Regional Studies in Marine Science, Год журнала: 2024, Номер unknown, С. 103946 - 103946
Опубликована: Ноя. 1, 2024
Язык: Английский
Integrative Zoology, Год журнала: 2025, Номер unknown
Опубликована: Апрель 1, 2025
DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due a significant lack reference sequences dedicated protocols. One such group the tardigrades-a charismatic phylum microinvertebrates known for their extremophilic cryptobiotic capabilities. In this study, we provide first curated database 3194 tardigrade COI sourced from public databases supplemented with newly produced barcodes. We demonstrate in action optimized PCR primers sample processing protocol using 78 samples collected Poland Italy. The revealed presence more than hundred operational units classified as Tardigrada, representing 23 genera. compared results morphological survey, which same genera, but lower number species-level taxa identified morphologically. observed congruent patterns richness composition between surveys both within-sample regional fauna levels. had higher discriminatory power, revealing cryptic diversity, distinguishing belonging taxonomically challenging complexes. By combining were able find rare taxa, including novel biogeographic records putative new science, showing also that approach can be extremely powerful effective meiofauna research.
Язык: Английский
Процитировано
0
Metabarcoding and Metagenomics, Год журнала: 2025, Номер 9
Опубликована: Апрель 7, 2025
Freshwater ecosystems are increasingly threatened by human activities, leading to biodiversity loss and ecosystem degradation. Effective monitoring, particularly through the use of aquatic macroinvertebrates as bioindicators, is crucial for assessing ecological health. While traditional morphological methods face limitations, DNA metabarcoding offers higher accuracy efficiency in species identification using environmental DNA. However, success contingent on quality reference libraries, which often incomplete or biased. This study aimed construct share a comprehensive COI-based barcode library freshwater France, specifically targeting short gene regions amplified with fwhF2/fwhR2N primers, suitable degraded A list occurring French was established from official national checklists Alpine lake surveys. The resulting analysed taxonomic completeness, coverage cryptic diversity. checklist consisted 2,841 across 10 phyla, 56% had at least one COI-5P sequence available Barcode Life Data System (BOLD). analysis diversity, based Index Numbers (BINs) highlighted potential high rate although it might have been overestimated due wide geographic origin sequences. Alignment challenges primers were identified certain taxa, amongst Coleoptera, Diptera Malacostraca. genetic diversity approached number haplotypes per that most limited only three having more than 100 haplotypes. Finally, this showed total 57 shared 116 distinct species. work emphasises need expanded sequencing efforts improve pitfalls associated these further assessment
Язык: Английский
Процитировано
0
Biodiversity and Conservation, Год журнала: 2024, Номер 33(13), С. 3871 - 3903
Опубликована: Ноя. 1, 2024
Abstract Expertise in biodiversity research (taxonomy, faunistics, conservation with taxonomic background) appears to decline worldwide. While the “taxonomic impediment” is discussed extensively literature, much fewer papers focus on identification crisis, i.e., decreasing number of experts who can identify species, and species-based research. As a test case explore gravity we chose Hungary, Central European country strong history comprehensive expertise output. We set out answer two main questions. (1) What proportion Hungarian fauna could currently be identified by experts, what factors determine which groups are covered; (2) trends underlying reasons for these trends? show that Hungary lacks active almost half nearly 36,000 animal species recorded country, more than quarter have only one or available. also faunistic experienced golden era between ca. 1990 2010. Since then, however, there has been decline, published decreased level like 1970s. Multiple causing this trend, such as increased pressure publish high impact journals increasing administrative duties professional scientists. The next generation needs fluent modern techniques publication strategies but maintain robust morphology-based knowledge equipped tasks difficult taxa. Despite being disadvantaged exclusive application citation-based evaluation, do need positions focused grants researchers country’s base avoid increasingly dependent on—equally declining—foreign expertise.
Язык: Английский
Процитировано
2
PLoS ONE, Год журнала: 2024, Номер 19(1), С. e0296305 - e0296305
Опубликована: Янв. 2, 2024
Peru ranks among the three countries with highest bird species diversity globally and a majority of those are found in Peruvian Amazon. However, birds this area currently facing serious anthropogenic threats. Genetic genomic methods becoming important tools for avian biodiversity monitoring conservation planning. Comprehensive molecular libraries that publicly available key to effective deployment these tools. We analyze information gaps four markers most genetic sequence databases, Barcode Life Data Systems (BOLD) NCBI GenBank, Amazonia. 64% Amazonian have gene sequences COI, 59.5% CYTB sequences, 16.4% 12S only 0.6% 18S sequences. numbers decrease drastically 4.3% COI when we consider specimens sampled Peru. Our data also showed 43.8% endemic (n = 32) missing any screened marker uploaded GenBank or BOLD. results will encourage guide efforts scientific community complete reference be useful future DNA-based projects include birds.
Язык: Английский
Процитировано
1
The European Zoological Journal, Год журнала: 2024, Номер 91(1), С. 162 - 171
Опубликована: Янв. 2, 2024
Plecoptera is a small order of aquatic insects that considered one the most endangered groups due to increasingly altered freshwater ecosystems. nymphs can be challenging identify at species level because diagnostic characters for are lacking, while adults difficult collect routinely given their short life span. Species identification by DNA barcoding used as an alternative morphological identification, but gaps and inaccuracies in reference databases needed taxonomic assignment undermine utility real case studies. Here we aim to: i) quantify number Italian with barcodes from specimens collected worldwide Italy; ii) perform regional assessment coverage; iii) calculate intraspecific distance among available sequences evaluate potential presence errors cryptic species. As databases, both non-curated database (BOLD) curated (MIDORI2) test effect sequence selection on availability sequences. We found 67.6% 51.8% were represented BOLD MIDORI2. Most obtained outside Italy, only 21.8% 13.5% having Italy. Endemisms poorly represented, distances some high, which suggest diversity or erroneous assignments. Our results support growing need increase international cooperation barcode initiatives promote integration between molecular biologists zoologists exploit full protect biodiversity.
