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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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(6), С. 873 - 888

Опубликована: Май 15, 2023

The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered invasive species detection, population genetics. Here we show that deep-sequencing-based approaches capture genomic information from humans (Homo sapiens) just as readily the intended target species. We term this phenomenon genetic bycatch (HGB). Additionally, high-quality could be intentionally recovered substrates (water, sand air), holding promise beneficial medical, forensic applications. However, also raises ethical dilemmas, consent, privacy surveillance to data ownership, requiring further consideration potentially novel regulation. present evidence detectable 'wildlife' samples bycatch, demonstrate identifiable can human-focused sampling discuss translational implications such findings.

Язык: Английский

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Key issues in assessing threats to sea turtles: knowledge gaps and future directions

Endangered Species Research, Год журнала: 2023, Номер 52, С. 303 - 341

Опубликована: Сен. 20, 2023

Sea turtles are an iconic group of marine megafauna that have been exposed to multiple anthropogenic threats across their different life stages, especially in the past decades. This has resulted population declines, and consequently many sea turtle populations now classified as threatened or endangered globally. Although some worldwide showing early signs recovery, still face fundamental threats. is problematic since important ecological roles. To encourage informed conservation planning direct future research, we surveyed experts identify key contemporary (climate change, take, fisheries, pollution, disease, predation, coastal development) faced by turtles. Using survey results current literature, also outline knowledge gaps our understanding impact these how targeted often involving emerging technologies, could close those gaps.

Язык: Английский

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Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance

Molecular Ecology, Год журнала: 2023, Номер 32(15), С. 4118 - 4132

Опубликована: Май 30, 2023

Abstract Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies explored the potential these detect within‐species variation, allowing population assessments abundance estimates from samples. However, we currently lack a framework outlining key considerations specific generating, analysing applying data two purposes. Here, discuss how various markers differ with regard information detectability samples analysis of differs common tissue‐based analyses. We then outline it may be possible obtain absolute by detecting intraspecific variation mixtures under multiple scenarios. also major causes contributing allele detection frequency errors data, their consequences population‐level analyses bioinformatic remove erroneous sequences. This review summarizes advances required harness full eDNA‐based inform questions ecology, evolutionary biology conservation management.

Язык: Английский

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Current status and topical issues on the use of eDNA-based targeted detection of rare animal species

The Science of The Total Environment, Год журнала: 2023, Номер 904, С. 166675 - 166675

Опубликована: Авг. 29, 2023

Язык: Английский

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Harnessing the omics revolution to address the global biodiversity crisis

Current Opinion in Biotechnology, Год журнала: 2023, Номер 80, С. 102901 - 102901

Опубликована: Фев. 10, 2023

Язык: Английский

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Playing “hide and seek” with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA)

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Фев. 14, 2023

Animal conservation relies on assessing the distribution and habitat use of species, but for endangered/elusive animals this can prove difficult. The Monk Seal, Monachus monachus, is one world's most endangered species pinniped, only endemic to Mediterranean Sea. During recent decades, direct observations have been few scattered, making it difficult determine its away from Aegean Sea (core area post-decline relict population). This study environmental DNA (eDNA) analysis detect presence Seal in 135 samples collected 120 locations central/western Sea, spanning about 1500 km longitudinally 1000 latitudinally. A recently described species-specific qPCR assay was used marine-water samples, mostly during 2021 by a Citizen Science (CS) project. Positive detections occurred throughout longitudinal range, including westernmost surveyed (Balearic archipelago). positive indicated six "hotspots", overlapping with historical sites, suggesting that habitat-specific characteristics play fundamental role. We applied single-season occupancy models correct detection probability assess importance site-specific characteristics. distance small islets protected (or access-restricted) areas correlated negatively probability. novel molecular approach, here first time an extensive CS study, proved potential as tool monitoring species.

Язык: Английский

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CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 2, 2024

ABSTRACT Metagenomics has enabled the rapid, unbiased detection of microbes across diverse sample types, leading to exciting discoveries in infectious disease, microbiome, and viral research. However, analysis metagenomic data is often complex computationally resource-intensive. CZ ID a free, cloud-based genomic platform that enables researchers detect using data, identify antimicrobial resistance genes, generate consensus genomes. With ID, can upload raw sequencing find matches NCBI databases, get per-sample taxon metrics, perform variety analyses visualizations. The intuitive interface interactive visualizations make exploring interpreting results simple. Here, we describe expansion with new long read mNGS pipeline accepts Oxford Nanopore generated ( czid.org ). We report benchmarking standard mock microbial community dataset against Kraken2, widely used tool for analysis. evaluated ability this divergent viruses simulated datasets. also assessed limit spiked-in virus cell line as proxy clinical samples. Lastly, detected known novel previously characterized disease vector (mosquitoes)

Язык: Английский

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Non-invasive real-time genomic monitoring of the critically endangered kākāpō

eLife, Год журнала: 2023, Номер 12

Опубликована: Март 17, 2023

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations critically endangered kākāpō ( Strigops habroptilus ). first established an environmental DNA metabarcoding protocol identify distribution and other vertebrate species in a highly localized manner using soil samples. Harnessing nanopore sequencing high-quality reference genome, we then extracted species-specific from soil. combined long read-based haplotype phasing with known individual variation population presence individuals, confirmed these genomically informed predictions through detailed metadata on distributions. This study shows that identification is feasible DNA, important implications for future efforts application genomics conservation rare species, potentially expanding research monitoring inferring fitness parameters such as diversity inbreeding.

Язык: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 1048 - 1064

Опубликована: Авг. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Язык: Английский

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