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Ganbaatar B, Li Q, Xi O, Cao H, Zhu C. One Step beyond Species Description: Unveiling a Fine-Scale Diversity within the Genus Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae). INSECTS 2024; 15:406. [PMID: 38921121 PMCID: PMC11203707 DOI: 10.3390/insects15060406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar & Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia.
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Affiliation(s)
- Bolormaa Ganbaatar
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (B.G.); (C.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Qin Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (Q.L.); (O.X.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830046, China
| | - Ouyan Xi
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (Q.L.); (O.X.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830046, China
| | - Huanxi Cao
- National Animal Collection Resource Center, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (B.G.); (C.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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2
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Cruaud A, Rasplus JY, Zhang J, Burks R, Delvare G, Fusu L, Gumovsky A, Huber JT, Janšta P, Mitroiu MD, Noyes JS, van Noort S, Baker A, Böhmová J, Baur H, Blaimer BB, Brady SG, Bubeníková K, Chartois M, Copeland RS, Dale-Skey Papilloud N, Dal Molin A, Dominguez C, Gebiola M, Guerrieri E, Kresslein RL, Krogmann L, Lemmon E, Murray EA, Nidelet S, Nieves-Aldrey JL, Perry RK, Peters RS, Polaszek A, Sauné L, Torréns J, Triapitsyn S, Tselikh EV, Yoder M, Lemmon AR, Woolley JB, Heraty JM. The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps. Cladistics 2024; 40:34-63. [PMID: 37919831 DOI: 10.1111/cla.12561] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023] Open
Abstract
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Roger Burks
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Gérard Delvare
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Lucian Fusu
- Faculty of Biology, Alexandru Ioan Cuza University, Iasi, Romania
| | - Alex Gumovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - John T Huber
- Natural Resources Canada, c/o Canadian National Collection of Insects, Ottawa, Ontario, Canada
| | - Petr Janšta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| | | | - John S Noyes
- Insects Division, Natural History Museum, London, UK
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Austin Baker
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Julie Böhmová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hannes Baur
- Department of Invertebrates, Natural History Museum Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Bonnie B Blaimer
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Seán G Brady
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Kristýna Bubeníková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marguerite Chartois
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Robert S Copeland
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | | | - Ana Dal Molin
- Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Chrysalyn Dominguez
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Marco Gebiola
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Emilio Guerrieri
- Insects Division, Natural History Museum, London, UK
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Robert L Kresslein
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Lars Krogmann
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
- Institute of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Emily Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Ryan K Perry
- Department of Plant Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Ralph S Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | | | - Laure Sauné
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Javier Torréns
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR-CONICET), Anillaco, Argentina
| | - Serguei Triapitsyn
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | | | - Matthew Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida, USA
| | - James B Woolley
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - John M Heraty
- Department of Entomology, University of California Riverside, Riverside, California, USA
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Xu X, Hoffmann AA, Umina PA, Ward SE, Coquilleau MP, Malipatil MB, Ridland PM. Molecular identification of hymenopteran parasitoids and their endosymbionts from agromyzids. BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:481-496. [PMID: 37278210 DOI: 10.1017/s0007485323000160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Three polyphagous pest Liriomyza spp. (Diptera: Agromyzidae) have recently invaded Australia and are damaging horticultural crops. Parasitic wasps are recognized as effective natural enemies of leafmining species globally and are expected to become important biocontrol agents in Australia. However, the hymenopteran parasitoid complex of agromyzids in Australia is poorly known and its use hindered due to taxonomic challenges when based on morphological characters. Here, we identified 14 parasitoid species of leafminers based on molecular and morphological data. We linked DNA barcodes (5' end cytochrome c oxidase subunit I (COI) sequences) to five adventive eulophid wasp species (Chrysocharis pubicornis (Zetterstedt), Diglyphus isaea (Walker), Hemiptarsenus varicornis (Girault), Neochrysocharis formosa (Westwood), and Neochrysocharis okazakii Kamijo) and two braconid species (Dacnusa areolaris (Nees) and Opius cinerariae Fischer). We also provide the first DNA barcodes (5' end COI sequences) with linked morphological characters for seven wasp species, with three identified to species level (Closterocerus mirabilis Edwards & La Salle, Trigonogastrella parasitica (Girault), and Zagrammosoma latilineatum Ubaidillah) and four identified to genus (Aprostocetus sp., Asecodes sp., Opius sp. 1, and Opius sp. 2). Phylogenetic analyses suggest C. pubicornis, D. isaea, H. varicornis, and O. cinerariae are likely cryptic species complexes. Neochrysocharis formosa and Aprostocetus sp. specimens were infected with Rickettsia. Five other species (Cl. mirabilis, D. isaea, H. varicornis, Opius sp. 1, and Opius sp. 2) were infected with Wolbachia, while two endosymbionts (Rickettsia and Wolbachia) co-infected N. okazakii. These findings provide background information about the parasitoid fauna expected to help control the leafminers.
