eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

Marine Biodiversity, Journal Year: 2024, Volume and Issue: 54(2)

Published: Feb. 23, 2024

Language: Английский

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General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(2), P. 326 - 342

Published: Dec. 18, 2022

Abstract Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive in samples. Continuous improvements the method and advances sequencing platforms over last decade have meant this approach now widely used biodiversity sciences biomonitoring. For its general use, hinges on correct identification taxa. However, past studies shown how crucially depends important decisions during sampling, sample processing, subsequent handling data. With no clear consensus to best practice, particularly latter has led varied bioinformatic approaches recommendations data preparation taxonomic identification. In study, using large freshwater fish eDNA sequence dataset, we compared frequently zero‐radius Operational Taxonomic Unit (zOTU) our raw reads assigned it taxonomically (i) combination with publicly available reference sequences (open databases) (ii) an OSU (Operational Sequence Units) database approach, curated generated from specimen barcoding (closed database). We show both gave comparable results common species. commonalities between decreased read abundance were thus less reliable not rare The success zOTU depended suitability, rather than size, database. Contrastingly, often enabled species‐level identifications, yet resolution recent phylogenetic age need include target group coverage, outgroups full annotation databases avoid misleading annotations that can occur when short amplicon sizes commonly metabarcoding studies. Finally, make suggestions improve construction use future.

Language: Английский

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Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(2005)

Published: Aug. 30, 2023

Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental retrieved archived marine sponge specimens can reconstruct fish communities at place sampling discriminate North Atlantic assemblages according biogeographic region (from Western Greenland Svalbard), depth habitat (80-1600 m), even level protection place. Given cost associated with ocean biodiversity surveys, argue targeted opportunistic samples - as well already stored museums other research collections represent an invaluable trove information significantly extend reach monitoring.

Language: Английский

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Integrative taxonomy of introduced Haplosclerida and four new species from Hawaiʻi

Zootaxa, Journal Year: 2025, Volume and Issue: 5566(2), P. 243 - 272

Published: Jan. 7, 2025

Haplosclerid sponges (Porifera: Demospongiae: Heteroscleromorpha), and particularly the family Chalinidae, are notoriously difficult to identify through taxonomic methods alone. Here we use an integrative approach confirm identification report both polymorphic characters different morphotypes exhibited from a recruitment stage that complicate of introduced haplosclerid species Haliclona (Soestella) caerulea Gelliodes conulosa sp. nov. in Hawai'i. Using these same methods, also describe three new (Gellius) pahua nov., (Reniera) kahoe (Rhizoniera) loe our collections Kāne'ohe Bay. combination mitochondrial ribosomal RNA sequences, compile phylogeny is consistent with previous molecular work but at odds morphological used classify belonging Chalinidae Niphatidae families within Haplosclerida. Although shared traits were distributed across taxa throughout tree, sequences diagnostic, average least 3 % sequence divergence among their closest relative. This study highlights standardized Autonomous Reef Monitoring Structures (ARMS) access hidden diversity sponges, potential for competition between newly described potentially endemic species.

Language: Английский

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Hydrological Connectivity Enhances Fish Biodiversity in Amazonian Mining Ponds: Insights from eDNA and Traditional Sampling

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

Abstract The expansion of artisanal and small-scale gold mining (ASGM) in the Madre de Dios region Peruvian Amazon has transformed primary forests into a novel wetland complex thousands abandoned ponds. Despite their ecological relevance, post-mining recovery these systems remains understudied, particularly regarding fish biodiversity recolonization. In this study, we evaluate community richness composition ponds different dimensions, years post abandonment, degree pulse flood connectivity using traditional collection-based methods environmental DNA (eDNA) with 12S COI markers. We compared two inventory contrasted results from ASGM waterbodies those obtained nearby pristine oxbow lakes. Overall, registered more at all sites eDNA vs methods, especially marker. identified 14 13 unique genera eDNA, respectively, 40 detected by both approaches, evidencing complementarity. Notably, found that flooding was main predictor species among (p-value < 0.05). 11 to 22, 23 71, 56 morphospecies non-flooded ponds, flooded lakes, respectively. Furthermore, most influenced were similar Our findings highlight role hydrological within mining-impacted wetlands. Future restoration efforts should enhance aquatic accelerate environments.

Language: Английский

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Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador

Metabarcoding and Metagenomics, Journal Year: 2025, Volume and Issue: 9

Published: Feb. 25, 2025

As unimpacted freshwater environments decline worldwide, developing effective and accurate biomonitoring approaches is critical for detecting ecosystem deterioration facilitating conservation efforts. Freshwater macroinvertebrate communities comprise several phyla thus a broad taxonomic expertise required to identify these precisely. Molecular characterizing invertebrate have the potential be more accurate, time-effective, less costly than traditional morphological methods. However, evaluations comparing two methods macroinvertebrates are lacking in Neotropics, where rapid deployment increased accuracy due escalating of environments. In this study, we compared performance DNA bulk tissue metabarcoding using an eDNA primer pair (fwhF2 & EPTDr2n) methodologies identifying communities. Our aim was evaluate suitability assessing biological quality Ecuadorian streams along altitudinal gradient. We found low overlap between at family genus ranks, though many molecular OTUs were unclassified levels. Morphological identification resulted higher Andean-Amazonian Biotic Index (AAMBI) scores each site, with only three sites classified into same category both methodologies. One reason that family-level information used AAMBI. Existing barcode reference libraries contained incomplete coverage taxa specimens determined approach, indicating need improve representation generate complete determinations. study suggests requires development Neotropics should, moment, complementary approaches.

