Risk Analysis and Bioeconomics of Invasive Species to Inform Policy and Management

Annual Review of Environment and Resources, Journal Year: 2016, Volume and Issue: 41(1), P. 453 - 488

Published: Sept. 12, 2016

Risk analysis of species invasions links biology and economics, is increasingly mandated by international national policies, enables improved management invasive species. Biological proceed through a series transition probabilities (i.e., introduction, establishment, spread, impact), each these presents opportunities for management. Recent research advances have estimates probability associated uncertainty. Improvements come from species-specific trait-based risk assessments (of impact probabilities, especially pathways commerce in living organisms), spatially explicit dispersal models (introduction transportation pathways), distribution (establishment, impact). Results forecasting combined with cheaper surveillance technologies practices [e.g., environmental DNA (eDNA), drones, citizen science] enable more efficient focusing surveillance, prevention, eradication, control efforts on the highest-risk locations. Bioeconomic account interacting dynamics within between ecological economic systems, allow decision makers to better understand financial consequences alternative strategies. In general, recent demonstrate that prevention policy greatest long-term net benefit.

Language: Английский

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Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

PLoS ONE, Journal Year: 2017, Volume and Issue: 12(4), P. e0175186 - e0175186

Published: April 12, 2017

The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental (eDNA) as an indicator fish presence in the lower Hudson River estuary. A checklist local and their relative abundance was prepared compiling 12 traditional surveys conducted between 1988-2015. To improve eDNA identification success, 31 specimens representing 18 species were sequenced two mitochondrial gene regions, boosting coverage 12S target sequence to 80% taxa. We collected 76 one-liter shoreline surface samples at contrasting estuary locations over six months beginning January 2016. amplified with vertebrate-specific primers. Bioinformatic analysis DNA, using a reference library GenBank our newly generated sequences, detected most (81%) locally abundant or common relatively few (23%) uncommon taxa, corresponded seasonal habitat preference determined surveys. Approximately 2% reads commonly consumed that are rare absent waters, consistent wastewater input. Freshwater rarely despite inflow. These results support further exploration suggest will facilitate fine-scale geographic temporal mapping low cost.

Language: Английский

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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Quaternary, Journal Year: 2021, Volume and Issue: 4(1), P. 6 - 6

Published: Feb. 13, 2021

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field paleoecological research. Although largely applied nowadays, knowledge gaps remain this there therefore still research be conducted ensure reliability signal. Building on most recent literature seven original case studies, we synthesize state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation inventories from ancient (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based current best practises.

Language: Английский

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Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation

PLoS ONE, Journal Year: 2018, Volume and Issue: 13(4), P. e0195403 - e0195403

Published: April 17, 2018

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree which taxa growing in vegetation are represented environmental DNA (eDNA) records. We analysed composition catchment vascular plant eDNA at 11 lakes northern Norway. Out 489 records within 2 m from shore, 17–49% (mean 31%) identifiable recorded were detected with eDNA. Of 217 47 lakes, 73% 12% matched surveys up 50 away lakeshore, respectively, whereas 16% not same lake. The latter include likely overlooked or outside survey area. percentages 61, 47, 25, 15 for dominant, common, scattered, rare taxa, respectively. Similar numbers aquatic plants 88, 33 62%, Detection rate taxonomic resolution varied among families functional groups good detection e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses aquatics. representation terrestrial depends on both their distance sampling site abundance sufficient recording types. For vegetation, may be comparable with, even superior to, in-lake therefore used as an tool biomonitoring. reconstruction technical improvements more intensive needed detect a higher proportion although some never reach due taphonomical constrains. Nevertheless, performs similar conventional methods pollen macrofossil analyses important vegetation.

Language: Английский

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Can we manage fisheries with the inherent uncertainty from eDNA?