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Affiliation(s)
- Xuefen Xu
- PEARG group, School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ary A Hoffmann
- PEARG group, School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul A Umina
- PEARG group, School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Cesar Australia, 95 Albert St, Brunswick, VIC 3056, Australia
| | - Samantha E Ward
- Cesar Australia, 95 Albert St, Brunswick, VIC 3056, Australia
| | - Marianne P Coquilleau
- PEARG group, School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mallik B Malipatil
- Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Peter M Ridland
- PEARG group, School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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4
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Wan WJ, Du SJ, Hansson C, Liu WX. A new species of Diglyphus Walker (Hymenoptera, Eulophidae) from China, with morphological characterizations and molecular analysis. Zookeys 2023; 1148:65-78. [DOI: 10.3897/zookeys.1148.98853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Diglyphus Walker, 1844 (Hymenoptera: Eulophidae) is an economically important genus including species acting as biocontrol agents against agromyzid leafminer pests. A new species of Diglyphus, Diglyphus difasciatus Liu, Hansson & Wan, sp. nov., was discovered during the identification of agromyzid leafminers and their associated parasitoid wasps collected from 2016 to 2022 in China, based on morphological characteristics and molecular analyses of COI, ITS2 and 28S genes. Diglyphus difasciatus is similar to D. bimaculatus Zhu, LaSalle & Huang, distinguished by two interconnected infuscate vertical bands on the fore wing and the color of the scape. Molecular data support D. difasciatus and D. bimaculatus as two different species. The mean genetic distances between D. difasciatus and D. bimaculatus were 11.33%, 8.62%, and 0.18%, based on the COI, ITS2, and 28S genes, respectively.
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CAO HUANXI, DALE-SKEY NATALIE, BURWELL CHRISJ, ZHU CHAODONG. Review of the genus Pleurotroppopsis Girault (Hymenoptera: Eulophidae) with interspecific phylogenetic relationships based on morphological characters. Zootaxa 2022; 5190:451-484. [PMID: 37045360 DOI: 10.11646/zootaxa.5190.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 11/04/2022]
Abstract
This study is dedicated to the late Dr. John LaSalle, and reviews the world species of Pleurotroppopsis Girault (Hymenoptera: Eulophidae); fourteen species are treated, of which two are newly described: P. dactylispae Cao & Zhu sp. nov. from China and P. peukscutella Cao & Zhu sp. nov. from Malaysia. On the basis of morphological characters, tentative relationships among genera allied to Pleurotroppopsis are discussed. A revised definition of Pleurotroppopsis is presented based on study of type specimens of all species and a critical review of previous studies on the genus. In addition, parsimony analyses were conducted to infer a phylogeny of Pleurotroppopsis species based on a unique data matrix of morphological characters. Keys to genera allied to Pleurotroppopsis and to known species of Pleurotroppopsis are provided.
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Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi JP, Rasplus JY. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics 2021; 37:1-35. [PMID: 34478176 DOI: 10.1111/cla.12416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2020] [Indexed: 11/30/2022] Open
Abstract
Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.
