DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to taxonomic problems, genus-specific barcoding gaps, and database errors DOI Open Access
Šet Janko,

Rok Šturm,

Blaž Koderman

et al.

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: March 25, 2024

Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification is inadequate for efficient standardized surveys. DNA barcoding has become standard approach molecular organisms, aiming overcome the shortcomings traditional monitoring. However, its efficacy depends completeness reference databases. Large efforts are (almost entirely) lacking European countries, such patchy data limit Europe-wide analyses precisely how apply bee identification. Here, we advance towards an effective bees. We conducted high-effort survey bees Slovenia, country where central Europe meets Balkan peninsula, barcoded all collected morpho-species. For global analyses, complemented our barcode dataset with relevant delimitation, general genus-specific gaps, examined error-rate repositories. found that i) sixth specimens from Slovenia could not be reliably identified, ii) delimitation methods show numerous systematic problems, iii) there no gap across bees, iv) genus-specific, but only after curating errors Intense sampling underrepresented regions strict curation repositories needed enhance use

Language: Английский

Taxonomy of the West Palaearctic butterfly genus Palaeophilotes Forster, 1938 (Lepidoptera: Lycaenidae) based on combined analysis of COI barcodes and multilocus nuclear markers DOI
Vladimir A. Lukhtanov, I. A. Makhov,

Anastasia V. Gagarina

et al.

Zootaxa, Journal Year: 2025, Volume and Issue: 5584(4), P. 570 - 580

Published: Feb. 10, 2025

Based on molecular phylogenetic analysis of all relevant taxa, we propose to consider the species previously classified as members Pseudophilotes, Palaeophilotes, Rubrapterus, and Inderskia belonging a single genus, valid name which is Palaeophilotes. This genus can be divided into two subgenera: Rubrapterus with P. bavius fatma, Palaeophilotes sensu stricto. The latter subgenus includes four lineages nine species: (1) abencerragus lineage (single abencerragus), (2) barbagiae barbagiae), (3) panope (P. triphysina), (4) baton panoptes, baton, vicrama, jacuticus sinaicus). Borisinia Korb, 2013, syn. nov. shown an objective synonym Forster, 1938. proposed synonymy svetlana marina supported by identity their DNA-barcodes. reported for Kazakhstan part Altai mountains first time. confirmed Lake Baikal region in Siberia.

Language: Английский

Citations

1
Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity DOI Creative Commons
Maurício M. Zenker, Tatiana Pineda Portella, Felipe Arley Costa Pessoa

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 28, 2024

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of terrestrial aquatic habitats world. DNA barcoding metabarcoding are now widely used in both research routine practices involving mosquitoes. However, these methodologies rely on information available databases consisting barcode sequences representing taxonomically identified voucher specimens. In this study, we assess availability public data for mosquitoes online databases, focusing specifically two most markers Culicidae: COI ITS2. addition, test hypotheses possible factors affecting species coverage (i.e., percentage covered databases) different countries occurrence gap COI. Our findings showed differences publicly repositories, with a taxonomic or 28.4-30.11% BOLD + GenBank, 12.32% ITS2 GenBank. Afrotropical, Australian Oriental biogeographic regions had lowest coverages, while Nearctic, Palearctic Oceanian highest. The Neotropical region an intermediate coverage. general, higher diversity numbers medically important lower Moreover, number endemic tended to have Although our analyses suggested that boundaries need be revised half mosquito additional must gathered confirm results allow explaining gap. We hope study can help guide regional inventories completion reference library barcodes all species.

Language: Английский

Citations

5
Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera DOI Creative Commons
Andrew W. Wilson, Ursula Eberhardt, Nhu H. Nguyen

et al.

