50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead

Csabai, Zoltán; Čiamporová‐Zaťovičová, Zuzana; Boda, Pál; Cĭampor, F

doi:10.1016/j.scitotenv.2022.160922

Cited by 12 publications

(7 citation statements)

References 70 publications

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“…Beetles are among the flagship groups of invertebrates for which barcode reference libraries are built (Pentinsaari et al, 2014; Hendrich et al, 2015). Still, even in Europe, progress reached above 50% of known species for freshwater aquatic beetles (Csabai et al, 2023).…”

Section: Discussionmentioning

confidence: 99%

“…Despite the potential of DNA barcoding, COI-based DNA reference databases remain incomplete (e.g., Weigand et al, 2019), including for adephagous aquatic beetles (Csabai et al, 2023). Currently, publicly available sequences exist for only two of the seven species within the uliginosus -group in databases such as BOLD (Ratnasingham & Hebert, 2007) and GenBank (Benson et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Age-dependent variation of aedeagal morphology inAgabus uliginosusand the status ofA. lotti(Coleoptera, Dytiscidae)

Dettner,

Kovács,

Rewicz

et al. 2024

Preprint

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The taxonomic status of Agabus lotti within the Agabus uliginosus species group has been a subject of debate due to morphological similarities and lack of molecular data. In this study, we conducted a comprehensive morphological and molecular analysis of specimens from Central Europe, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A. lotti to A. uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A. lotti should be regarded as a junior synonym of A. uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Age-dependent variation of aedeagal morphology inAgabus uliginosusand the status ofA. lotti(Coleoptera, Dytiscidae)

Dettner,

Kovács,

Rewicz

et al. 2024

Preprint

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“…This is crucial for assessing the strengths and deficiencies of reference libraries. Without in-depth analysis, information gaps can be missed because major databases may not update their nomenclature regularly enough [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Lack of local genetic representation in one of the regions with the highest bird species richness, the Peruvian Amazonia

Arana,

Watsa

et al. 2024

PLoS ONE

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Peru ranks among the three countries with the highest bird species diversity globally and a majority of those species are found in the Peruvian Amazon. However, birds in this area are currently facing serious anthropogenic threats. Genetic and genomic methods are becoming important tools for avian biodiversity monitoring and conservation planning. Comprehensive molecular libraries that are publicly available are key to the effective deployment of these tools. We analyze the information gaps for four molecular markers in the most important genetic sequence databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, for bird species of the Peruvian Amazonia. We found that 64% of Peruvian Amazonian bird species have gene sequences for COI, 59.5% have CYTB sequences, 16.4% have 12S sequences, and only 0.6% have 18S sequences. However, these numbers decrease drastically to 4.3% for COI sequences when we only consider specimens sampled in Peru. Our data also showed that 43.8% of Peruvian Amazonian endemic species (n = 32) are missing sequences of any screened marker uploaded to GenBank or BOLD. Our results will encourage and guide efforts of the scientific community to complete reference libraries for Peruvian avian species that will be useful for future DNA-based monitoring projects that include birds.

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“…In conclusion, despite the small focus area, this study revealed a number of new cryptic and potentially endemic mitochondrial lineages, barcodes of species new to BOLD and previously unrecorded taxa that cannot be clearly distinguished using COI alone. Above all, however, it has significantly improved the BOLD database by expertly identifying mayfly species and has clearly indicated the path to follow if we are to achieve an error‐free, feasible DNA barcode library (Csabai et al., 2023). However, other initiatives from areas without barcode‐based records, such as known biodiversity hotspots in the Carpathians or the Mediterranean, are more than crucial for the meaningful enrichment of the BOLD database.…”

Section: Discussionmentioning

confidence: 99%

“…Above all, however, it has significantly improved the BOLD database by expertly identifying mayfly species and has clearly indicated the path to follow if we are to achieve an error-free, feasible DNA barcode library (Csabai et al, 2023). However, other initiatives from areas without barcode-based records, such as known biodiversity hotspots in the Carpathians or the Mediterranean, are more than crucial for the meaningful enrichment of the BOLD database.…”

Section: Species With Low Genetic Divergence As Warnings For Dna Barc...mentioning

confidence: 99%

Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries

Macko,

Derka,

Čiamporová‐Zaťovičová

et al. 2024

Molecular Ecology Resources

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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 in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second‐most species‐rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non‐existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum‐likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.

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50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead

Cited by 12 publications

References 70 publications

Age-dependent variation of aedeagal morphology inAgabus uliginosusand the status ofA. lotti(Coleoptera, Dytiscidae)

Age-dependent variation of aedeagal morphology inAgabus uliginosusand the status ofA. lotti(Coleoptera, Dytiscidae)

Lack of local genetic representation in one of the regions with the highest bird species richness, the Peruvian Amazonia

Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries

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