Next‐generation species delimitation and taxonomy: Implications for biogeography

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(9), P. 1709 - 1722

Published: Feb. 13, 2024

Abstract An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, data are of importance species delimitation. We here review recent developments future perspectives direct relevance biogeographers. The understanding that independently evolving segments population‐level lineages, the rise integrative approaches to delimit such advent high‐throughput sequencing have considerably renewed discipline taxonomy. Using genome‐scale molecular datasets, extent admixture across hybrid zones can now be effectively assessed evolutionary independence lineages inferred, leading more reliable comparable delimitation criteria. Substantially divergent but admixing phylogeographical conveniently named as subspecies, thus avoiding taxonomic oversplitting inflation. At same time, comprehensive DNA barcoding metabarcoding efforts uncovering an enormous proportion undiscovered biotic diversity, we encourage development bioinformatic pipelines combine discovery with diagnosis scientific naming, approach a inventory globe without abandoning established Linnaean system.

Language: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1048 - 1064

Published: Aug. 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.

Language: Английский

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Investigating pelagic biodiversity and gelatinous zooplankton communities in the rapidly changing European Arctic: An eDNA metabarcoding survey

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(3)

Published: May 1, 2024

Abstract Fram Strait, the gateway between Arctic and Atlantic Oceans, is undergoing major climate change‐induced physical biological transformations. In particular, rapid warming ongoing “Atlantification” are driving species range shifts altering food web structures in Arctic. Understanding predicting consequences of these processes on future ecosystems requires detailed assessments local pelagic biodiversity. Gelatinous zooplankton (GZP) an important component communities, recent evidence indicates that such communities changes Strait. However, as sampling GZP challenging, they regularly underestimated biodiversity, distribution, abundance. To overcome this address existing ecological knowledge gaps, we investigated patterns metazoan diversity Strait using environmental DNA (eDNA) metabarcoding cytochrome c oxidase I (COI) gene. We successfully detected a broad taxa from marine across locations ocean depth zones. demonstrate vertical structuring elucidate relationships water mass indicators, salinity temperature. Furthermore, when comparing eDNA data with net video transect for at same period location, found uncovered higher number taxa, including several were not by other methods. This study contribution to formation baseline biodiversity datasets, well research changing community composition.

Language: Английский

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Estimating Rapid Diversity Changes During Acute Herbicide Contamination Using Environmental DNA

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 1, 2025

ABSTRACT The biodiversity of freshwater ecosystems globally is facing severe threats due to various anthropogenic stressors, such as habitat degradation, introduction invasive species, and pollution. Assessing the effects human‐induced environmental stressors on population community persistence requires accurate estimates. While DNA (eDNA) metabarcoding has emerged a promising tool, its effectiveness in capturing rapid responses acute across levels biological organization (community, population, intra‐specific levels) remains be investigated. In this study, we tested efficacy eDNA assessing changes aquatic zooplankton insect communities by conducting two‐month mesocosm experiment with pulses glyphosate‐based herbicide under contrasting nutrient (mesotrophic eutrophic). We examined treatments assemblages, family richness, intraspecific diversity, compared our findings those obtained through microscopy approach. Metabarcoding revealed partially congruent ecological microscopy, indicating potential changes. induced shifts composition differentially impacted richness (increase insects, decrease crustaceans rotifers), suggesting gradient tolerance among taxa top‐down regulation larvae that may counteract advantage gained herbicide‐tolerant zooplankton. Finally, showed enrichment exacerbated negative highlighting concerns about genetic erosion. Our underscore complexity ecosystems. conclude can not only used estimate invertebrate but also provides additional value offering broader perspective diversity dynamics cascading at different scales organization.

Language: Английский

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A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Molecular methods such as DNA/eDNA metabarcoding have emerged useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with for genetic marine hard-bottom benthic communities. Here, we present data our first campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved 2018-2020 across 15 observatories along coasts Europe adjacent regions. describe open-access set (image, metadata) explore show its potential ecological research. Our analysis shows that recovered more than 60 eukaryotic phyla capturing diversity up ~5500 amplicon sequence variants ~1800 operational taxonomic units, ~250 ~50 species per observatory cytochrome c oxidase subunit I (COI) 18S rRNA marker genes, respectively. Further, detected threatened, vulnerable non-indigenous often targeted biological monitoring. while deployment duration does not drive estimates, effort sequencing depth do. recommend should be at least 3-6 months during main growth season use resources efficiently possible post-sequencing curation is applied enable statistical comparison entities. suggest used programs long-term research encourage adoption ARMS-MBON protocols.