Journal of Fish Biology, Journal Year: 2019, Volume and Issue: 98(2), P. 341 - 353

Published: Nov. 26, 2019

Abstract Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material water and hence infer physical presence. However, fisheries managers face making decisions with risk uncertainty when eDNA indicates fish is present but traditional methods fail capture fish. In comparison such nets, electrofishing piscicides, approaches have more sources underlying error that could give rise false positives. This has resulted some question whether can be used make management because there no hand. As relatively new approach, techniques quickly evolved improve confidence eDNA. By evaluating an based research programmes through pattern signal, assay design, experimental quality assurance control checks, data analyses concurrent search for using gears, evidence evaluated build approach. The benefits from adopting are numerous include cost effectiveness, broader geographic coverage habitat occupancy, early detection invasive species, non‐lethal stock assessments, exploration previously inaccessible environments discovery species hidden beneath water's surface. At time global freshwater marine facing growing threats over‐harvest, pollution climate change, we anticipate will overcome inherent not having hand empower informed actions necessary protect restore our fisheries.

Language: Английский

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Improving the reliability of eDNA data interpretation

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(5), P. 1422 - 1433

Published: March 3, 2021

Abstract Global declines in biodiversity highlight the need to effectively monitor density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target‐species into their environment (eDNA) have been rapidly on rise. Despite providing new, cost‐effective tools for conservation, eDNA‐based are prone errors. Best field laboratory practices can mitigate some, but risks errors cannot be eliminated accounted for. Here, we synthesize advances data processing that increase reliability interpretations drawn from eDNA data. We review occupancy models consider spatial data‐structures simultaneously assess rates false positive negative results. Further, introduce process‐based integration metabarcoding as complementing approaches assessments. These will most effective when capitalizing multi‐source sets collating with classical citizen‐science approaches, paving way more robust decision‐making processes conservation planning.

Language: Английский

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Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(20), P. 5132 - 5164

Published: Aug. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Language: Английский

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Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: Increasing efficacy of sampling designs

The Science of The Total Environment, Journal Year: 2018, Volume and Issue: 633, P. 695 - 703

Published: March 28, 2018

Language: Английский

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Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

PeerJ, Journal Year: 2017, Volume and Issue: 5, P. e3006 - e3006

Published: March 22, 2017

DNA metabarcoding, the PCR-based profiling of natural communities, is becoming method choice for biodiversity monitoring because it circumvents some limitations inherent to traditional ecological surveys. However, potential sources bias that can affect reproducibility this remain be quantified. The interpretation differences in patterns sequence abundance and relevance rare sequences particularly uncertain. Here we used one artificial mock community explore significance disentangle effects two biases on data reproducibility: indexed PCR primers random sampling during Illumina MiSeq sequencing. We amplified a short fragment mitochondrial Cytochrome c Oxidase Subunit I (COI) single sample containing equimolar amounts total genomic from 34 marine invertebrates belonging six phyla. seven broad-range sequenced resulting library consecutive runs. number Operational Taxonomic Units (OTUs) was ∼4 times higher than expected based composition sample. Moreover, reads components differed by up three orders magnitude. 79 out 86 unexpected OTUs were represented <10 did not appear consistently across replicates. Our suggest (e.g., small associated fauna such as parasites) accounted most variation OTU presence–absence, whereas with PCRs larger amount relative patterns. These results sequencing leads low OTUs. strategy handling should depend objectives study. Systematic removal may avoid inflating diversity common β descriptors but will exclude positive records taxa are functionally important. further reinforce need technical replicates (parallel same sample) metabarcoding experimental designs. Data determined empirically upon depth, type sample, analysis pipeline, estimating biomasses or abundances read counts remains elusive at level.

Language: Английский

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Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

PLoS ONE, Journal Year: 2016, Volume and Issue: 11(3), P. e0148698 - e0148698

Published: March 7, 2016

Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression ecological community assemblage. However, the number of reads produced per run far exceeds required sample for many applications, compelling researchers sequence multiple samples in order maximize efficiency. For studies that include a PCR step, this can be accomplished using primers index allowing origin determined after sequencing. The use indexed assumes they behave no differently than standard primers; however, we found cause substantial template sequence-specific bias, resulting radically different profiles same environmental sample. Likely outcome differential amplification efficiency due primer-template mismatch, two primer sets spuriously change inferred abundance DNA extraction by up 77.1%. We demonstrate double approach alleviates these effects applications where are necessary.

Language: Английский

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