Towards the fully automated monitoring of ecological communities

Ecology Letters, Год журнала: 2022, Номер 25(12), С. 2753 - 2775

Опубликована: Окт. 20, 2022

Abstract High‐resolution monitoring is fundamental to understand ecosystems dynamics in an era of global change and biodiversity declines. While real‐time automated abiotic components has been possible for some time, biotic components—for example, individual behaviours traits, species abundance distribution—is far more challenging. Recent technological advancements offer potential solutions achieve this through: (i) increasingly affordable high‐throughput recording hardware, which can collect rich multidimensional data, (ii) accessible artificial intelligence approaches, extract ecological knowledge from large datasets. However, automating the facets communities via such technologies primarily achieved at low spatiotemporal resolutions within limited steps workflow. Here, we review existing data processing that enable communities. We then present novel frameworks combine technologies, forming fully pipelines detect, track, classify count multiple species, record behavioural morphological have previously impossible achieve. Based on these rapidly developing illustrate a solution one greatest challenges ecology: ability generate high‐resolution, standardised across complex ecologies.

Язык: Английский

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Measuring biodiversity from DNA in the air

Current Biology, Год журнала: 2022, Номер 32(3), С. 693 - 700.e5

Опубликована: Янв. 6, 2022

The crisis of declining biodiversity1 exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential quantify the causes and consequences global change. Environmental DNA2 has revolutionized aquatic ecology,3 permitting population monitoring4 remote diversity assessments matching or outperforming conventional methods community sampling.3-5 Despite this model, similar have not been widely adopted Here, we demonstrate that DNA from animals can be filtered, amplified, then sequenced air samples collected natural settings representing a powerful tool for ecology. We at zoological park, where spatially confined non-native species allowed us track sources. show used identify their ecological interactions. Air contained 25 mammals birds, including 17 known resident zoo species. also identified food items sampled enclosures detected taxa native local area, Eurasian hedgehog, endangered United Kingdom. Our data airborne eDNA concentrates around recently inhabited areas but disperses away sources, suggesting an ecology potential sampling distance. findings profound as source biomonitoring.

Язык: Английский

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Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(42)

Опубликована: Окт. 10, 2022

COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine reduce risk future events. We review major outbreaks since 1967 identify common features opportunities prevent emergence, including ancestral viral origins in birds, bats, other mammals; animal reservoirs intermediate hosts; pathways for spillover community spread, leading local, regional, or international outbreaks. The increasing scientific evidence concerning Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) most consistent with a origin pathway from wildlife people via farming trade. apply what we know about these relevant, feasible, implementable interventions. three primary targets pandemic prevention preparedness: first, smart surveillance coupled epidemiological assessment across wildlife–livestock–human (One Health) interfaces; second, research enhance preparedness expedite development vaccines therapeutics; third, strategies underlying drivers influence misinformation. For all three, continued efforts improve integrate biosafety biosecurity implementation One Health approach are essential. discuss new models address challenges creating an inclusive effective governance structure, necessary stable funding cross-disciplinary collaborative research. Finally, offer recommendations feasible actions close knowledge gaps continuum response future.

Язык: Английский

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Toward quantitative metabarcoding

Ecology, Год журнала: 2022, Номер 104(2)

Опубликована: Ноя. 2, 2022

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary consist of targeted, amplified fragments sequenced many taxa a mixture-struggle to link genetic observations underlying biology quantitative way, but applications require about or systems under scrutiny. As proliferate it becomes more develop ways make them ensure that their conclusions are adequately supported. Here we previously disparate sets techniques making such quantitative, showing polymerase chain reaction mechanism explains observed patterns amplicon general way. By modeling process through amplicon-sequence arise, rather than transforming post hoc, show how estimate starting proportions mixture taxa. We illustrate calibrate model using mock communities apply approach simulated series empirical examples. Our opens door improve use wide range public health, related fields.

Язык: Английский

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Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects—A proof of concept from the field

Environmental DNA, Год журнала: 2022, Номер 4(4), С. 790 - 807

Опубликована: Март 11, 2022

Abstract Biodiversity is in decline due to human‐induced pressures on ecosystems around the world. To be able counteract this alarming trend, it paramount closely monitor biodiversity at global scales. Because practically impossible with traditional methods, last decade has seen a strong push for new solutions. In aquatic ecosystems, monitoring of species from environmental DNA (eDNA) emerged as one most powerful tools our disposal, but terrestrial power eDNA so far been hampered by local scale samples. study, we report successful detection insects airborne samples taken field. We compare results two insect methods (1) light traps moth and (2) transect walks butterflies wild bees. Airborne metabarcoding revealed six classes arthropods, twelve order insects—including representatives four largest orders: Diptera (flies), Lepidoptera (butterflies moths), Coleoptera (beetles), Hymenoptera (bees, wasps, ants). did not detect all observed using suggest further directions development metabarcoding. also recovered nine vertebrates, including frogs, birds, mammals well 12 other phyla. potential become tool monitoring, many impactful applications pests, invasive, or endangered disease vectors.