Language: Английский

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Eukaryotic biodiversity of sub-ice water in the marginal ice zone of the European Arctic: A multi-marker eDNA metabarcoding survey

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 968, P. 178840 - 178840

Published: Feb. 21, 2025

The effects of climate change, including warming waters, loss sea ice habitat and the resulting changes in primary production, are inducing shifts marine communities across Arctic Ocean. marginal zone (MIZ) is a highly dynamic ecosystem transition between pack open ocean. It for wide range organisms, sympagic pelagic taxa, all which affected by changing physical dynamics MIZ. Here we use multi-marker (18S rRNA V1-2 COI Leray-XT) approach to investigate eukaryotic biodiversity upper water column this understudied habitat. Environmental DNA (eDNA) was sequenced from seawater samples collected directly beneath at depth 5 m, sourced floes representing different regimes. To explore abiotic factors influencing under-ice diversity, combined satellite-derived environmental data with simultaneous situ hydrographic measurements. Our analysis identified metazoans, along producers typical region, as well substantial uncharacterised diversity. Alpha diversity indices were higher immediately below ice, community composition differed depths floe stations. We show that properties meltwater stratification ocean, concentration distance edge, significantly shape composition. These findings highlight effectiveness eDNA metabarcoding monitoring sub-ice enhance our understanding

Language: Английский

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Metabarcoding identifies macroalgal composition as a driver of benthic invertebrate assemblages in restored habitats

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 21, 2025

Abstract Large brown macroalgal forests support diverse communities of associated invertebrates. However, human activities have led to their degradation, replacing the original assemblages with less-complex habitats and altering invertebrate communities. To counteract this, restoration actions are currently being performed aiming at recovery. Here, we used metabarcoding COI gene describe community a 10-year restored forest dominated by Gongolaria barbata . This assemblage was compared an adjacent site where G. is absent, two healthy also , as references. Results showed that arthropods, molluscs, annelids were most abundant groups. Specific MOTUs representing sponge ascidian species exclusively found in assemblages, suggesting particularly benefited some these organisms. Crustaceans however, similarly across including one photophilous macroalgae (without ), thus indicating mobile groups may equally colonise alternative habitats. The overall composition did not completely resemble references, recovering all diversity complex process, likely influenced multiple factors require further investigation.

Language: Английский

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Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in subtropical coastal vegetated ecosystems

Journal of Fish Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Abstract In South Africa, mangrove forests and seagrass meadows often co‐occur in estuarine systems combination host rich, endemic biodiversity. There is an urgent need to explore community diversity coastal vegetated ecosystems, given the degrading effects of climate change anthropogenic pressures. Environmental DNA metabarcoding a promising biomonitoring tool African although studies highlight optimise standardise sampling protocols. This study aimed contribute developing protocols by understanding applicability environmental (eDNA) within habitats investigating using two different sample types. Aquatic sedimentary samples from three estuaries along east coast with MiFish metabarcoding, detected 148 operational taxonomic units (OTUs) representing 67 fish genera 50 families, only 16% were resolved species. We observed that aquatic eDNA 97% total diversity, suggesting this efficient comprehensively detect ichthyofaunal diversity. did not communities between mangroves seagrasses our findings underscore importance taking hydrological connectivity into consideration for design. Overall, work reinforces key considerations future focused on fauna estuaries, therefore contributes optimising support

Language: Английский

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Detecting Threatened Ichthyofauna in a Mediterranean Intensive Agricultural Landscape: From DNA Traces to Electrofishing

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(4)

Published: April 1, 2025

ABSTRACT Intensive agriculture and farming activities, industry, as well human settlement can seriously affect freshwater ecosystems the species they host. These disturbances have been previously monitored using traditional catch surveys. New methods, such environmental DNA (eDNA) metabarcoding, significantly improve biodiversity mapping by accessing rarely visited areas enhancing detection of rare invasive species. We conducted an eDNA survey in a complex river tributary system at Tenagi, Philippi that hosts approximately 12.5% Greek ichthyofauna. A primer pair targeting 12S rRNA was used to analyse samples from 30 sites. reference sequence database generated regional diversity monitoring endemic, native fishes. Results were compared with data collected electrofishing stations allowed access. Two three invasive, two translocated 10 detected their current known distribution both methods. Overall, metabarcoding being more sensitive, consistently than methods on single fieldwork expedition. Co‐occurrence also investigated for first time, revealing minor variations composition within fish communities. Stations intensive agricultural zones potentially high accumulation organic inorganic pollutants (Tributary D), exhibited lower number reads richness other tributaries Tenagi. Our results demonstrate need complementary use assess assemblages habitats, combined approach address reliability issues biases associated each method.

Language: Английский

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Towards DNA metabarcoding‐based haplotype for monitoring terrestrial arthropod communities

Insect Conservation and Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: June 2, 2025

Abstract Whole organism community DNA (wocDNA) metabarcoding has become a necessary and powerful tool to study mixed communities from bulk samples by detecting short sequences. This review integrates the use of arthropods as ecological indicators through wocDNA metabarcoding, covering key methodological aspects sampling design bioinformatics highlighting amplicon sequence variants (ASV)‐based pipelines for incorporating haplotype‐level variation. The success relies on proper methods, good laboratory practices, cleaning bulk‐samples, selecting suitable arthropod sizes, efficient extractions, accurate library quantification, appropriate genetic markers taxonomic identification effective filtering. Incorporating haplotype data into monitoring unveils intraspecific variation that could complement species‐level diversity, thus enhancing conventional analyses. Choosing abundance‐ or incidence‐based approaches is statistical methods. WocDNA provides biodiversity estimates entire allows researchers derive insights can inform formulation refinement hypotheses. These refined hypotheses, based obtained estimates, then guide ecosystem conservation.

Language: Английский

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