Journal of Fungi, Journal Year: 2023, Volume and Issue: 9(8), P. 788 - 788

Published: July 26, 2023

The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding increased the importance of DNA barcode documenting and distribution. gap is seen as difference between intra- inter-specific pairwise distances a barcode. current understanding macrofungi limited, inhibiting development best practices applying nrITS toward research on diversity. This study examined using 5146 sequences representing 717 species from eleven genera, eight orders two phyla datasets assembled by taxonomic experts. Intra- were measured sequence phylogenetic data. results demonstrate that gaps are influenced differences variance distances. In terms behavior, greater ITS1 than ITS2, both relative to combined region. Due variance, ITS2 ITS1. Additionally, approach "splitting" taxa into numerous units produces when compared "lumping". show variability taxa, demonstrating need understand accuracy barcoding quantifying richness. For studies, data supports application multiple molecular markers corroborate systematic delineation species.

Language: Английский

Citations

12
Environmental DNA and biodiversity patterns: a call for a community phylogenetics approach DOI Creative Commons
José Alexandre Felizola Diniz‐Filho, Luís Maurício Bini, Cíntia Pelegrineti Targueta

et al.

Perspectives in Ecology and Conservation, Journal Year: 2024, Volume and Issue: 22(1), P. 15 - 23

Published: Jan. 1, 2024

Environmental DNA (eDNA) metabarcoding is a relatively new technology allowing effective non-invasive analyses and monitoring of biodiversity patterns. Studies on eDNA focus using sequence data to delimit basic units (i.e., such as Molecular Operational Taxonomic Units – MOTUS or Amplicon Sequence Variation ASVs), after this definition standard analytical approaches from community ecology are applied. However, there more information inherent it now straightforward use general in which based directly phylogenies genetic distances between MOTUs ASVs, rather than discrete without any accounting for hierarchical structure, providing continuum understanding Here we briefly review the concepts methods incorporate phylogenetic patterns into analyses, illustrating some main issues with eukaryote diversity along Araguaia River Basin. Hopefully perspective stimulates researchers obtaining perform their under phylogenetics framework instead (or addition to) approach.

Language: Английский

Citations

4
DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus‐specific barcoding gaps and database errors DOI Creative Commons
Šet Janko, Šturm Rok,

Koderman Blaž

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(5)

Published: March 25, 2024

Abstract Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification is inadequate for efficient standardized surveys. DNA barcoding has become standard approach molecular organisms, aiming overcome the shortcomings traditional biodiversity monitoring. However, its efficacy depends completeness reference databases. Large efforts are (almost entirely) lacking European countries such patchy data limit Europe‐wide analyses precisely how apply bee identification. Here, we advance towards an effective bees. We conducted high‐effort survey bees at junction central southern Europe barcoded all collected morphospecies. For global analyses, complemented our barcode dataset with relevant delimitation, general genus‐specific gaps examined error rate repositories. found that (i) sixth specimens from Slovenia could not be reliably identified, (ii) delimitation methods show numerous systematic discrepancies, (iii) there no gap across (iv) genus specific, but only after curating errors Intense sampling underrepresented regions strict curation repositories needed enhance use

Language: Английский

Citations

4
DNA Barcoding: Bioinformatics and Phylogenetic Workflow in R DOI
Voon-Ching Lim, Sree Kanthaswamy, John‐James Wilson

et al.

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 126 - 147

Published: Jan. 1, 2025

Language: Английский

Citations

0
Protein Coding Low‐Copy rpb2 and ef1‐α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy DOI Creative Commons
Vasilii Shapkin, Miroslav Caboň, Miroslav Kolařík

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks significant barcoding gap between sister taxa. Here we tested the reliability of protein coding low‐copy genes alternative markers. Mock communities three unrelated agaric genera ( Dermoloma , Hodophilus and Russula ) representing lineages closely related species were sequenced by Illumina platform targeting ITS1, ITS2, second largest subunit RNA polymerase II gene rpb2 transcription elongation factor 1‐alpha ef1‐α regions. Species representation their relative abundances similar across all regions, despite lower copy number in ITS1 ITS2 required more sophisticated sequence filtering because they produced high chimeric sequences requiring reference‐based chimera removal had higher variants per species. Although clustering filtered ITS resulted an average correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best‐fitted markers consistent frequently lacked resolution due to low intraspecific variability. At some observed multiple lumped together, same time, split into partial clusters, which should be taken consideration when assessing best taxonomic identity clusters. To achieve improve detection, recommend combining different applying additional sorting current availability reference public databases far from being complete for groups, combined marker approach can group‐specific studies that build data own purposes.