Язык: Английский
Процитировано
1
Molecular Ecology Resources, Год журнала: 2024, Номер 24(5)
Опубликована: Март 23, 2024
Abstract Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long‐term use in various studies, more reliable mayfly DNA barcode data have been produced a negligible number of countries, only ~40% European species had barcoded with less than 50% families covered. Despite being carried out small area, our study presents second‐most species‐rich reference library mayflies from Europe first comprehensive view an important biodiversity hotspot such as Western Carpathians. Within 1153 sequences, 76 morphologically determined were recorded added to Barcode Life Data System (BOLD) database. All obtained sequences assigned 97 BINs, 11 which unique three represented never before. Sequences 16 high intraspecific variability divided into 40 confirming presence cryptic lineages. Due low interspecific divergence non‐existing barcoding gap, six shared BINs. Delimitation analyses resulted 79 107 putative respectively. Bayesian maximum‐likelihood phylogenies confirmed monophyly almost all complexes taxa proved that distinguishes studied species. We shown it is still sufficient thoroughly investigate fauna but geographically area enrich global databases greatly. In particular, insights gained here transcend local context may broader implications for advancing efforts.
Язык: Английский
Процитировано
1
Ecology and Evolution, Год журнала: 2024, Номер 14(8)
Опубликована: Авг. 1, 2024
Abstract Rivers are crucial ecosystems supporting biodiversity and human well‐being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms taxonomic resolution scalability. This study explores the application DNA metabarcoding analysis both bulk environmental (eDNA) samples for comprehensive assessment macrozoobenthic biodiversity, detection invasive endangered species, evaluation ecological status northwestern Spain. homogenized water eDNA revealed a mean 100 87 macrozoobenthos species per sample respectively. However, specific composition was significantly different with only 27.3% total being shared. It not possible to identify all OTUs level; 17.43% 49.4% generated could be identified level samples, Additionally, 11 exotic (two first records Iberian Peninsula another three Asturias region) one were detected by molecular tools. Molecular showed significant correlations EQR values (Ecological Quality Ratio) IBMWP index, differences inferred noted, tending indicate higher status. Overall, offers promising approach biomonitoring, providing insights into within single analysis. Further optimization intercalibration required its implementation routine programmes, but scalability multi‐tasking capabilities position it as valuable tool integrated monitoring ecosystems.
Язык: Английский
Процитировано
1
Biology, Год журнала: 2024, Номер 13(11), С. 951 - 951
Опубликована: Ноя. 19, 2024
Aquatic biodiversity includes a variety of unique species, their habitats, and interactions with each other. Albania has large hydrographic network including rivers, lakes, wetlands coastal marine areas, contributing to high level aquatic biodiversity. Currently, evaluating relies on morphological species identification methods, but DNA-based taxonomic could improve the monitoring assessment ecosystems. This study aims evaluate coverage COI DNA barcodes in reference libraries for known animal present lagoons Albania. In this study, six most studied were selected. Species data gathered from scientific literature publicly available sites studies. The collected lists taxonomically standardised using global public databases like WORMS. used analyse barcode gap based two libraries: Barcode Life Data Systems (BOLD) NCBI GenBank. results show that ranges 7% (Lagoon Patok) 33% (Karavasta Lagoon). Fishes Amphibia represent groups lowest (8% each), while Annelida shows highest (47%). conclusion, gene marker assessments is reliable
Язык: Английский
Процитировано
1
Estuarine Coastal and Shelf Science, Год журнала: 2024, Номер 313, С. 109092 - 109092
Опубликована: Дек. 17, 2024
Язык: Английский
Процитировано
1
Ecological Indicators, Год журнала: 2023, Номер 158, С. 111454 - 111454
Опубликована: Дек. 22, 2023
Water resources play a vital role in sustaining ecosystems, human life, food security, and biodiversity. However, these currently face serious threats caused primarily by activities. Because of that, European Union have mandated that all its member states monitor the ecological status their water bodies. One most commonly used bioindicator groups for routine river biomonitoring is benthic macroinvertebrates, which rely mainly on morphological identification at family level use diverse indices to estimate ecosystem. The approach has certain limitations, metabarcoding now considered an alternative technique biodiversity studies surface waters. efficacy this depends comparison sequencing data with genetic databases, are often incomplete geographically biased. In study, we collected 92 macroinvertebrate samples from rivers northern Iberian Peninsula identify possible species generate new DNA sequences COI-5P region. objectives were perform region-specific enrichment reference databases geographical area Spain assess impact, before after strategy, taxonomic assignments inference samples. results showed 21% morphospecies lacked BOLD or GenBank indicating significant number northwestern lack major databases. Enriching led detection average 17.25 more BINs (species-assimilable gene cluster) 1.54 IBMWP taxa (river indicator taxa) per sample, causing changes determination 16% samples, clearly shows improving local could enhance taxa, potentially impacting molecular data. Additionally, historical analysis addition database using public records revealed asymptotic trend can be partially mitigated enrichment. These indicate biota effort considerably improve rather than waiting gradual improvement conclusion, advocate creation freshwater checklist then initiation coordinated any unsequenced
Язык: Английский
Процитировано
2