Language: Английский

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A Confidence Scoring Procedure for eDNA Metabarcoding Records and Its Application to a Global Marine Fish Dataset

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is changing the way biodiversity surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into monitoring programs public databases. Although it widely recognized that records require interpretation light taxonomy biogeography, there remains a range perceptions about how thoroughly should be evaluated which ones reported. Here, we present modular procedure, available as an R script, uses set five steps to assess confidence species‐level by assigning them score from 0 5. This procedure includes evaluations known geographic distribution each taxon, taxonomic resolution marker used, regional completeness reference database, diversification rate, map taxon. We tested on large‐scale marine fish dataset (572 samples) covering 15 ecoregions worldwide, poles tropics, using teleo mitochondrial 12S ribosomal gene. Our analysis revealed broad variation average among regions, with highest scores occurring along European Eastern Atlantic coasts. Generalized linear models applied record covariates highlighted significant influences latitude species richness low (< 2.5). The polar regions notably displayed high proportions scores, probably due limited databases marker. conclude only (> 2.5) medium (2.5) relatively low‐confidence correspond further investigation may after inspection ensure high‐quality records.

Language: Английский

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Environmental DNA Reveals Ecologically Relevant Temporal and Spatial Variation of Fish Community in Silver Carp- and Bighead Carp-Dominant Drinking Water Reservoirs

Water, Journal Year: 2025, Volume and Issue: 17(7), P. 1057 - 1057

Published: April 3, 2025

Environmental DNA (eDNA) metabarcoding was utilized to compare the fish species composition, diversity, and their relationships with environmental factors in four medium-sized drinking water reservoirs (Tongjiqiao, Andi, Shafan, Jinlan) within Qiantang River Basin during both wet dry seasons. A total of 44 belonging 6 orders, 15 families, 40 genera were detected, Cyprinidae being identified as dominant family (68.2%). Silver carp (Hypophthalmichthys molitrix) bighead nobilis) most abundant species, representing 81.94% 99.98% relative eDNA abundance, respectively. The communities characterized by river-resident (59.1%), pelagic (43.2%), omnivorous (43.2%) carnivorous feeding habits. Significant influences seasonal reservoir-specific variations on physicochemical parameters, ecological traits observed. However, no significant differences community diversity (Chao1, Pielou_e, Shannon, Simpson indices) or distribution patterns detected between In contrast, Jinlan Reservoir found exhibit distinct compared other three reservoirs, which consistent abundance H. molitrix nobilis. Through a Spearman correlation analysis, revealed be negatively correlated while nobilis shown have positive correlations (except Chao1). This suggests that excessive stocking may lead reduced whereas moderate could promote restoration. Among factors, Chao1 richness conductivity, pH, phosphate–phosphorus (PO4-P), nitrogen phosphorus ratio (TN/TP), Shannon indices nitrate (NO3-N) concentrations. redundancy analysis (RDA) NO3-N permanganate index (CODMn) primary drivers structure, indicating influence composition effects considered relatively limited. These findings suggest overwhelming dominance reduce cross-reservoir disparities dynamics.

Language: Английский

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Hydrological Connectivity Enhances Fish Biodiversity in Amazonian Mining Ponds: Insights From eDNA and Traditional Sampling

Molecular Ecology, Journal Year: 2025, Volume and Issue: 34(11)

Published: May 9, 2025

ABSTRACT Artisanal and small‐scale gold mining (ASGM) expansion in the Madre de Dios region of Peruvian Amazon has transformed primary forests into a novel wetland complex thousands abandoned ponds. Despite their ecological relevance, post‐mining recovery these systems remains understudied, particularly regarding fish biodiversity recolonisation. In this study, we evaluate community richness composition ponds different dimensions, years post abandonment, physicochemical properties degree pulse flood connectivity using traditional collection‐based methods environmental DNA (eDNA) with 12S COI markers. We compared two inventory contrasted results from ASGM waterbodies those obtained nearby pristine oxbow lakes. Overall, registered more at all sites eDNA versus methods, especially marker. identified 14 13 unique genera eDNA, respectively, 40 detected by both approaches, evidencing complementarity. Notably, found that flooding was main predictor species among ( p ‐value < 0.05). 11–22, 23–71 56 morphospecies non‐flooded ponds, flooded lakes, respectively. Furthermore, most influenced similar to Our findings highlight role hydrological within mining‐impacted wetlands. Future restoration efforts should enhance aquatic accelerate environments.

Language: Английский

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Identification of Variable Importance for Predictions of Mortality From COVID-19 Using AI Models for Ontario, Canada

Frontiers in Public Health, Journal Year: 2021, Volume and Issue: 9

Published: June 21, 2021

The Severe Acute Respiratory Syndrome Coronavirus 2 pandemic has challenged medical systems to the brink of collapse around globe. In this paper, logistic regression and three other artificial intelligence models (XGBoost, Artificial Neural Network Random Forest) are described used predict mortality risk individual patients. database is based on census data for designated area co-morbidities obtained using from Ontario Health Data Platform. dataset consisted more than 280,000 COVID-19 cases in a wide-range age groups; 0–9, 10–19, 20–29, 30–39, 40–49, 50–59, 60–69, 70–79, 80–89, 90+. Findings resulting regression, XGBoost, Forest, all demonstrate excellent discrimination (area under curve exceeded 0.948 with best performance being 0.956 an XGBoost model). Based SHapley Additive exPlanations values, importance 24 variables identified, findings indicated highest are, order importance, age, date test, sex, presence/absence chronic dementia. study allow identification out-patients who likely deteriorate into severe cases, allowing professionals make decisions timely treatments. Furthermore, methodology results may be extended public health regions.

Language: Английский

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