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Affiliation(s)
- Astrid Cruaud
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gérard Delvare
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.,UMR CBGP, CIRAD, F-34398, Montpellier, France
| | - Sabine Nidelet
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Laure Sauné
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marguerite Chartois
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Michael Gates
- USDA, ARS, SEL, c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Seán G Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sariana Faure
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town, 8000, South Africa.,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Pierre Rossi
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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Gumovsky A. Review of the species of Pediobius (Hymenoptera, Eulophidae) having extreme dorsal setation and description of a new species from East Africa. Zootaxa 2021; 4999:423-438. [PMID: 34811336 DOI: 10.11646/zootaxa.4999.5.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/04/2022]
Abstract
The Afrotropical species of the genus Pediobius (Hymenoptera, Eulophidae) characterized by extreme setation on the dorsal mesosoma are reviewed and grouped into a newly proposed setigerus group. This group is characterized by the broad attachment of the third funicular and first claval segments, so that the funicle is functionally 2-segmented with a 3-segmented clava. Four species are recognized for the group: P. setigerus Kerrich (from Ghana, Ivory Coast, Republic of Guinea, the Democratic Republic of the Congo, Uganda), P. multisetis Bouek (from Ivory Coast), P. sp. indet. aff. multisetis (from Uganda), and P. erinaceus Gumovsky sp. n. (from Uganda). This last species is associated with a leaf miner, and is easily recognizable in having numerous strong bristles on the lateral areas of the mesoscutum, along the notauli, and anterior margin of the mesoscutum, a smooth mesoscutellum with only one pair of thin setae, and the pronotal collar with only 6 thin setae. By contrast, in P. setigerus and P. multisetis the mesoscutellum is sculptured and bears a row of about 20 strong bristles on each side, and the pronotal collar also bears about 20 strong bristles. The differences between P. setigerus and P. multisetis, as well as issues on their biology and type material, are discussed.
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Affiliation(s)
- Alex Gumovsky
- Schmalhausen Institute of Zoology, 15 Bogdan Khmelnitsky St., 01601 Kiev-30, Ukraine; School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa..
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8
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Rasplus JY, Blaimer BB, Brady SG, Burks RA, Delvare G, Fisher N, Gates M, Gauthier N, Gumovsky AV, Hansson C, Heraty JM, Fusu L, Nidelet S, Pereira RA, Sauné L, Ubaidillah R, Cruaud A. A first phylogenomic hypothesis for Eulophidae (Hymenoptera, Chalcidoidea). J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1762941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Bonnie B. Blaimer
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Seán G. Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Roger A. Burks
- Department of Entomology, University of California, Riverside, CA, USA
| | | | - Nicole Fisher
- Digital Collections and Informatics, National Research Collections Australia (NRCA), CSIRO, Canberra, Australia
| | - Michael Gates
- USDA, ARS, SEL, C/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Nathalie Gauthier
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Alex V. Gumovsky
- Schmalhausen Institute of Zoology, NAS of Ukraine, Kiev, Ukraine
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christer Hansson
- Museum of Biology (Entomology), Lund University, Lund, Sweden
- Faculty of Biology and CERNESIM, Al. I. Cuza University, Iasi, Romania
| | - John M. Heraty
- Department of Entomology, University of California, Riverside, CA, USA
| | - Lucian Fusu
- Departamento de Biologia, FFCLRP – USP, Ribeirão Preto, Brazil
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Laure Sauné
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Astrid Cruaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
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Sperm morphology of Elasmus polistis Burks, 1971 (Hymenoptera: Chalcidoidea: Eulophidae). Micron 2019; 127:102757. [PMID: 31574380 DOI: 10.1016/j.micron.2019.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/08/2019] [Accepted: 09/20/2019] [Indexed: 11/22/2022]
Abstract
The sperm morphology of the parasitoid Elasmus polistis (Eulophidae) has been investigated with light and transmission electron microscopy. The sperm were filiform and spiraled, with 165.6 (± 4.6) μm in length, and showed a distinctive head, formed by a one-layered small acrosome and a nucleus, and a flagellar region. An extracellular sheath from which many long filaments radiated out covered the acrosome and part of the nucleus. The spiral nucleus, with 24.1 (± 1.3) μm in length, was filled with homogeneously compact chromatin. In the nucleus-flagellum transition, the centriole adjunct extended posteriorly from the nuclear base in a spiral around the basal body, which has two central microtubules, and axoneme for approximately 1.1 μm. The two mitochondrial derivatives began roughly at the same level and at the base of the centriole adjunct. In cross-section, they were symmetrical, with a slightly oval shape and a smaller diameter in comparison to the axoneme. The latter, also spiraled, consisted of 9 + 9 + 2 microtubules that was formed from the basal body situated just below and aligned with the nucleus. The E. polistis sperm showed the same basic structures and morphological characteristics as observed in other Chalcidoidea. However, it was possible to distinguish the sperm of this species from those of other Eulophidae by (i) the long length of the centriole adjunct on the flagellum, and (ii) the presence of two central microtubules within the basal body. The sperm characteristics suggest that Eulophidae is closely related to Trichogrammatidae and both families are more similar to Eurytomidae, Pteromalidae, and Torymidae than Agaonidae.
