TICI: a taxon-independent community index for eDNA-based ecological health assessment

PeerJ, Год журнала: 2024, Номер 12, С. e16963 - e16963

Опубликована: Фев. 26, 2024

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods difficult scale, limited in scope, suffer prohibitive costs, skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible scalable solution survey across the tree-of-life with relatively low cost minimal expertise for sample collection. However, there remains need condense complex, multidimensional community information into simple, interpretable metrics of ecological health environmental management purposes. We developed riverine taxon-independent index (TICI) objectively assigns indicator values amplicon sequence variants (ASVs), significantly improves statistical power utility eDNA-based bioassessments. The TICI model training step uses Chessman iterative learning algorithm assign scores large number ASVs commonly encountered wide geographic range. New sites then evaluated by averaging value present site. trained on eDNA dataset from 53 well-studied monitoring Zealand, each sampled high level biological replication ( n = 16). Eight short-amplicon assays were used generate broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, animals. Site-specific strongly correlated historical stream macroinvertebrate assessments (macroinvertebrate MCI; R 2 0.82), variation replicates was (CV 0.013). Taken together, this demonstrates potential analysis provide reliable, robust low-cost assessment accessible managers, decision makers, wider community.

Язык: Английский

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Targeted eDNA Metabarcoding Reveals New Populations of a Range‐Limited Stonefly

Ecology and Evolution, Год журнала: 2025, Номер 15(4)

Опубликована: Апрель 1, 2025

ABSTRACT Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer potential to efficiently document endangered species, but date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA assess distribution Maungatua stonefly, Zelandoperla maungatuaensis , a flightless insect previously known from only handful streams draining 4‐km section mountain range in southern Zealand. We analyzed 12 stream localities across range. Screening with commercial COI primers failed detect focal Z. . However, newly designed species‐specific detected this taxon four adjacent east‐flowing contain and two which it had not been detected. Subsequent manual surveys confirmed presence discovered populations, barcoding revealing that they together represent unknown, genetically divergent subclade. Our results illustrate metabarcoding help delineate ranges taxa, highlight importance primer specificity when These findings also have considerable implications companies offering biodiversity health services targeting invertebrates.

Язык: Английский

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Promoting Community‐Led Monitoring of Taonga (Treasured) Species and Freshwater Health Through eDNA Metabarcoding

Environmental DNA, Год журнала: 2025, Номер 7(3)

Опубликована: Май 1, 2025

ABSTRACT In response to intensified agricultural impacts on Aotearoa New Zealand's river systems, our study sought demonstrate a novel approach for assessing freshwater quality through environmental DNA (eDNA) and promote holistic understanding of ecological health. Employing 13 eDNA tree‐of‐life metabarcoding assays alongside 11 standard physicochemical attributes, we generated comprehensive temporal spatial dataset along 3.5 km section an upper catchment. The catchment moves from culturally significant native bush area, sheep beef farming, organic dairy farm, capturing the transition varying land uses. Our analysis focused detections key taonga (treasured) species, known animal sources fecal contamination, taxon‐independent community index (TICI) as measure We identified 479 species including whīo/native blue duck, long short finned tuna/eels, kaharore bully/cockabully, kōkopu/dwarf galaxias, kōura/freshwater crayfish. Although Escherichia coli ( E. ) levels did not significantly vary across sites, sequence counts cattle deer were predictors site's levels, suggesting that could be valuable indicator contamination sources. TICI scores strongly correlated with changes in water attributes (Adj‐ R 2 = 0.92) consistently detected subtle declines driven by increased pastoral use. Community leadership was central methodology, enabling local stakeholders, mana whenua farmers, actively participate monitoring data interpretation. This only fulfilled regulatory requirements but also fostered deep connection river, enhancing community‐led conservation efforts. By mauri (life force) active participation capacity building, this exemplifies sustainable, collaborative efforts management revitalization.

Язык: Английский

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Do freshwater insect assemblages in exotic plantations resemble those from native forest? Evidence from environmental DNA

Restoration Ecology, Год журнала: 2025, Номер unknown

Опубликована: Май 21, 2025

Widespread deforestation has impacted biodiversity patterns globally, but the potential for forest plantations to restore remains unclear. Here we used environmental DNA (eDNA) analysis compare freshwater insect assemblages between native and exotic forests in New Zealand, a region that experienced heavy over recent centuries. Our of mayfly, stonefly, caddisfly (Ephemeroptera, Plecoptera, Trichoptera [EPT]) eDNA from 15 plantation streams southern Zealand yielded 85 taxa, most which were shared across these habitat types. Assemblages structured primarily by rather than type. Although taxonomic diversity EPT was lower relative forest, highly similar those streams. These findings suggest can broadly previously deforested aquatic communities resemble forest.

Язык: Английский

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Human-driven evolution of color in a stonefly mimic

Science, Год журнала: 2024, Номер 386(6720), С. 453 - 458

Опубликована: Окт. 24, 2024

Rapid adaptation is thought to be critical for the survival of species under global change, but our understanding human-induced evolution in wild remains limited. We show that widespread deforestation has underpinned repeated color shifts insect populations. Specifically, loss forest led changes across lineages mimic warning coloration a toxic stonefly. Predation experiments suggest relative fitness phenotypes varies between forested and deforested habitats. Genomic analyses 1200 specimens selection at

Язык: Английский

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Disturbance drives concordant functional biodiversity shifts across regions: new evidence from river eDNA

Ecography, Год журнала: 2024, Номер unknown

Опубликована: Дек. 16, 2024

Major disturbance events can profoundly influence biodiversity patterns, although the extent to which such shifts are predictable remains poorly understood. We used environmental DNA (eDNA) compare forested versus recently deforested stream insect communities across disjunct regions of New Zealand, test for parallel in response widescale disturbance. Although eDNA analyses revealed highly distinct species pools regions, they detected concordant functional diversity linked recent deforestation, including decreases grazing taxa. The finding that taxonomically freshwater biotas have experienced broadly wake deforestation indicates drive deterministic ecological change. By contrast, some closely related within groups show discordant responses suggests differentiation among cryptic taxa may contribute idiosyncratic shifts. These findings highlight potential resolving subtle species‐level differences anthropogenically impacted assemblages.

Язык: Английский

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