Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels DOI Creative Commons
Gurutzeta Guillera‐Arroita, José J. Lahoz‐Monfort, Anthony van Rooyen

et al.

Methods in Ecology and Evolution, Journal Year: 2017, Volume and Issue: 8(9), P. 1081 - 1091

Published: Jan. 28, 2017

Summary Accurate knowledge of species occurrence is fundamental to a wide variety ecological, evolutionary and conservation applications. Assessing the presence or absence at sites often complicated by imperfect detection, with different mechanisms potentially contributing false‐negative and/or false‐positive errors sampling stages. Ambiguities in data mean that estimation relevant parameters might be confounded unless additional information available resolve those uncertainties. Here, we consider analysis detection multiple levels. We develop examine two‐stage occupancy‐detection model for this purpose. use profile likelihoods identifiability estimation, study types required reliable estimation. test simulated data, then analyse from environmental DNA ( eDNA ) surveys four Australian frog species. In our case study, false positives may arise due contamination water sample quantitative PCR ‐sample levels, whereas negatives not being captured field sample, sensitivity laboratory tests. augment survey aural calibration experiments. demonstrate identifiable if only prone are available. At least two sources extra (e.g. records method unambiguous detections, experiment). Alternatively, can achieved setting plausible bounds on rates as prior Bayesian setting. The results matched simulations respect requirements, revealed greater than zero all provide statistical modelling tools account uncertainties when could occur Such needed support management policy decisions. Dealing these traditional methods, but also promising new techniques, such sampling.

Language: Английский

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects DOI
Kingsly C. Beng, Richard T. Corlett

Biodiversity and Conservation, Journal Year: 2020, Volume and Issue: 29(7), P. 2089 - 2121

Published: April 8, 2020

Language: Английский

Citations

506
Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA DOI Creative Commons

Jesse A. Port,

James L. O’Donnell,

Ofelia C. Romero‐Maraccini

et al.

Molecular Ecology, Journal Year: 2015, Volume and Issue: 25(2), P. 527 - 541

Published: Nov. 19, 2015

Abstract Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic temporal scales. However, traditional methods to survey mobile in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA ( eDNA ) offers new means assess much larger scales, but adoption this approach for surveying whole animal communities large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates detection relevant spatial resolution surveys. Here, we report the results 2.5 km transect vertebrate fauna present along gradation diverse habitats associated with kelp forest ecosystem. Using PCR primers that target mitochondrial 12S rRNA gene fishes mammals, generated sequence compared it simultaneous visual dive We find concordance between individual trends, able distinguish community assemblages from separated as little ~60 m. reliably detected vertebrates low false‐negative (1/12 taxa) when surveys, revealed cryptic species known occupy overlooked methods. This study also presents an explicit accounting false negatives positives metabarcoding data, which illustrate influence marker selection, replication, contamination, biases impacting count ecology open

Language: Английский

Citations

406
Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities DOI Creative Commons
Gurutzeta Guillera‐Arroita

Ecography, Journal Year: 2016, Volume and Issue: 40(2), P. 281 - 295

Published: June 20, 2016

Building useful models of species distributions requires attention to several important issues, one being imperfect detection species. Data sets detections are likely suffer from false absence records. Depending on the type survey, positive records can also be a problem. Disregarding these observation errors may lead biases in model estimation as well overconfidence about precision. The severity problem depends intensity and how they correlate with environmental characteristics (e.g. where detectability strongly habitat features). A powerful modelling framework that accounts for has developed last 10–15 yr. Fundamental this is data must collected way informative process. For instance, such form multiple detection/non‐detection obtained visits/observers/detection methods at (at least) some sites, or times within survey visit. extend studying species’ range dynamics communities, approaches analysing abundance occupancy states (rather than binary presence/absence). This paper summarizes advances, discusses evidence effects difficulties working it, concludes current outlook future research application methods.

Language: Английский

Citations

361
Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales DOI Creative Commons
Michael D. Tillotson, Ryan P. Kelly, Jeffrey J. Duda

et al.

Biological Conservation, Journal Year: 2018, Volume and Issue: 220, P. 1 - 11

Published: Feb. 7, 2018

Language: Английский

Citations

256
Ancient plant DNA in lake sediments DOI Open Access
Laura Parducci, K. D. Bennett, Gentile Francesco Ficetola

et al.

New Phytologist, Journal Year: 2017, Volume and Issue: 214(3), P. 924 - 942

Published: April 3, 2017

Contents 924 I. 925 II. III. 927 IV. 929 V. 930 VI. VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 References SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient DNA, aDNA), and thus enable molecular reconstruction palaeofloras. Hitherto, ancient frozen soils have proved excellent preserving molecules, been most commonly used source aDNA. However, soil mainly represents taxa growing a few metres sampling point. Lakes larger catchment areas recent studies suggested that aDNA lake sediments is more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally nearly all environments, are therefore not limited to perennially areas. Here, we review latest approaches methods study discuss progress made up present. We argue add new additional perspectives populations and, time, will provide higher taxonomic resolution precise estimation abundance. Despite this, key questions challenges remain such studies. Finally, guidelines on technical issues, including selection, suggest directions future research sediments.

Language: Английский

Citations

250
Environmental DNA reveals seasonal shifts and potential interactions in a marine community DOI Creative Commons
Anni Djurhuus, Collin J. Closek, Ryan P. Kelly

et al.

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Jan. 14, 2020

Abstract Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains life, providing critical information about complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing eDNA survey biodiversity from an eighteen-month (2015–2016) time-series seawater samples Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher rank) ranging microorganisms mammals. We inferred changes in composition communities, revealing putative among taxa identifying correlations between these communities environmental properties over time. Community network provided evidence expected predator-prey relationships, linkages, seasonal shifts all life. conclude that eDNA-based analyses can provide detailed marine dynamics identify sensitive biological indicators suggest inform conservation strategies.

Language: Английский

Citations

238
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance DOI Creative Commons
Alexander M. Piper, Jana Batovska, Noel O. I. Cogan

et al.

GigaScience, Journal Year: 2019, Volume and Issue: 8(8)

Published: July 30, 2019

Abstract Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well track the population levels established or endemic pests. Where these traps have low specificity and capture non-target species in excess target pests, need extensive specimen sorting identification creates a major diagnostic bottleneck. While recent development standardized molecular diagnostics has partly alleviated this requirement, single per reaction nature methods does not readily scale sheer number insects trapped programmes. Consequently, lists often restricted few high-priority allowing unanticipated avoid detection potentially establish populations. DNA metabarcoding recently emerged method conducting simultaneous, multi-species complex mixed communities may lend itself ideally rapid bulk trap samples. Moreover, high-throughput sequencing platforms could enable multiplexing hundreds diverse samples on flow cell, thereby providing means dramatically up terms both quantity that can be processed concurrently pest targeted. In review literature, we explore how tailored context highlight unique technical regulatory challenges must considered when implementing technologies into sensitive applications.

Language: Английский

Citations

220
Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding DOI Creative Commons

Elizabeth A. Andruszkiewicz,

Hilary Starks, Francisco P. Chávez

et al.

PLoS ONE, Journal Year: 2017, Volume and Issue: 12(4), P. e0176343 - e0176343

Published: April 25, 2017

Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies marine waters. Further, there is understanding the spatial distribution Here, we use an metabarcoding approach target and amplify a hypervariable region mitochondrial 12S rRNA gene characterize communities at 10 oceanographic stations spanning 45 km within Monterey Bay National Marine Sanctuary (MBNMS). In this study, collected three biological replicates small volume water samples (1 L) 2 depths each stations. We amplified fish using universal primer set. obtained 5,644,299 high quality Illumina sequence reads from samples. The were annotated lowest taxonomic assignment bioinformatics pipeline. survey identified, rank, 7 families, 3 subfamilies, genera, 72 species vertebrates study sites. These 92 distinct taxa come 33 unique families. observed significantly different community composition between sampling (0 m 20/40 deep) across all located on continental shelf (<200 bottom depth) versus deeper waters canyons (>200 depth). All 1 family identified known occur MBNMS. informs implementation for biomonitoring.

Language: Английский

Citations

218
Minimizing polymerase biases in metabarcoding DOI Creative Commons
Ruth V. Nichols, Christopher Vollmers,

Lee A. Newsom

et al.

Molecular Ecology Resources, Journal Year: 2018, Volume and Issue: 18(5), P. 927 - 939

Published: May 24, 2018

DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal flanking conserved regions. Results of these experiments are reported as occurrence data, which provide list taxa amplified sample, relative abundance measure contribution each taxon overall composition product. The accuracy both estimates can be affected by variety biological technical biases. For example, with larger biomass may better represented samples than those smaller biomass. Here, we explore how choice, potential source bias, might influence results experiments. We compared biases six commercially available polymerases combination mixtures amplifiable synthetic sequences real sedimentary extracts. find choice affect main this bias appears preference for specific GC contents. further recommend experimental approach based on our

Language: Английский

Citations

217
How to limit false positives in environmental DNA and metabarcoding? DOI Open Access
Gentile Francesco Ficetola, Pierre Taberlet, Éric Coissac

et al.

Molecular Ecology Resources, Journal Year: 2016, Volume and Issue: 16(3), P. 604 - 607

Published: April 7, 2016

Environmental DNA ( eDNA ) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most sampling approaches, is not perfect. It can fail detect that actually present, even false positives possible: may be apparently detected areas where it absent. Controlling remains main challenge for analyses: this issue Molecular Ecology Resources, Lahoz‐Monfort et al . test the performance multiple statistical modelling approaches estimate rate detection from data. Here, we discuss importance controlling early steps analyses (laboratory, bioinformatics), improve quality results allow an efficient use site occupancy‐detection SODM framework limiting presences analysis.

Language: Английский

Citations

205