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Cruaud A, Nidelet S, Arnal P, Weber A, Fusu L, Gumovsky A, Huber J, Polaszek A, Rasplus JY. Optimized DNA extraction and library preparation for minute arthropods: Application to target enrichment in chalcid wasps used for biocontrol. Mol Ecol Resour 2019; 19:702-710. [PMID: 30758892 DOI: 10.1111/1755-0998.13006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/18/2019] [Accepted: 02/01/2019] [Indexed: 01/04/2023]
Abstract
Target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as microarthropods can be challenging. Here, we propose easy to set up optimizations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1,432 ultraconserved elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250 ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs on an Illumina MiSeq. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment) allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Sabine Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Pierre Arnal
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France.,ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Audrey Weber
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Lucian Fusu
- Faculty of Biology, Alexandru Ioan Cuza University, Iasi, Romania
| | - Alex Gumovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - John Huber
- Natural Resources Canada, c/o Canadian National Collection of Insects, Ottawa, Canada
| | - Andrew Polaszek
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jean-Yves Rasplus
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
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11
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Powell C, Caleca V, Sinno M, van Staden M, van Noort S, Rhode C, Allsopp E, van Asch B. Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa. Genome 2019; 62:183-199. [DOI: 10.1139/gen-2018-0068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.
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Affiliation(s)
- Chante Powell
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Virgilio Caleca
- Department of Agricultural and Forestry Sciences, University of Palermo, Italy
| | - Martina Sinno
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Michaela van Staden
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Simon van Noort
- Division of Entomology, Department of Natural History, Iziko South African Museum, Cape Town, South Africa
| | - Clint Rhode
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Elleunorah Allsopp
- Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch, South Africa
| | - Barbara van Asch
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
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12
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Haas M, Burks RA, Krogmann L. A new lineage of Cretaceous jewel wasps (Chalcidoidea: Diversinitidae). PeerJ 2018; 6:e4633. [PMID: 29682418 PMCID: PMC5907778 DOI: 10.7717/peerj.4633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/28/2018] [Indexed: 11/20/2022] Open
Abstract
Jewel wasps (Hymenoptera: Chalcidoidea) are extremely species-rich today, but have a sparse fossil record from the Cretaceous, the period of their early diversification. Three genera and three species, Diversinitus attenboroughi gen. & sp. n., Burminata caputaeria gen. & sp. n. and Glabiala barbata gen. & sp. n. are described in the family Diversinitidae fam. n., from Lower Cretaceous Burmese amber. Placement in Chalcidoidea is supported by the presence of multiporous plate sensilla on the antennal flagellum and a laterally exposed prepectus. The new taxa can be excluded from all extant family level chalcidoid lineages by the presence of multiporous plate sensilla on the first flagellomere in both sexes and lack of any synapomorphies. Accordingly, a new family is proposed for the fossils and its probable phylogenetic position within Chalcidoidea is discussed. Morphological cladistic analyses of the new fossils within the Heraty et al. (2013) dataset did not resolve the phylogenetic placement of Diversinitidae, but indicated its monophyly. Phylogenetically relevant morphological characters of the new fossils are discussed with reference to Cretaceous and extant chalcidoid taxa. Along with mymarid fossils and a few species of uncertain phylogenetic placement, the newly described members of Diversinitidae are among the earliest known chalcidoids and advance our knowledge of their Cretaceous diversity.
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Affiliation(s)
- Michael Haas
- Department of Entomology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Roger A Burks
- Department of Entomology, University of California, Riverside, Riverside, United States of America
| | - Lars Krogmann
- Department of Entomology, State Museum of Natural History Stuttgart, Stuttgart, Germany
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13
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Janšta P, Cruaud A, Delvare G, Genson G, Heraty J, Křížková B, Rasplus J. Torymidae (Hymenoptera, Chalcidoidea) revised: molecular phylogeny, circumscription and reclassification of the family with discussion of its biogeography and evolution of life‐history traits. Cladistics 2017; 34:627-651. [DOI: 10.1111/cla.12228] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2017] [Indexed: 11/30/2022] Open
Affiliation(s)
- Petr Janšta
- Faculty of Science Department of Zoology Charles University Viničná 7 128 44 Prague 2 Czech Republic
| | - Astrid Cruaud
- CBGP, INRA, CIRAD, IRD Montpellier SupAgro Université de Montpellier Montpellier France
| | - Gérard Delvare
- CBGP, CIRAD Montpellier SupAgro INRA, IRD Université de Montpellier Montpellier France
| | - Guénaëlle Genson
- CBGP, INRA, CIRAD, IRD Montpellier SupAgro Université de Montpellier Montpellier France
| | - John Heraty
- Department of Entomology University of California Riverside CA 92521 USA
| | - Barbora Křížková
- Faculty of Science Department of Zoology Charles University Viničná 7 128 44 Prague 2 Czech Republic
| | - Jean‐Yves Rasplus
- CBGP, INRA, CIRAD, IRD Montpellier SupAgro Université de Montpellier Montpellier France
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14
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van Oudenhove L, Mailleret L, Fauvergue X. Infochemical use and dietary specialization in parasitoids: a meta-analysis. Ecol Evol 2017; 7:4804-4811. [PMID: 28690809 PMCID: PMC5496531 DOI: 10.1002/ece3.2888] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 11/12/2022] Open
Abstract
Many parasitoid species use olfactory cues to locate their hosts. In tritrophic systems, parasitoids of herbivores can exploit the chemical blends emitted by plants in reaction to herbivore-induced damage, known as herbivore-induced plant volatiles (HIPVs). In this study, we explored the specificity and innateness of parasitoid responses to HIPVs using a meta-analysis of data from the literature. Based on the concept of dietary specialization and infochemical use, we hypothesized that (i) specialist parasitoids (i.e., with narrow host ranges) should be attracted to specific HIPV signals, whereas generalist parasitoids (i.e., with broad host ranges) should be attracted to more generic HIPV signals and (ii) specialist parasitoids should innately respond to HIPVs, whereas generalist parasitoids should have to learn to associate HIPVs with host presence. We characterized the responses of 66 parasitoid species based on published studies of parasitoid behavior. Our meta-analysis showed that (i) as predicted, specialist parasitoids were attracted to more specific signals than were generalist parasitoids but, (ii) contrary to expectations, response innateness depended on a parasitoid's target host life stage rather than on its degree of host specialization: parasitoids of larvae were more likely to show an innate response to HIPVs than were parasitoids of adults. This result changes our understanding of dietary specialization and highlights the need for further theoretical research that will help clarify infochemical use by parasitoids.
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Affiliation(s)
| | - Ludovic Mailleret
- Université Côte d'AzurINRACNRSISASophia AntipolisFrance
- Université Côte d'AzurINRIAINRACNRSUPMC Univ. Paris 06Sophia AntipolisFrance
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15
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Dale-Skey N, Askew RR, Noyes JS, Livermore L, Broad GR. Checklist of British and Irish Hymenoptera - Chalcidoidea and Mymarommatoidea. Biodivers Data J 2016; 4:e8013. [PMID: 27346954 PMCID: PMC4910507 DOI: 10.3897/bdj.4.e8013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/05/2016] [Indexed: 11/16/2022] Open
Abstract
Background A revised checklist of the British and Irish Chalcidoidea and Mymarommatoidea substantially updates the previous comprehensive checklist, dating from 1978. Country level data (i.e. occurrence in England, Scotland, Wales, Ireland and the Isle of Man) is reported where known. New information A total of 1754 British and Irish Chalcidoidea species represents a 22% increase on the number of British species known in 1978.
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Affiliation(s)
| | | | | | | | - Gavin R. Broad
- The Natural History Museum, London, London, United Kingdom
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16
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Blacket MJ, Rice AD, Semeraro L, Malipatil MB. DNA-based identifications reveal multiple introductions of the vegetable leafminer Liriomyza sativae (Diptera: Agromyzidae) into the Torres Strait Islands and Papua New Guinea. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:533-544. [PMID: 25991411 DOI: 10.1017/s0007485315000383] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Leafmining flies (Diptera: Agromyzidae) can be serious economic pests of horticultural crops. Some genera such as Liriomyza are particularly problematic with numerous species, some of which are highly polyphagous (wide host range), which can only be confidently identified morphologically from adult males. In our study, DNA barcoding was employed to establish new locality records of the vegetable leafminer fly, Liriomyza sativae, from the islands of Torres Strait (Queensland, Australia) and the central highlands of Papua New Guinea (PNG). These records represent significant range extensions of this highly invasive plant pest. Specimens of immature leafminers (from leaf mines) were collected over a 5-year period during routine plant health surveys in ethanol or on FTA® filter paper cards, both methods proved effective at preserving and transporting insect DNA under tropical conditions, with FTA cards possessing some additional logistical benefits. Specimens were identified through sequencing two sections of the cytochrome oxidase I gene and the utility of each was assessed for the identification of species and intra-specific genetic lineages. Our study indicates that multiple haplotypes of L. sativae occur in PNG, while a different haplotype is present in the Torres Strait, with genetic regionalization between these areas apart from a single possible instance - one haplotype 'S.7' appears to be common between these two regions - interestingly this has also been the most common haplotype detected in previous studies of invasive L. sativae populations. The DNA barcoding methods employed here not only identified multiple introductions of L. sativae, but also appear generally applicable to the identification of other agromyzid leafminers (Phytomyzinae and Agromyzinae) and should decrease the likelihood of potentially co-amplifying internal hymenopteran parasitoids. Currently, L. sativae is still not recorded from the Australian mainland; however, further sampling of leafminer flies from Northern Australia and surrounding areas is required, as surveillance for possible Liriomyza incursions, as well as to characterize endemic species with which Liriomyza species might be confused.
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Affiliation(s)
- M J Blacket
- Department of Economic Development (DEDJTR),Biosciences Research Division (BRD),AgriBio,Centre for AgriBioscience,Bundoora,Victoria 3083,Australia
| | - A D Rice
- Department of Agriculture,Northern Australian Quarantine Strategy (NAQS),Cairns,Queensland 4870,Australia
| | - L Semeraro
- Department of Economic Development (DEDJTR),Biosciences Research Division (BRD),AgriBio,Centre for AgriBioscience,Bundoora,Victoria 3083,Australia
| | - M B Malipatil
- Department of Economic Development (DEDJTR),Biosciences Research Division (BRD),AgriBio,Centre for AgriBioscience,Bundoora,Victoria 3083,Australia
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17
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Burks RA, Mottern JL, Pownall NG, Waterworth R, Paine TD. First record of Closteroceruschamaeleon, parasitoid of the Eucalyptus Gall Wasp Ophelimusmaskelli (Hymenoptera, Chalcidoidea, Eulophidae), in the New World. Zookeys 2015; 504:149-52. [PMID: 26019681 PMCID: PMC4443530 DOI: 10.3897/zookeys.504.9728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 05/05/2015] [Indexed: 11/12/2022] Open
Abstract
The uniparental parasitoid Closteroceruschamaeleon (Girault) is discovered to be fortuitously present on a population of the invasive Eucalyptus Gall Wasp Ophelimusmaskelli (Ashmead) in Riverside, California. This is the first report from the New World of Closteroceruschamaeleon, which has proven to be a highly effective natural enemy of Ophelimusmaskelli in the Mediterranean Basin. The taxonomy and identification of Closteroceruschamaeleon is discussed.
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Affiliation(s)
- Roger A. Burks
- Entomology Department, University of California, Riverside, Riverside, CA, USA 92521
| | - Jason L. Mottern
- Entomology Department, University of California, Riverside, Riverside, CA, USA 92521
| | - Nicole G. Pownall
- Entomology Department, University of California, Riverside, Riverside, CA, USA 92521
| | - Rebeccah Waterworth
- Entomology Department, University of California, Riverside, Riverside, CA, USA 92521
| | - Timothy D. Paine
- Entomology Department, University of California, Riverside, Riverside, CA, USA 92521
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18
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Guastella D, Lulah H, Tajebe LS, Cavalieri V, Evans GA, Pedata PA, Rapisarda C, Legg JP. Survey on whiteflies and their parasitoids in cassava mosaic pandemic areas of Tanzania using morphological and molecular techniques. PEST MANAGEMENT SCIENCE 2015; 71:383-94. [PMID: 24753389 DOI: 10.1002/ps.3810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 04/13/2014] [Accepted: 04/16/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND Bemisia tabaci (Gennadius) is the vector of cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) in Africa, which cause devastating yield losses. As a prerequisite to developing biological control methods and enhancing knowledge of the fauna of whitefly parasitoids in sub-Saharan Africa, endemic parasitoids were surveyed in the cassava-growing regions of Tanzania and analysed using both morphological and molecular methods. An attempt was made to corroborate the identification of the parasitoid species on the basis of consideration of their morphology and sequence analyses of three DNA fragments, namely partial cytochrome oxidase I (COI), the D2 expansion segment of the 28S rRNA and the internal transcribed spacer I (ITS1). RESULTS Eight whitefly species colonising cassava and twelve species of parasitoids were detected. A species in the Encarsia strenua group and a species in the Eretmocerus mundus group were the most common parasitoids. Molecular systematics indicated the occurrence of two new species of Eretmocerus Haldeman parasitising B. tabaci. CONCLUSION The accurate identification of natural enemies is an essential first step in developing effective biological control solutions for B. tabaci in Tanzania and the wider cassava-growing environments of Africa. The new data provided here represent an important contribution to this goal.
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19
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Chesters D, Zhu CD. A protocol for species delineation of public DNA databases, applied to the Insecta. Syst Biol 2014; 63:712-25. [PMID: 24929897 DOI: 10.1093/sysbio/syu038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L × S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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20
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Cruaud A, Underhill JG, Huguin M, Genson G, Jabbour-Zahab R, Tolley KA, Rasplus JY, van Noort S. A multilocus phylogeny of the world Sycoecinae fig wasps (Chalcidoidea: Pteromalidae). PLoS One 2013; 8:e79291. [PMID: 24223925 PMCID: PMC3818460 DOI: 10.1371/journal.pone.0079291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 09/22/2013] [Indexed: 11/25/2022] Open
Abstract
The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.
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Affiliation(s)
- Astrid Cruaud
- INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | - Jenny G. Underhill
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Maïlis Huguin
- INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | - Gwenaëlle Genson
- INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | - Roula Jabbour-Zahab
- INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | - Krystal A. Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Department of Zoology, University of Cape Town, Rondebosch, South Africa
| | - Jean-Yves Rasplus
- INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France
| | - Simon van Noort
- Natural History Division, South African Museum, Iziko Museums of Cape Town, Cape Town, South Africa
- Department of Zoology, University of Cape Town, Rondebosch, South Africa
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21
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Symonds MRE, Elgar MA. The evolution of body size, antennal size and host use in parasitoid wasps (Hymenoptera: Chalcidoidea): a phylogenetic comparative analysis. PLoS One 2013; 8:e78297. [PMID: 24205189 PMCID: PMC3818564 DOI: 10.1371/journal.pone.0078297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/17/2013] [Indexed: 11/19/2022] Open
Abstract
Chalcidoid wasps represent one of the most speciose superfamilies of animals known, with ca. 23,000 species described of which many are parasitoids. They are extremely diverse in body size, morphology and, among the parasitoids, insect hosts. Parasitic chalcidoids utilise a range of behavioural adaptations to facilitate exploitation of their diverse insect hosts, but how host use might influence the evolution of body size and morphology is not known in this group. We used a phylogenetic comparative analysis of 126 chalcidoid species to examine whether body size and antennal size showed evolutionary correlations with aspects of host use, including host breadth (specificity), host identity (orders of insects parasitized) and number of plant associates. Both morphological features and identity of exploited host orders show strong phylogenetic signal, but host breadth does not. Larger body size in these wasps was weakly associated with few plant genera, and with more specialised host use, and chalcidoid wasps that parasitize coleopteran hosts tend to be larger. Intriguingly, chalcidoid wasps that parasitize hemipteran hosts are both smaller in size in the case of those parasitizing the suborder Sternorrhyncha and have relatively larger antennae, particularly in those that parasitize other hemipteran suborders. These results suggest there are adaptations in chalcidoid wasps that are specifically associated with host detection and exploitation.
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Affiliation(s)
- Matthew R. E. Symonds
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria, Australia
- Department of Zoology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A. Elgar
- Department of Zoology, University of Melbourne, Melbourne, Victoria, Australia
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22
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Heraty JM, Burks RA, Cruaud A, Gibson GAP, Liljeblad J, Munro J, Rasplus JY, Delvare G, Janšta P, Gumovsky A, Huber J, Woolley JB, Krogmann L, Heydon S, Polaszek A, Schmidt S, Darling DC, Gates MW, Mottern J, Murray E, Dal Molin A, Triapitsyn S, Baur H, Pinto JD, van Noort S, George J, Yoder M. A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera). Cladistics 2013; 29:466-542. [DOI: 10.1111/cla.12006] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2012] [Indexed: 01/28/2023] Open
Affiliation(s)
- John M. Heraty
- Department of Entomology; University of California; Riverside; CA; 92521; USA
| | | | | | - Gary A. P. Gibson
- Agriculture and Agri-Food Canada; 960 Carling Avenue; Ottawa; ON; K1A 0C6; Canada
| | | | | | | | - Gerard Delvare
- Cirad; INRA; UMR 1062 CBGP CS30016; F-34988; Montferrier-sur-Lez; France
| | - Peter Janšta
- Department of Zoology; Charles University; Vinicna 7; CZ-128 44; Praha 2; Czech Republic
| | - Alex Gumovsky
- Schmalhausen Institute of Zoology; National Academy of Sciences of Ukraine; Kiev; 30 01601; Ukraine
| | - John Huber
- Natural Resources Canada; c/o Canadian National Collection of Insects; 960 Carling Ave; Ottawa; ON; K1A 0C6; Canada
| | - James B. Woolley
- Department of Entomology; Texas A&M University; College Station; TX; 77843; USA
| | - Lars Krogmann
- Department of Entomology; State Museum of Natural History Stuttgart; Rosenstein 1; 70191; Stuttgart; Germany
| | - Steve Heydon
- Bohart Museum of Entomology; University of California; Davis; CA; 95616; USA
| | - Andrew Polaszek
- Department of Entomology; Natural History Museum; London; SW7 5BD; UK
| | - Stefan Schmidt
- Staatliche Naturwissenschaftliche Sammlungen Bayerns; Zoologische Staatssammlung; Münchhausenstr. 21; 81247; Munich; Germany
| | | | - Michael W. Gates
- