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Janko Š, Rok Š, Blaž K, Danilo B, Andrej G, Denis K, Klemen Č, Matjaž G. DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors. Mol Ecol Resour 2024; 24:e13953. [PMID: 38523561 DOI: 10.1111/1755-0998.13953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.
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Affiliation(s)
- Šet Janko
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Šturm Rok
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Koderman Blaž
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Bevk Danilo
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Gogala Andrej
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Kutnjak Denis
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Čandek Klemen
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Gregorič Matjaž
- Jovan Hadži Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
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2
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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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3
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Vuataz L, Reding JP, Reding A, Roesti C, Stoffel C, Vinçon G, Gattolliat JL. A comprehensive DNA barcoding reference database for Plecoptera of Switzerland. Sci Rep 2024; 14:6322. [PMID: 38491157 PMCID: PMC10943188 DOI: 10.1038/s41598-024-56930-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.
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Affiliation(s)
- Laurent Vuataz
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland.
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland.
| | | | | | | | - Céline Stoffel
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland
| | | | - Jean-Luc Gattolliat
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland
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4
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Jospin A, Chittaro Y, Bolt D, Demergès D, Gurcel K, Hensle J, Sanchez A, Praz C, Lucek K. Genomic evidence for three distinct species in the Erebia manto complex in Central Europe (Lepidoptera, Nymphalidae). CONSERV GENET 2023; 24:293-304. [PMID: 37187800 PMCID: PMC10175325 DOI: 10.1007/s10592-023-01501-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringlet Erebia manto, which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priorities. Using several thousand nuclear genomic markers, we evaluated to which degree the bubastis lineage from the Alps and the vogesiaca lineage from the Vosges, are genetically isolated from the widespread manto lineage. Our results suggest that both lineages are genetically as strongly differentiated from manto as other taxonomically well separated sibling species in this genus from each other, supporting a delineation of bubastis and vogesiaca as independent species. Given the restricted and isolated range of vogesiaca as well as the disjunct distribution of bubastis, our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01501-w.
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Affiliation(s)
- Amanda Jospin
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | | | | | - David Demergès
- Conservatoire d’espaces Naturels de Lorraine, 20 Chemin de L’école Des Xettes, 88400 Gérardmer, France
| | | | | | - Andreas Sanchez
- Info Fauna, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Christophe Praz
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Info Fauna, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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5
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Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, Ahrens D. Standardized nuclear markers improve and homogenize species delimitation in Metazoa. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Paris‐Lodron‐University Salzburg Austria
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Sandra Kukowka
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Hannes Baur
- Naturhistorisches Museum Bern/Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Marianne Espeland
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Bernhard A. Huber
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Carl Hutter
- Museum of Natural Sciences and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Ximo Mengual
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Ralph S. Peters
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Miguel Vences
- Technische Universität Braunschweig Braunschweig Germany
| | - Thomas Wesener
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Keith Willmott
- Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert‐Ludwigs‐Universität Freiburg Freiburg im Breisgau Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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6
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Zhang YM, Sheikh SI, Ward AKG, Forbes AA, Prior KM, Stone GN, Gates MW, Egan SP, Zhang L, Davis C, Weinersmith KL, Melika G, Lucky A. Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data. Mol Ecol 2022; 31:4417-4433. [PMID: 35762844 DOI: 10.1111/mec.16582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.
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Affiliation(s)
- Y Miles Zhang
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Washington, DC, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Sofia I Sheikh
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Anna K G Ward
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Kirsten M Prior
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Washington, DC, USA
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Linyi Zhang
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Charles Davis
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Entomology, Pennsylvania State University, University Park, PA, USA
| | | | - George Melika
- Plant Health and Molecular Biology Laboratory, Directorate of Plant Protection, Budapest, Hungary
| | - Andrea Lucky
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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7
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Azevedo GHF, Bougie T, Carboni M, Hedin M, Ramírez MJ. Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha). Mol Phylogenet Evol 2021; 166:107327. [PMID: 34666169 DOI: 10.1016/j.ympev.2021.107327] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.
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Affiliation(s)
- Guilherme H F Azevedo
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina; Dept of Biology, San Diego State University, San Diego, CA 92182, United States.