Language: Английский

Citations

0
Molecular Taxonomy and Biogeography of the Copper Butterfly Genus Phoenicurusia and Genus‐Level Classification of the Subfamily Lycaeninae (Lepidoptera, Lycaenidae) DOI
Vladimir A. Lukhtanov, Vazrick Nazari, Wolfgang ten Hagen

et al.

Zoologica Scripta, Journal Year: 2025, Volume and Issue: unknown

Published: May 8, 2025

ABSTRACT We investigate a group of small‐sized, phenotypically similar copper species known under the generic names Phoenicurusia , Athamanthia and Margelycaena all which are sometimes considered as subgenera genus Lycaena . This group, consisting ~15–16 species, is distributed in Central Asia (including Mongolia, West China, Afghanistan Pakistan), Caucasus Middle East. It characterised by distinctive wing pattern male genitalia to have very specific ecological preferences larval food plants being associated with ligneous bushes Atraphaxis (Polygonaceae). demonstrate that this monophyletic confirm both synonyms show although most inhabit Asia, itself likely originated Western about 13.5 million years ago soon after populated territory where intense radiation occurred due allopatric speciation subsequent formation zones secondary sympatry. Based on molecular morphological data, we revise taxonomy provide synonymic checklist taxa belonging group. Finally, discuss systematics subfamily Lycaeninae at level light new data obtained review literature.

Language: Английский

Citations

0
Applicability and perspectives for DNA barcoding of soil invertebrates DOI Creative Commons
Jéhan Le Cadre,

Finn Luca Klemp,

Miklós Bálint

et al.

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e17709 - e17709

Published: July 24, 2024

Belowground invertebrate communities are dominated by species-rich and very small microarthropods that require long handling times high taxonomic expertise for species determination. Molecular based methods like metabarcoding circumvent the morphological determination process assigning taxa bioinformatically on sequence information. The potential to analyse diverse cryptic in short time at resolution is promising. However, studies revealed assignment below family-level Collembola (Hexapoda) Oribatida (Acariformes) difficult often fails. These most abundant soil-living microarthropods, application of molecular-based, automated would be beneficial these . In this study, we analysed presence a barcoding gap standard gene cytochrome oxidase I (COI) Oribatida. describes significant difference between intra- interspecific genetic distances among essential bioinformatic assignment. We collected COI sequences from BOLD NCBI focused with wide geographic sampling capture range their intraspecific variance. Our results show overlapped species, impeding accurate When was present, it exceeded threshold 3% also differed species. Automatic specimen assignments showed comprised multiple lineages caused ambiguous taxon distance-based methods. Character-based using phylogenetic trees monophyletic clades as criteria worked some but failed completely Collembola. Notably, parthenogenetic lower variance more than sexual different patterns diversity suggest degrees result deep evolutionary distances. This indicates single threshold, or gene, will probably not sufficient molecular identification many taxa. haplotype investigated even nearly covered, coverage better Additional use secondary genes long-read sequencing marker can improve studies. recommend construction pan-genomes pan-barcodes lacking gap. allow both identify boundaries, cover full variability genes, making possible highly barcode sequences.

Language: Английский

Citations

2
New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests DOI Creative Commons

Marie Pollmann,

Denise Kuhn,

Christian König

et al.

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(9)

Published: Sept. 1, 2023

The pteromalid parasitoid

Language: Английский

Citations

4