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Dominiak P, Szadziewski R. Taxonomic status of two European sibling and barcode-sharing species of Brachypogon Kieffer, 1899 (Diptera: Ceratopogonidae). Zootaxa 2023; 5319:145-147. [PMID: 37518242 DOI: 10.11646/zootaxa.5319.1.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Patrycja Dominiak
- Tromsø University Museum; UiT - The Arctic University of Norway; NO-9037 Tromsø; Norway.
| | - Ryszard Szadziewski
- Department of Invertebrate Zoology and Parasitology; Faculty of Biology; University of Gdańsk; Wita Stwosza 59; 80-308 Gdańsk; Poland.
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2
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Bourque DA, Morey KC, Bradley DL, Fost B, Daley JM, Jacobson N, Naaum AM, Hanner RH. Dimethyldimethyl Hydantoin: An Alternative Fluid for Morphological and Genetic Preservation. Biopreserv Biobank 2020; 18:283-289. [PMID: 32522020 DOI: 10.1089/bio.2020.0001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Modern taxonomy requires the preservation of biospecimens for both morphological and molecular applications. The utility of a previously identified preservative, dimethyldimethylhydantoin hydantoin (Dekafald®), to retain both physical diagnostic traits and the DNA integrity of biological specimens remains unknown. Using 439 eggs and 414 larvae from two North American fish species, we compared three hydantoin solutions at different concentrations (5%, 10%, and 20%) with gold standard preservatives (10% buffered formalin, 95% ethanol) to evaluate morphological trait retention up to 90 days, and DNA barcoding success up to 56 days. While the 5% hydantoin solution had the most sequencing success by 56 days, the 10% hydantoin solution was the best multipurpose preservative. Future work should assess the performance of ∼10% hydantoin solution over longer time periods, and its applicability to other taxa such as Arthropoda.
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Affiliation(s)
- Danielle A Bourque
- Department of Integrative Biology, The University of Guelph, Guelph, Ontario, Canada
| | - Kevin C Morey
- Department of Integrative Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Brooks Fost
- ASA Analysis and Communication, Marlboro, New York, USA
| | | | | | - Amanda M Naaum
- Department of Integrative Biology, The University of Guelph, Guelph, Ontario, Canada
| | - Robert H Hanner
- Department of Integrative Biology, The University of Guelph, Guelph, Ontario, Canada
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3
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Salvi D, Berrilli E, D'Alessandro P, Biondi M. Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae). PLoS One 2020; 15:e0233573. [PMID: 32437469 PMCID: PMC7241800 DOI: 10.1371/journal.pone.0233573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Emanuele Berrilli
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Paola D'Alessandro
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Maurizio Biondi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
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4
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Jiruskova A, Motyka M, Bocek M, Bocak L. The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles. PeerJ 2019; 7:e6511. [PMID: 30863675 PMCID: PMC6407506 DOI: 10.7717/peerj.6511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 01/22/2019] [Indexed: 02/04/2023] Open
Abstract
We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
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Affiliation(s)
- Alice Jiruskova
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Michal Motyka
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
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5
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Bocek M, Bocak L. Species limits in polymorphic mimetic Eniclases net-winged beetles from New Guinean mountains (Coleoptera, Lycidae). Zookeys 2016:15-35. [PMID: 27408550 PMCID: PMC4926628 DOI: 10.3897/zookeys.593.7728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/20/2016] [Indexed: 01/31/2023] Open
Abstract
Species delimitation was compared in a group of closely related lineages of aposematically colored Eniclases (Coleoptera, Lycidae) using morphology, genetic distances, and Bayesian implementation of the Poisson Tree Processes model. A high diversity of net-winged beetles was found in previously unsampled regions of New Guinea and ten new species are described: Eniclasesbicolorsp. n., Eniclasesbokondinensissp. n., Eniclasesbrancucciisp. n., Eniclaseselelimensissp. n., Eniclasesinfuscatussp. n., Eniclasesnigersp. n., Eniclasespseudoapertussp. n., Eniclasespseudoluteolussp. n., Eniclasestikapurensissp. n., and Eniclasesvariabilissp. n. Different levels of genetic and morphological diversification were identified in various sister-species pairs. As a result, both morphological and molecular analyses are used to delimit species. Sister-species with uncorrected pairwise genetic divergence as low as 0.45% were morphologically distinct not only in color pattern, but also in the relative size of eyes. Conversely, differences in color pattern regardless of their magnitude did not necessarily indicate genetic distance and intraspecific mimicry polymorphism was common. Additionally, genetic divergence without morphological differentiation was detected in one sister-species pair. Low dispersal propensity, diverse mimicry patterns, and mimetic polymorphism resulted in complex diversification of Eniclases and uncertain species delimitation in recently diversified lineages.
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Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. Listopadu 50, 771 46 Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. Listopadu 50, 771 46 Olomouc, Czech Republic
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Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015; 32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Matthew L Gimmel
- Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic
| | | | - Timothy D Cockerill
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chey Vun Khen
- Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
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Gómez‐Rodríguez C, Crampton‐Platt A, Timmermans MJTN, Baselga A, Vogler AP. Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12376] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Carola Gómez‐Rodríguez
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Departamento de Zoología Facultad de Biología Universidad de Santiago de Compostela c/Lope Gómez de Marzoa s/n 15782 Santiago de Compostela Spain
| | - Alex Crampton‐Platt
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Genetics, Evolution and Environment University College London Gower Street London WC1E 6BT UK
| | - Martijn J. T. N. Timmermans
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Life Sciences Silwood Park Campus Imperial College London Ascot SL5 7PY UK
- Department of Natural Sciences Hendon Campus Middlesex University London NW4 4BT UK
| | - Andrés Baselga
- Departamento de Zoología Facultad de Biología Universidad de Santiago de Compostela c/Lope Gómez de Marzoa s/n 15782 Santiago de Compostela Spain
| | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum London SW7 5BD UK
- Department of Life Sciences Silwood Park Campus Imperial College London Ascot SL5 7PY UK
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