Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

Sales, Naiara Guimarães; Wangensteen, Owen S.; Carvalho, Daniel C.; Deiner, Kristy; Præbel, Kim; Coscia, Ilaria; McDevitt, Allan D.; Mariani, Stefano

doi:10.22541/au.158093489.92340788

Cited by 19 publications

(50 citation statements)

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“…Preferentially sampling sites downstream (which may represent 'eDNA reservoirs'; Sales et al, 2021) does not seem to represent an optimal sampling strategy for species which are not fully aquatic based on the results presented here.…”

Section: Discussionmentioning

confidence: 85%

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Broadhurst

Gregory

Bleakley

et al. 2021

Preprint

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Aim: Finding more efficient ways to monitor, and estimate the diversity of, mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Yet, most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. In this study, we focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding rivers. Location: Southeastern England Methods: We used eDNA metabarcoding on water samples collected along two rivers and a beaver enclosure over two days, targeting terrestrial and semi-aquatic mammals. Mammalian community diversity and composition was assessed based on species richness and β-diversity. Differences between river communities were calculated and partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. Results: eDNA metabarcoding efficiently detected 25 wild mammal species from five orders in two days of sampling, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorph species) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. Main conclusions: eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

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Section: Discussionmentioning

confidence: 85%

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Broadhurst

Gregory

Bleakley

et al. 2021

Preprint

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“…Information from eDNA often needs to be followed up with traditional surveys, but eDNA can help guide these surveys in the right direction (Rose et al 2019;Ji et al 2020;Sales et al 2020).…”

Section: Minimum Sequence Thresholdmentioning

confidence: 99%

“…Traditional surveys are also generally labor intensive and time consuming, and can be inefficient at detecting the true biodiversity present (van der Heyde et al ;Basset et al 2012;Gómez-Zurita et al 2016;Stoeckle et al 2016;Evans et al 2017b;Rodriguez-Estrella et al 2019;Zhang et al 2020b). The advent of rapid and relatively cheap DNA sequencing techniques has significantly enhanced biodiversity research by overcoming some of the challenges of labor-intensive traditional surveys and offering the opportunity to efficiently characterize biodiversity in time and space, using standardized methods (Corlett 2017;Alexander et al 2020;Cowart et al 2020;Ji et al 2020;Leempoel et al 2020;Sales et al 2020;Yang & Zhang 2020). Among these techniques, environmental DNA (eDNA) sampling has attracted worldwide attention, and interest in using this tool for biodiversity assessment has grown rapidly in the past few years (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

“…The utilization of eDNA has the potential to revolutionize conservation science and practice in several ways. First, eDNA techniques are fast, efficient and relatively cheap, thus providing the opportunity to monitor the dynamics of species, populations and communities, and to map their geographic distribution over long time periods and across large spatial scales (Ficetola et al 2019;Itakura et al 2019;Lecaudey et al 2019;Preissler et al 2019;Reinhardt et al 2019;Sutter & Kinziger 2019;Sales et al 2020). Second, eDNA sampling is simple, non-destructive, and non-invasive, causing no significant damage to the target species or its habitats (Antognazza et al 2019b;Mora et al 2019;Leempoel et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

2020

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“…eDNA technology has been shown to be useful in spatial and temporal monitoring in a wide variety of settings, as the methods are relatively inexpensive, reliable and quicker than conventional monitoring (Lecaudey et al 2019;Preissler et al 2019;Reinhardt et al 2019;Sutter and Kinziger 2019;Sales et al 2020). The breakthrough in eDNA barcoding technology is in its ability to monitor the ecosystem without causing unnecessary harm to ecosystem or their organisms by non-invasive sampling strategy (Antognazza et al 2019;Mora et al 2019;Leempoel et al 2020) and to detect elusive, rare, and cryptic species effectively even in low density occurrences (Franklin et al 2019;Shelton et al 2019;Takahara et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

PrasannaKumar

Manikantan

Vijaylaxmi

et al. 2020

Preprint

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Environmental DNA (eDNA) barcoding technology is finding innovative applications in monitoring terrestrial and marine biodiversity. DNA barcode reference libraries containing barcodes for wide range of species is vital for the success of monitoring any environments using eDNA barcodes. Since amphipods are used as bio-indicators for monitoring environmental quality and its health, we used DNA barcodes of amphipods to test the efficacy of present DNA libraries for species identification. We barcoded 22 amphipod species belonging to 17 genera of 13 families. 50% of barcodes produced in the present study was generated for the first time, as the sequences were absent in GenBank and Barcode of Life Databases (BOLD). Tree based identification method used in the present study precisely clustered the generated sequences with reference sequences. Besides exploring the distribution of recorded amphipod species, we show that with advent of next generation sequencing technologies, reference datasets such as ours will become essential for assessing health and monitoring various environments using amphipod barcodes.

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Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

Cited by 19 publications

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Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

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