environmental samples is higher when using ddPCR compared to qPCR technology (Doi et al, 2015a;Mauvisseau et al, 2019a;Wood et al, 2019;Brys et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Johnsen

Strand

Rusch

et al. 2020

Front. Environ. Sci.

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Noble crayfish is the most widespread native freshwater crayfish species in Europe. It is threatened in its entire distribution range and listed on the International Union for Concervation Nature- and national red lists. Reliable monitoring data is a prerequisite for implementing conservation measures, and population trends are traditionally obtained from catch per unit effort (CPUE) data. Recently developed environmental DNA (eDNA) tools can potentially improve the effort. In the past decade, eDNA monitoring has emerged as a promising tool for species surveillance, and some studies have established that eDNA methods yield adequate presence-absence data for crayfish. There are also high expectations that eDNA concentrations in the water can predict biomass or relative density. However, eDNA studies for crayfish have not yet been able to establish a convincing relationship between eDNA concentrations and crayfish density. This study compared eDNA and CPUE data obtained the same day and with high sampling effort, and evaluated whether eDNA concentrations can predict relative density of crayfish. We also compared two analytical methods [Quantitative real-time PCR (qPCR) and digital droplet PCR (ddPCR)], and estimated the detection probability for eDNA monitoring compared to trapping using occupancy modeling. In all lakes investigated, we detected eDNA from noble crayfish, even in lakes with very low densities. The eDNA method is reliable for presence-absence monitoring of noble crayfish, and the probability of detecting noble crayfish from eDNA samples increased with increasing relative crayfish densities. However, the crayfish eDNA concentrations were consistently low and mostly below the limit of quantification, even in lakes with very high crayfish densities. The hypothesis that eDNA concentrations can predict relative crayfish density was consequently not supported. Our study underlines the importance of intensified sampling effort for successful detection of very low-density populations, and for substantiating presumed absence, inferred from negative results. Surprisingly, we found a higher likelihood of eDNA detection using qPCR compared to ddPCR. We conclude that eDNA monitoring cannot substitute CPUE data, but is a reliable supplement for rapid presence-absence overviews. Combined with eDNA analyses of alien crayfish species and diseases such as crayfish plague, this is a cost-efficient supplement offering a more holistic monitoring approach for aquatic environments and native crayfish conservation.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Johnsen

Strand

Rusch

et al. 2020

Front. Environ. Sci.

View full text Add to dashboard Cite

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“…Since the inception of eDNA-based biodiversity assessment, there has been an emphasis on comparing detection performance with well-established biomonitoring approaches that use capture, visual or acoustic identification (Jerde et al 2011; Foote et al 2012; Thomsen et al 2012; Yamamoto et al 2016). The popularity of eDNA-based analysis today owes much to the realisation that, in many important contexts, the new tool offered significant advantages over conventional sampling methods, either through sheer improvement of detection efficacy (Boussarie et al 2018; McElroy et al 2020), through the discovery of its unique complementarity (Aglieri et al 2020; Harper et al 2020), or by simply being less resource-intensive (Bálint et al 2018; Aglieri et al 2020). On the other hand, little effort has gone into evaluating the intrinsically serendipitous nature of high-throughput sequencing, which, irrespective of the metabarcoding markers chosen, consistently yields substantial amounts of non-target sequences.…”

Section: Discussionmentioning

confidence: 99%

“…Fundamental to the success of multi-species eDNA investigations is the choice of the genetic marker, which should be ‘universal’ across the whole taxonomic group of interest, and ‘specific’ enough to minimise the amplification of DNA from non-target taxa (Collins et al 2019; Leese et al 2020). As the most abundant and speciose vertebrate class on Earth, bony fishes (Osteichthyes) have played a major role in the development and consolidation of eDNA applications in marine and freshwater systems (McElroy et al 2020), and there are now a widely recognised set of procedures that have proven successful globally (Miya et al 2020). Interestingly, even the most efficient ‘fish’ primers tend to also amplify some DNA from other vertebrates, and whilst such components typically amount to rather pervasive biological material shed by humans and farmed animals (e.g.…”

Section: Introductionmentioning

confidence: 99%

Estuarine molecular bycatch as a landscape-wide biomonitoring tool

Mariani

Harper

Collins

et al. 2021

Preprint

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Environmental DNA analysis is rapidly transforming biodiversity monitoring and bolstering conservation applications worldwide. This approach has been assisted by the development of metabarcoding PCR primers that are suited for detection of a wide range of taxa. However, little effort has gone into exploring the value of the non-target DNA sequences that are generated in every survey, but subsequently discarded. Here we demonstrate that fish-targeted markers widely employed in aquatic biomonitoring can also detect birds and mammals present in the surrounding habitats. We showcase this feature in three temperate estuaries over multiple seasons, where dozens of bird and mammal species offer valuable insights into spatial and temporal faunal variation. Our results indicate that existing metabarcode sequence data sets are suitable for mining and exploration of this ‘molecular by-catch’, and that any future eDNA-based surveys can be designed to accommodate this enhanced property of this widely applicable tool.

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“…Advances in next-generation sequencing (NGS) have unlocked the potential use of eDNA metabarcoding for monitoring whole communities within specific taxonomic groups (e.g., fishes; Miya, Gotoh & Sado, 2020). Recent studies display its efficiency in different aquatic environments and show how it compares favourably to, or even outperforms, traditional sampling methods in terms of species detections (McDevitt et al, 2019;McElroy et al, 2020) and facilitates investigations into patterns of extirpation, invasive species detection, and dynamics of species richness (Lacoursière-Roussel et al, 2018;Sales et al, 2021). Despite the increase of eDNA surveys in megadiverse systems, several limiting factors prevent its full application (Cilleros et al, 2019;Doble el al., 2020;Sales et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

Jackman

Benvenuto

Coscia

et al. 2021

Preprint

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The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

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Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

Cited by 96 publications

References 88 publications

Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Estuarine molecular bycatch as a landscape-wide biomonitoring tool

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

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