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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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Krivosheeva V, Solodovnikov A, Shulepov A, Semerikova D, Ivanova A, Salnitska M. Assessment of the DNA barcode libraries for the study of the poorly-known rove beetle (Staphylinidae) fauna of West Siberia. Biodivers Data J 2023; 11:e115477. [PMID: 38161489 PMCID: PMC10755746 DOI: 10.3897/bdj.11.e115477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024] Open
Abstract
Staphylinidae, or rove beetles, are one of the mega-diverse and abundant families of the ground-living terrestrial arthropods that is taxonomically poorly known even in the regions adjacent to Europe where the fauna has been investigated for the longest time. Since DNA barcoding is a tool to accelerate biodiversity research, here we explored if the currently-available COI barcode libraries are representative enough for the study of rove beetles of West Siberia. This is a vast region adjacent to Europe with poorly-known fauna of rove beetles and from where not a single DNA barcode has hitherto been produced for Staphylinidae. First, we investigated the faunal similarity between the rove beetle faunas of the climatically compatible West Siberia in Asia, Fennoscandia in Europe and Canada and Alaska in North America. Second, we investigated barcodes available for Staphylinidae from the latter two regions in BOLD and GenBank, the world's largest DNA barcode libraries. We conclude that the rather different rove beetle faunas of Fennoscandia, on the one hand and Canada and Alaska on the other hand, are well covered in both barcode libraries that complement each other. We also find that even without any barcodes originating from specimens collected in West Siberia, this coverage is helpful for the study of rove beetles there due to the significant number of widespread species shared between West Siberia and Fennoscandia and due to the even larger number of shared genera amongst all three investigated regions. For the first time, we compiled a literature-based checklist for 726 species of the West Siberian Staphylinidae supplemented by their occurrence dataset submitted to GBIF. Our script written for mining unique (i.e. not redundant) barcodes for a given geographic area across global libraries is made available here and can be adopted for any other regions.
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Affiliation(s)
- Valeria Krivosheeva
- X-BIO Institute, University of Tyumen, Tyumen, RussiaX-BIO Institute, University of TyumenTyumenRussia
| | - Alexey Solodovnikov
- Natural History Museum of Denmark, Copenhagen, DenmarkNatural History Museum of DenmarkCopenhagenDenmark
| | - Aleksandr Shulepov
- MAGNIT information technologies, Krasnodar, RussiaMAGNIT information technologiesKrasnodarRussia
| | - Darya Semerikova
- X-BIO Institute, University of Tyumen, Tyumen, RussiaX-BIO Institute, University of TyumenTyumenRussia
| | - Anastasiya Ivanova
- X-BIO Institute, University of Tyumen, Tyumen, RussiaX-BIO Institute, University of TyumenTyumenRussia
| | - Maria Salnitska
- X-BIO Institute, University of Tyumen, Tyumen, RussiaX-BIO Institute, University of TyumenTyumenRussia
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Mugnai F, Costantini F, Chenuil A, Leduc M, Gutiérrez Ortega JM, Meglécz E. Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies. PeerJ 2023; 11:e14616. [PMID: 36643652 PMCID: PMC9835706 DOI: 10.7717/peerj.14616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments. Methods We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency. Results The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).
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Affiliation(s)
- Francesco Mugnai
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy
| | - Federica Costantini
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | | | | | - Emese Meglécz
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
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Ottati S, Eberle J, Rulik B, Köhler F, Ahrens D. From DNA barcodes to ecology: Meta-analysis of central European beetles reveal link with species ecology but also to data pattern and gaps. Ecol Evol 2022; 12:e9650. [PMID: 36568864 PMCID: PMC9771709 DOI: 10.1002/ece3.9650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.
