Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities

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

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The recent past and promising future for data integration methods to estimate species’ distributions

Methods in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(1), P. 22 - 37

Published: Jan. 1, 2019

Abstract With the advance of methods for estimating species distribution models has come an interest in how to best combine datasets improve estimates distributions. This spurred development data integration that simultaneously harness information from multiple while dealing with specific strengths and weaknesses each dataset. We outline general principles have guided review recent developments field. then key areas allow a more framework integrating provide suggestions improving sampling design validation integrated models. Key advances been using point‐process thinking estimators developed different types. Extending this new types will further our inferences, as well relaxing assumptions about parameters are jointly estimated. These along better use regarding effort spatial autocorrelation inferences. Recent form strong foundation implementation Wider adoption can inferences distributions dynamic processes lead distributional shifts.

Language: Английский

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Analytical guidelines to increase the value of community science data: An example using eBird data to estimate species distributions

Diversity and Distributions, Journal Year: 2021, Volume and Issue: 27(7), P. 1265 - 1277

Published: May 7, 2021

Abstract Aim Ecological data collected by the general public are valuable for addressing a wide range of ecological research and conservation planning, there has been rapid increase in scope volume available. However, from eBird or other large‐scale projects with volunteer observers typically present several challenges that can impede robust inferences. These include spatial bias, variation effort species reporting bias. Innovation We use example estimating distributions eBird, community science citizen (CS) project. estimate two widely used metrics distributions: encounter rate occupancy probability. For each metric, we critically assess impact processing steps either degrade refine analyses. CS density varies across globe, so also test whether differences model performance to sample size. Main conclusions Model improved when analytical methods addressed arising data; however, degree improvement varied density. The largest gains observed were achieved 1) complete checklists (where report all they detect identify, allowing non‐detections be inferred) 2) covariates describing detectability checklist. Occupancy models more lack checklists. Improvements refinement evident larger sizes. In general, found value situation encourage researchers benefits scenarios. approaches will enable effectively harness vast knowledge exists within basic research.

Language: Английский

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Detecting the Multiple Facets of Biodiversity

Trends in Ecology & Evolution, Journal Year: 2016, Volume and Issue: 31(7), P. 527 - 538

Published: May 8, 2016

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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Outstanding challenges and future directions for biodiversity monitoring using citizen science data

Methods in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 14(1), P. 103 - 116

Published: Feb. 20, 2022

Abstract There is increasing availability and use of unstructured semi‐structured citizen science data in biodiversity research conservation. This expansion a rich source ‘big data’ has sparked numerous directions, driving the development analytical approaches that account for complex observation processes these datasets. We review outstanding challenges analysis monitoring. For many challenges, potential impact on ecological inference unknown. Further can document explore ways to address it. In addition outlining describing may be useful considering design future projects or additions existing projects. outline monitoring using four partially overlapping categories: arise as result (a) observer behaviour; (b) structures; (c) statistical models; (d) communication. Potential solutions are combinations of: collecting additional metadata; analytically combining different datasets; developing refining models. While there been important progress develop methods tackle most remain substantial gains subsequent conservation actions we believe will possible by further areas. The degree challenge opportunity each presents varies substantially across datasets, taxa questions. some cases, route forward clear, while other cases more scope exploration creativity.

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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Statistical approaches to account for false‐positive errors in environmental DNA samples

Molecular Ecology Resources, Journal Year: 2015, Volume and Issue: 16(3), P. 673 - 685

Published: Nov. 12, 2015

Abstract Environmental DNA ( eDNA ) sampling is prone to both false‐positive and false‐negative errors. We review statistical methods account for such errors in the analysis of data use simulations compare performance different modelling approaches. Our illustrate that even low rates can produce biased estimates occupancy detectability. further show removing or classifying single PCR detections an ad hoc manner under suspicion records represent false positives, as sometimes advocated literature, also results estimation occupancy, detectability rates. advocate alternative approaches rely on prior information, collection ancillary detection at a subset sites using method not advantages these over classifications provide practical advice code fitting models maximum likelihood Bayesian frameworks. Given severe bias induced by errors, presented here should be more routinely adopted studies.

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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