| | - Tierney Bougie
- Dept of Biology, San Diego State University, San Diego, CA 92182, United States; Evolution, Ecology, and Organismal Biology Department, University of California, Riverside, Riverside, CA 92521, United States
| | - Martin Carboni
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Marshal Hedin
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Martín J Ramírez
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"- CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
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8
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Litman JR, Fateryga AV, Griswold TL, Aubert M, Proshchalykin MY, Le Divelec R, Burrows S, Praz CJ. Paraphyly and low levels of genetic divergence in morphologically distinct taxa: revision of the Pseudoanthidium scapulare complex of carder bees (Apoidea: Megachilidae: Anthidiini). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Palaearctic complex of anthidiine bees closely related to Pseudoanthidium scapulare has long been a source of unresolved taxonomic and systematic issues. Until now, the number of species in the complex and their geographical distributions were largely unclear, thus complicating the compilation of accurate species checklists and hindering conservation efforts. In order to address these issues, we use morphology and mitochondrial cytochrome c oxidase subunit I (COI) sequences, combined with a thorough examination of the relevant literature and type material, to delimit species within this complex, assign names to species and clarify geographical ranges. An unexpected result was that a certain number of morphologically distinct taxa exhibited low levels of genetic divergence at the COI locus, resulting in species paraphyly. A set of ultra-conserved elements (UCEs) was also sequenced in order to further investigate relationships among these taxa. One morphologically distinct species was also paraphyletic using UCE data, hinting at recent species divergences and genetic exchange at zones of contact between morphologically well-differentiated taxa. The results of our study reveal the presence of ten species in this complex, including a previously overlooked species for western continental Europe. A complete diagnosis of the males and females of these species is provided, as are maps detailing the geographic distributions of each. An illustrated identification key to the males and females of each species is presented. Two new species are described, Pseudoanthidium kaspareki sp. nov. and P. rozeni sp. nov. New synonymy is established for several species and Pseudoanthidium palestinicum and P. tropicum are raised to species level. The new combination, Icteranthidium floripetum comb. nov. is also established. Lectotypes are designated for the following species: Anthidium eversmanni, A. floripetum, A. frontale, A. karakalense, A. nanum and A. reptans. Previously unpublished lectotype designations are published here for A. sinuatum and A. tenellum.
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Affiliation(s)
- Jessica R Litman
- Muséum d’histoire naturelle de Neuchâtel, Terreaux 14, 2000 Neuchâtel, Switzerland
| | - Alexander V Fateryga
- T. I. Vyazemsky Karadag Scientific Station – Nature Reserve of RAS – Branch of A. O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Feodosiya, 298188, Crimea, Russia
| | - Terry L Griswold
- USDA-ARS Pollinating Insects Research Unit, Logan, Utah 84322, USA
| | - Matthieu Aubert
- Observatoire des Abeilles, Route de Pégairolles, 34380 Saint-Jean-de-Buèges, France
| | - Maxim Yu Proshchalykin
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Romain Le Divelec
- Observatoire des Abeilles, 87 rue de Courcelles, 75017 Paris, France
| | - Skyler Burrows
- Utah State University, Department of Biology, 5200 Old Main Hill, Logan, Utah, USA
| | - Christophe J Praz
- University of Neuchâtel, Institute of Biology, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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9
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Maggioni D, Assandri G, Ramazzotti F, Magnani D, Pellegrino I, Valsecchi E, Galimberti A. Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1896795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- D. Maggioni
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
- Marine Research and High Education (MaRHE) Center, University of Milano - Bicocca, Faafu Magoodhoo, Maldives
| | - G. Assandri
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Italy
| | - F. Ramazzotti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - D. Magnani
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - I. Pellegrino
- Department of Sciences and Technological Innovation (DISIT), University of Eastern Piedmont, Alessandria, Italy
| | - E. Valsecchi
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
| | - A. Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
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10
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Villalta I, Ledet R, Baude M, Genoud D, Bouget C, Cornillon M, Moreau S, Courtial B, Lopez-Vaamonde C. A DNA barcode-based survey of wild urban bees in the Loire Valley, France. Sci Rep 2021; 11:4770. [PMID: 33637824 PMCID: PMC7910470 DOI: 10.1038/s41598-021-83631-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/08/2021] [Indexed: 11/11/2022] Open
Abstract
The current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes of wild bee decline. Effective insect monitoring relies on both mass-trapping methods coupled with rapid and accurate identifications. Identifying wild bees using only morphology can be challenging, in particular, specimens from mass-trapped samples which are often in poor condition. We generated DNA barcodes for 2931 specimens representing 157 species (156 named and one unnamed species) and 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total of 36 species (22.93%) were found in highly urbanized areas. The majority of specimens, representing 96.17% of the species barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related species notoriously difficult to identify. A total of 137 species (87.26%) show a "one-to-one" match between a named species and the BIN assignment. Fourteen species (8.92%) show deep conspecific lineages with no apparent morphological differentiation. Only two species pairs shared the same BIN making their identification with DNA barcodes alone uncertain. Therefore, our DNA barcoding reference library allows reliable identification by non-experts for the vast majority of wild bee species in the Loire Valley.
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Affiliation(s)
- Irene Villalta
- IRBI, UMR 7261, CNRS, Université de Tours, Tours, France.
| | - Romain Ledet
- INRAE USC 1328, LBLGC EA 1207, Université d'Orléans, Orléans, France
| | - Mathilde Baude
- INRAE USC 1328, LBLGC EA 1207, Université d'Orléans, Orléans, France
| | | | | | | | | | | | - Carlos Lopez-Vaamonde
- IRBI, UMR 7261, CNRS, Université de Tours, Tours, France
- INRAE, URZF, Orléans, France
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Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry JF, Laštůvka A, Laštůvka Z, Lee KM, Lees DC, Mutanen M, van Nieukerken EJ, Segerer AH, Triberti P, Wieser C, Rougerie R. Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.
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