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Affiliation(s)
- Sara Ottati
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Jonas Eberle
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
- Department of Environment & BiodiversityUniversity of SalzburgSalzburgAustria
| | - Björn Rulik
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoTurinItaly
| | - Frank Köhler
- Coleopterological Research OfficeBornheimGermany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum A. Koenig (LIB)BonnGermany
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Goh KS, Wang LJ, Ni JH, Wang TY. Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies. PeerJ 2022; 10:e14195. [PMID: 36325176 PMCID: PMC9620971 DOI: 10.7717/peerj.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
Background Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat. Methods In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016-2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species. Results Nine species-eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta-were morphologically identified. The nine species could be found in April-August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the λ max of studied species ranged from 552-572 nm (yellow-green to orange-yellow). The average luminescent intensity range of these species was about 1.2-14 lux (182.1-2,048 nW/cm2) for males and 0.8-5.8 lux (122.8-850 nW/cm2) for females, and the maximum luminescent intensity of males was 1.01-7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different λ max, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49-28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8-2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%-12.3% variation. This study renews the idea that fireflies' luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange-yellow color in some derived species.
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Affiliation(s)
- King-Siang Goh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Jing-Han Ni
- Department of Ecological Humanities, Providence University, Taichung, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Sánchez-Vialas A, Ruiz JL, Recuero E, Gutiérrez-Pérez F, García-París M. A new systematic arrangement for the blister beetle genus Eurymeloe (Meloini, Meloidae, Coleoptera) with the description of a new species from Spain. Zookeys 2022; 1109:17-48. [PMID: 36762342 PMCID: PMC9848860 DOI: 10.3897/zookeys.1109.83863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
The taxonomic status and subgeneric arrangement of the genus Eurymeloe have been debated for decades. In this work, the internal taxonomy of Eurymeloe is redefined by recognising three subgenera: Eurymeloe for the former Eurymeloebrevicollis species group, Coelomeloe for Eurymeloetuccia, and Bolognaia Ruiz, García-París, Sánchez-Vialas & Recuero, subgen. nov., to accommodate the species of the formerly recognised Eurymeloerugosus species group. Additionally, a new species of the newly described subgenus Bolognaia is described from the Iberian Peninsula based on molecular and morphological traits. The new species, Eurymeloe (Bolognaia) orobatessp. nov., can be distinguished from all other species of Eurymeloe by the following combination of morphological traits: dispersed brownish setae over the body that are arranged in small tufts on the abdominal terga; a small, very transverse pronotum that presents a unique macrosculpture; a deeply and densely punctured integument of the head and pronotum; and the very rugose elytra. The characters displayed by E.orobates suggest that the species groups that were previously defined and recognised for Eurymeloe, and that are now integrated within the newly erected subgenus Bolognaia, are non-monophyletic.
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Affiliation(s)
- Alberto Sánchez-Vialas
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), calle José Gutiérrez Abascal 2, 28006, Madrid, SpainMuseo Nacional de Ciencias NaturalesMadridSpain
| | - José L. Ruiz
- Instituto de Estudios Ceutíes, Paseo del Revellín 30, 51001 Ceuta, SpainInstituto de Estudios CeutíesCeutaSpain
| | - Ernesto Recuero
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), calle José Gutiérrez Abascal 2, 28006, Madrid, SpainMuseo Nacional de Ciencias NaturalesMadridSpain,Department of Plant & Environmental Sciences, Clemson University, Clemson, SC 29634, USAClemson UniversityClemsonUnited States of America
| | | | - Mario García-París
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), calle José Gutiérrez Abascal 2, 28006, Madrid, SpainMuseo Nacional de Ciencias NaturalesMadridSpain
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Kaczmarek M, Entling MH, Hoffmann C. Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort. INSECTS 2022; 13:insects13060507. [PMID: 35735844 PMCID: PMC9224819 DOI: 10.3390/insects13060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.
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Affiliation(s)
- Marvin Kaczmarek
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
- Correspondence:
| | - Martin H. Entling
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
| | - Christoph Hoffmann
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
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Ranasinghe UGSL, Eberle J, Thormann J, Bohacz C, Benjamin SP, Ahrens D. Multiple species delimitation approaches with
COI
barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae). Ecol Evol 2022; 12:e8942. [PMID: 35600695 PMCID: PMC9120212 DOI: 10.1002/ece3.8942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022] Open
Abstract
DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.