Язык: Английский

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MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

Environmental DNA, Год журнала: 2022, Номер 4(4), С. 894 - 907

Опубликована: Апрель 11, 2022

Abstract Analysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness this approach depends on accuracy taxonomic reference databases. The MIDORI databases, first released in 2017, were built improve for mitochondrial metazoan (animal) sequences. has now been significantly improved and renamed MIDORI2 (available at http://www.reference‐midori.info ). Like MIDORI, from GenBank contains curated sequences thirteen protein‐coding two ribosomal RNA genes. Coverage substantially expanded cover all eukaryotes, including fungi, green algae land plants, other multicellular algal groups, diverse protist lineages. also includes not only species with full binomials, taxa referred by genus left unspecified (“sp.”). Another new feature updating databases approximately every months version numbers corresponding each release. Additional potentially erroneously annotated have removed. Finally, ability export data files BLAST+ added original preformatted five assignment programs, amino acid are made available As a technical validation, we conducted preliminary comparison performance programs. Results suggest that top hits performed better assigning CO1 than alignment‐free methods based compositional features. Comparing commonly sequences, CO‐ARBitrator BOLD, show broader range non‐metazoan taxa. Overall, many contexts, offers clear advantages: higher diversity variety user‐friendly features, regular updates. particularly well‐suited studies target genes broad primers.

Язык: Английский

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Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring

Science Robotics, Год журнала: 2023, Номер 8(74)

Опубликована: Янв. 18, 2023

The protection and restoration of the biosphere is crucial for human resilience well-being, but scarcity data on status distribution biodiversity puts these efforts at risk. DNA released into environment by organisms, i.e., environmental (eDNA), can be used to monitor in a scalable manner if equipped with appropriate tool. However, collection eDNA terrestrial environments remains challenge because many potential surfaces sources that need surveyed their limited accessibility. Here, we propose survey sampling outer branches tree canopies an aerial robot. drone combines force-sensing cage haptic-based control strategy establish maintain contact upper surface branches. Surface then collected using adhesive integrated drone. We show autonomously land variety stiffnesses between 1 103 newton/meter without prior knowledge structural stiffness robustness linear angular misalignments. Validation natural demonstrates our method successful detecting animal species, including arthropods vertebrates. Combining robotics from unreachable aboveground substrates offer solution broad-scale monitoring biodiversity.

Язык: Английский

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Targeting Terrestrial Vertebrates With eDNA: Trends, Perspectives, and Considerations for Sampling

Environmental DNA, Год журнала: 2025, Номер 7(1)

Опубликована: Янв. 1, 2025

ABSTRACT Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations species, rapid, cost‐effective, scalable methods needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)‐based approaches being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA onto land, presented with new set challenges. This necessitates the development “best‐practice” sample collection guidelines systems purpose detecting vertebrates. address these needs, conducted systematic literature review 143 peer‐reviewed papers applying (excluding Lissamphibia) that were published between 2012 2023. We summarize use biomonitoring, focusing on study design field techniques. Over decade observe steady growth in annual number publications, 3 33 The majority reviewed studies targeted mammals temperate forest regions. While an equal focused metabarcoding approach assess community taxon composition and/or species‐specific detection methods, novel uses increasingly published. These include animal behavior genetics. record three types sampling strategies, eight different substrate types, seven preservation suggesting there is no “one size fits all” eDNA‐based methodology when With multitude aims, across environments, target organisms ecologies, standardization extremely challenging. table known factors influencing Furthermore, identify five key considerations be addressed targeting aim guiding decision making.

Язык: Английский

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Strategies for sample labelling and library preparation in DNA metabarcoding studies

Molecular Ecology Resources, Год журнала: 2021, Номер 22(4), С. 1231 - 1246

Опубликована: Сен. 22, 2021

Abstract Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because its targeted nature that allows sequencing genetic markers many parallel. To achieve this, PCR amplification carried out with primers designed target a taxonomically informative marker within taxonomic group, sample‐specific nucleotide identifiers are added the amplicons prior sequencing. The latter enables assignment sequences back they originated from. Nucleotide can be during metabarcoding “library preparation”, is, when prepared for Different strategies this labelling exist. All have advantages, challenges limitations, some which lead misleading results, worst case compromise fidelity data. Given range questions addressed using metabarcoding, ensuring data generation robust fit chosen purpose critically important practitioners seeking employ assessments. Here, we present an overview three main workflows library preparation studies on Illumina platforms; one‐step PCR, two‐step tagged PCR. Further, distill key considerations researchers select appropriate strategy their specific study. Ultimately, by gaining insights into consequences different workflows, hope further consolidate power as tool assess across applications.

Язык: Английский

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Existing and emerging uses of drones in restoration ecology

Methods in Ecology and Evolution, Год журнала: 2022, Номер 13(9), С. 1899 - 1911

Опубликована: Июнь 26, 2022

Abstract In the absence of effective and scalable human intervention, up to 95% world's ecosystems will be affected by anthropogenic degradation 2050. Therefore, immediate large‐scale ecological restoration is imperative stem biodiversity loss ecosystem decline. Ecologists must draw upon most efficient tools available achieve successful goals. Drones (i.e., unmanned aerial vehicles) are a valuable set in environmental, forestry, agriculture sectors; however, there has been limited uptake ecology. Here, we aim highlight existing emerging uses drones science practice. We discuss strengths weaknesses these applications provide roadmap for increasing utilisation refine enhance objectives. Our article presented with continuum mind, including sections planning, implementation monitoring. also take novel approach describing how relate globally recognised tool published Society Ecological Restoration . used several scenarios from mapping habitats managing wildfires, monitoring effectiveness interventions. Many other disciplines can transferred scenarios. However, use context‐dependent, technical practical constraints need addressed. have considerable potential improve practice at all stages project, which vital realising goals UN Decade on Ecosystem Restoration.

Язык: Английский

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