DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification
The <i>COI</i> gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences of Tetrigidae, an understudied ortho...
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MDPI AG
2023-05-01
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| Online Access: | https://www.mdpi.com/1424-2818/15/6/696 |
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| author | Niko Kasalo Josip Skejo Martin Husemann |
| author_facet | Niko Kasalo Josip Skejo Martin Husemann |
| author_sort | Niko Kasalo |
| collection | DOAJ |
| description | The <i>COI</i> gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences of Tetrigidae, an understudied orthopteran family with unresolved taxonomy and species that are difficult to identify. In this paper, we provide a summary of the metadata provided with the <i>COI</i> sequences and present a phylogenetic analysis of photographically vouchered sequences using Maximum Likelihood and Bayesian analysis. We found that (1) the subfamily Tetriginae is disproportionately represented in the dataset, (2) most of the records are not identified beyond the family level, (3) most regions, except for Costa Rica, are undersampled, (4) most of the sequences do not have photographic vouchers, and (5) the taxonomic backbone of BOLD is out of date. The phylogenetic analysis showed that the clusters of <i>COI</i> barcodes mostly correspond to species, but some clusters remain ambiguous. The deeper nodes in the phylogenetic trees are not well-supported, indicating that this gene has a very weak phylogenetic signal beyond the specific level. |
| first_indexed | 2024-03-11T02:35:18Z |
| format | Article |
| id | doaj.art-e57ae4582a8b4750b1d72bbf67e49f2a |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-11T02:35:18Z |
| publishDate | 2023-05-01 |
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| record_format | Article |
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| spelling | doaj.art-e57ae4582a8b4750b1d72bbf67e49f2a2023-11-18T10:02:14ZengMDPI AGDiversity1424-28182023-05-0115669610.3390/d15060696DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species IdentificationNiko Kasalo0Josip Skejo1Martin Husemann2Matice hrvatske 11, 80101 Livno, Bosnia and HerzegovinaEvolution Lab, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, CroatiaZoologisches Museum Hamburg, Leibniz Institut zur Analyse des Biodiversitätswandels, Martin-Luther-King-Platz 3, 20146 Hamburg, GermanyThe <i>COI</i> gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences of Tetrigidae, an understudied orthopteran family with unresolved taxonomy and species that are difficult to identify. In this paper, we provide a summary of the metadata provided with the <i>COI</i> sequences and present a phylogenetic analysis of photographically vouchered sequences using Maximum Likelihood and Bayesian analysis. We found that (1) the subfamily Tetriginae is disproportionately represented in the dataset, (2) most of the records are not identified beyond the family level, (3) most regions, except for Costa Rica, are undersampled, (4) most of the sequences do not have photographic vouchers, and (5) the taxonomic backbone of BOLD is out of date. The phylogenetic analysis showed that the clusters of <i>COI</i> barcodes mostly correspond to species, but some clusters remain ambiguous. The deeper nodes in the phylogenetic trees are not well-supported, indicating that this gene has a very weak phylogenetic signal beyond the specific level.https://www.mdpi.com/1424-2818/15/6/696batrachideinaeBOLD Systems<i>COI</i>taxonomydatabase curationmetadata |
| spellingShingle | Niko Kasalo Josip Skejo Martin Husemann DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification Diversity batrachideinae BOLD Systems <i>COI</i> taxonomy database curation metadata |
| title | DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification |
| title_full | DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification |
| title_fullStr | DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification |
| title_full_unstemmed | DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification |
| title_short | DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification |
| title_sort | dna barcoding of pygmy hoppers the first comprehensive overview of the bold systems data shows promise for species identification |
| topic | batrachideinae BOLD Systems <i>COI</i> taxonomy database curation metadata |
| url | https://www.mdpi.com/1424-2818/15/6/696 |
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