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Affiliation(s)
| | - Jonas Eberle
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- University of Salzburg Salzburg Austria
| | - Jana Thormann
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Suresh P. Benjamin
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- National Institute of Fundamental Studies Kandy Sri Lanka
| | - Dirk Ahrens
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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Drake LE, Cuff JP, Young RE, Marchbank A, Chadwick EA, Symondson WOC. An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Jordan P. Cuff
- School of Biosciences Cardiff University Cardiff UK
- Rothamsted Insect Survey, Rothamsted Research West Common Harpenden UK
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DNA barcoding in Dorcadionini (Coleoptera, Cerambycidae) uncovers mitochondrial-morphological discordance and the hybridogenic origin of several subspecies. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Rajabizadeh M, Morinière J, Rajaei H. Adaptation to the hottest spot on earth: Dietary ecology of an enigmatic desert gecko based on DNA metabarcoding. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahdi Rajabizadeh
- Department of Biodiversity Institute of Science and High Technology and Environmental Sciences Graduate University of Advanced Technology Kerman Iran
- Inria Startup StudioAI.Nature Team Paris France
| | - Jérôme Morinière
- Advanced Identification Methods – AIM GmbH Niemeyerstr 1 Leipzig Germany
| | - Hossein Rajaei
- Entomology Department State Museum of Natural History Stuttgart Germany
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Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
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Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
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Lukic D, Eberle J, Thormann J, Holzschuh C, Ahrens D. Excluding spatial sampling bias does not eliminate oversplitting in DNA-based species delimitation analyses. Ecol Evol 2021; 11:10327-10337. [PMID: 34367578 PMCID: PMC8328443 DOI: 10.1002/ece3.7836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.
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Affiliation(s)
- Daniel Lukic
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | - Jonas Eberle
- Zoologische EvolutionsbiologieParis‐Lodron‐UniversitätSalzburgAustria
| | - Jana Thormann
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | | | - Dirk Ahrens
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
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14
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Brunke AJ, Pentinsaari M, Klimaszewski J. Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae). Zookeys 2021; 1041:27-99. [PMID: 34140825 PMCID: PMC8184736 DOI: 10.3897/zookeys.1041.64460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022] Open
Abstract
A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossatriangularis Klimaszewski, Brunke & Pentinsaari, sp. nov. from British Columbia; Gnypetaimpressicollis Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconotapseudogregaria Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygrapseudolaevicollis Klimaszewski, Brunke & Pentinsaari, sp. nov. from eastern Canada. Dasygnypetavelata and Philhygraangusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypetavelata (Erichson, 1839) = Gnypetaminuta Klimaszewski & Webster, 2008, syn. nov. and Philhygraangusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylotaochracea (and genus Hylota), Thecturotatenuissima, and Trichiusarobustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylotaochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturotatenuissima Casey, 1893 = Athetamarchii Dodero, 1922, syn. nov.; and Trichiusarobustula Casey, 1893 = T.immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarocharaforticornis, Anomognathuscuspidatus, Oligotapumilio, and Parocyusarubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusarubicunda (Erichson, 1837) = Chiloporaamericana Casey, 1906, syn. nov. and Anomognathuscuspidatus (Erichson, 1839) = Thecturaamericana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacradensissima (Bernhauer, 1909) = Gnypetasaccharina Klimaszewski & Webster, 2008, syn. nov. Native Cypheawallisi is newly reported from across Canada and C.curtula is removed from the Nearctic fauna. The status of both Gyrophaenaaffinis and Homalotaplana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypetabaranowskii (Klimaszewski, 2020) and D.nigrella (LeConte, 1863) (both from Gnypeta) and Mocytascopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronotascopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant & Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.
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Affiliation(s)
- Adam J Brunke
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada Canadian National Collection of Insects, Arachnids and Nematodes Ottawa Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, 50 Stone Road East, University of Guelph, Guelph, Ontario, N1G 2W1, Canada University of Guelph Guelph Canada
| | - Jan Klimaszewski
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, PO Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec Sainte-Foy, Québec Canada
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15
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Geiger M, Koblmüller S, Assandri G, Chovanec A, Ekrem T, Fischer I, Galimberti A, Grabowski M, Haring E, Hausmann A, Hendrich L, Koch S, Mamos T, Rothe U, Rulik B, Rewicz T, Sittenthaler M, Stur E, Tończyk G, Zangl L, Moriniere J. Coverage and quality of DNA barcode references for Central and Northern European Odonata. PeerJ 2021; 9:e11192. [PMID: 33986985 PMCID: PMC8101477 DOI: 10.7717/peerj.11192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background Dragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches. Methods This study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD. Results Over 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges.
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Affiliation(s)
- Matthias Geiger
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK) - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | - Giacomo Assandri
- Area per l'Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, BO, Italy
| | - Andreas Chovanec
- Federal Ministry of Agriculture, Regions and Tourism, Vienna, Austria
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Iris Fischer
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Andrea Galimberti
- Department of Biotechnology and Biosciences, ZooPlantLab, University of Milano - Bicocca, Milano, Italy
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Łódź, Poland
| | - Elisabeth Haring
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung, München, BY, Germany
| | - Lars Hendrich
- SNSB-Zoologische Staatssammlung, München, BY, Germany
| | - Stefan Koch
- Independent Researcher, Mindelheim, BY, Germany
| | - Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Łódź, Poland
| | - Udo Rothe
- Naturkundemuseum Potsdam, Potsdam, BB, Germany
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK) - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Łódź, Poland
| | - Marcia Sittenthaler
- Central Research Laboratories, Natural History Museum Vienna, Vienna, Austria
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Grzegorz Tończyk
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Łódź, Poland
| | - Lukas Zangl
- Institute of Biology, University of Graz, Graz, Steiermark, Austria.,ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Graz, Steiermark, Austria.,Universalmuseum Joanneum, Studienzentrum Naturkunde, Graz, Steiermark, Austria
| | - Jerome Moriniere
- AIM - Advanced Identification Methods GmbH, Leipzig, SN, Germany
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16
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Freitag H, de Vries R, Paterno M, Maestri S, Delledonne M, Thompson CG, Lamed H, Lambert R, Fox MF, Gonzalez MC, Delocado ED, Sabordo MR, Pangantihon CV, Njunjić I. Hydraena (s.str.) dinarica, new species (Coleoptera: Hydraenidae) along with further records of Hydraena spp. from Durmitor National Park, Montenegro and comments on the DNA barcoding problem with the genus. Biodivers Data J 2021; 9:e59892. [PMID: 33519262 PMCID: PMC7815695 DOI: 10.3897/bdj.9.e59892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
Background Long-palped Water Beetles were collected during a taxon expedition in Montenegro which involved citizen scientists, students and taxonomists. The material was collected from springs, brooks, fens and the Tara River, at altitudes between 600 m and 1450 m above sea level, using fine-meshed hand-nets and by manual checking of submerged substrates. The morphological species delimitation was supplemented and congruent with mtDNA sequences mainly obtained in the field using the newly-developed MinION-based ONTrack pipeline. New information The new species Hydraenadinarica Freitag & de Vries, sp. n. from Durmitor Mt. is described, illustrated and compared in detail to closely-related congeners of the H.saga d'Orchymont, 1930/H.emarginata Rey, 1885 species complex. Five additional species and female specimens of two unidentified morphospecies of the genus were also recorded in the vicinity of Durmitor National Park. New records and the first DNA barcodes for Hydraenabiltoni Jäch & Díaz, 2012 (endemic to Montenegro) and H.morio Kiesenwetter, 1849 are provided. Further records of H.nigrita Germar, 1824, H.minutissima Stephens, 1829, H.subintegra Ganglbauer, 1901 and females of two unidentified morphospecies are commented upon. The resulting inter- and intraspecific genetic distances and some observations of low or zero sequence divergence between recently-diverged species of Hydraena Kugelann, 1794 are briefly discussed.
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Affiliation(s)
- Hendrik Freitag
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Rick de Vries
- Amstelveenseweg 980B, Amsterdam, Netherlands Amstelveenseweg 980B Amsterdam Netherlands
| | - Marta Paterno
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Simone Maestri
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Massimo Delledonne
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Cameron G Thompson
- Oxford Brookes University, Department of Health and Life Sciences, Oxford, United Kingdom Oxford Brookes University, Department of Health and Life Sciences Oxford United Kingdom
| | - Helena Lamed
- 39 av Melbourne, Mont-Royal, Quebec, Canada 39 av Melbourne, Mont-Royal Quebec Canada
| | - Rebekah Lambert
- 340 N. Adams Street, Eugene, Oregon, United States of America 340 N. Adams Street Eugene, Oregon United States of America
| | - Michael F Fox
- 340 N. Adams Street, Eugene, Oregon, United States of America 340 N. Adams Street Eugene, Oregon United States of America
| | - Mariela C Gonzalez
- Taxon Expeditions, Rembrandtstraat 20, Leiden, Netherlands Taxon Expeditions, Rembrandtstraat 20 Leiden Netherlands
| | - Emmanuel D Delocado
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Marc R Sabordo
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Clister V Pangantihon
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Iva Njunjić
- Taxon Expeditions, Rembrandtstraat 20, Leiden, Netherlands Taxon Expeditions, Rembrandtstraat 20 Leiden Netherlands.,Naturalis Biodiversity Center, Darwinweg 2, Leiden, Netherlands Naturalis Biodiversity Center, Darwinweg 2 Leiden Netherlands
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17
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Behrens-Chapuis S, Herder F, Geiger MF. Adding DNA barcoding to stream monitoring protocols - What's the additional value and congruence between morphological and molecular identification approaches? PLoS One 2021; 16:e0244598. [PMID: 33395693 PMCID: PMC7781668 DOI: 10.1371/journal.pone.0244598] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.
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Affiliation(s)
| | - Fabian Herder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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18
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Fontes JT, Vieira PE, Ekrem T, Soares P, Costa FO. BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries. Mol Ecol Resour 2020; 21:573-583. [PMID: 33000878 DOI: 10.1111/1755-0998.13262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023]
Abstract
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
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Affiliation(s)
- João T Fontes
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Pedro E Vieira
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Pedro Soares
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Filipe O Costa
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
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19
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Hardulak LA, Morinière J, Hausmann A, Hendrich L, Schmidt S, Doczkal D, Müller J, Hebert PDN, Haszprunar G. DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species. Mol Ecol Resour 2020; 20:1542-1557. [PMID: 32559020 DOI: 10.1111/1755-0998.13212] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.
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Affiliation(s)
- Laura A Hardulak
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Lars Hendrich
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Jörg Müller
- National Park Bavarian Forest, Grafenau, Germany.,Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Rauhenebrach, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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20
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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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21
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Hausmann A, Segerer AH, Greifenstein T, Knubben J, Morinière J, Bozicevic V, Doczkal D, Günter A, Ulrich W, Habel JC. Toward a standardized quantitative and qualitative insect monitoring scheme. Ecol Evol 2020; 10:4009-4020. [PMID: 32489627 PMCID: PMC7244892 DOI: 10.1002/ece3.6166] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/19/2020] [Indexed: 12/21/2022] Open
Abstract
The number of insect species and insect abundances decreased severely during the past decades over major parts of Central Europe. Previous studies documented declines of species richness, abundances, shifts in species composition, and decreasing biomass of flying insects. In this study, we present a standardized approach to quantitatively and qualitatively assess insect diversity, biomass, and the abundance of taxa, in parallel. We applied two methods: Malaise traps, and automated and active light trapping. Sampling was conducted from April to October 2018 in southern Germany, at four sites representing conventional and organic farming. Bulk samples obtained from Malaise traps were further analyzed using DNA metabarcoding. Larger moths (Macroheterocera) collected with light trapping were further classified according to their degree of endangerment. Our methods provide valuable quantitative and qualitative data. Our results indicate more biomass and higher species richness, as well as twice the number of Red List lepidopterans in organic farmland than in conventional farmland. This combination of sampling methods with subsequent DNA metabarcoding and assignments of individuals according depending on ecological characteristics and the degree of endangerment allows to evaluate the status of landscapes and represents a suitable setup for large-scale long-term insect monitoring across Central Europe, and elsewhere.
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Affiliation(s)
| | | | | | | | - Jerôme Morinière
- Bavarian Natural History CollectionsMunichGermany
- Advanced Identification Methods GmbH (AIM)MunichGermany
| | | | | | | | - Werner Ulrich
- Department of Ecology and BiogeographyNicolaus Copernicus University TorunToruńPoland
| | - Jan Christian Habel
- Evolutionary ZoologyDepartment of BiosciencesUniversity of SalzburgSalzburgAustria
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22
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Richardson RT, Sponsler DB, McMinn‐Sauder H, Johnson RM. MetaCurator: A hidden Markov model‐based toolkit for extracting and curating sequences from taxonomically‐informative genetic markers. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13314] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Douglas B. Sponsler
- Department of Entomology Pennsylvania State University University Park PA USA
- Department of Botany The Academy of Natural Sciences of Drexel University Philadelphia PA USA
| | | | - Reed M. Johnson
- Department of Entomology The Ohio State University Columbus OH USA
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23
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Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele JW, Hebert PDN. A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Mol Ecol Resour 2019; 19:900-928. [PMID: 30977972 PMCID: PMC6851627 DOI: 10.1111/1755-0998.13022] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 11/29/2022]
Abstract
This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.
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Affiliation(s)
| | | | | | - Matthias F Geiger
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | | | | | | | | | - Björn Rulik
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | - Johann-Wolfgang Wägele
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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24
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Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, Pokorny L, Rahbek C, Sandel B, Smith SA, Stamatakis A, Vos RA, Warnow T, Baker WJ. A roadmap for global synthesis of the plant tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:614-622. [PMID: 29603138 DOI: 10.1002/ajb2.1041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/08/2017] [Indexed: 06/08/2023]
Abstract
Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.
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Affiliation(s)
- Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
- Department of Bioscience, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs Gata 22B, SE-413 19, Gothenburg, Sweden
| | - Dominic J Bennett
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs Gata 22B, SE-413 19, Gothenburg, Sweden
| | | | | | | | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
| | - Jan T Kim
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
| | - Alexey M Kozlov
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118, Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
| | - Brian S Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, 92093, USA
| | - William H Piel
- Yale-NUS College, 16 College Avenue West, Singapore, 138527, Republic of Singapore
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen O, Denmark
- Imperial College London, Silwood Park, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Brody Sandel
- Department of Biology, Santa Clara University, Santa Clara, CA, 95053, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76128, Karlsruhe, Germany
| | - Rutger A Vos
- Naturalis Biodiversity Center, P.O. Box 9517, 2300RA, Leiden, The Netherlands
- Institute of Biology Leiden, P.O. Box 9505, 2300RA, Leiden, The Netherlands
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Suprayitno N, Narakusumo RP, von Rintelen T, Hendrich L, Balke M. Taxonomy and Biogeography without frontiers - WhatsApp, Facebook and smartphone digital photography let citizen scientists in more remote localities step out of the dark. Biodivers Data J 2017:e19938. [PMID: 29104436 PMCID: PMC5665057 DOI: 10.3897/bdj.5.e19938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/22/2017] [Indexed: 11/12/2022] Open
Abstract
Background Taxonomy and biogeography can benefit from citizen scientists. The use of social networking and open access cooperative publishing can easily connect naturalists even in more remote areas with in-country scientists and institutions, as well as those abroad. This enables taxonomic efforts without frontiers and at the same time adequate benefit sharing measures. New information We present new distribution and habitat data for diving beetles of Bali island, Indonesia, as a proof of concept. The species Hydaticusluczonicus Aubé, 1838 and Eretesgriseus (Fabricius, 1781) are reported from Bali for the first time. The total number of Dytiscidae species known from Bali is now 34.
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Affiliation(s)
| | - Raden Pramesa Narakusumo
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
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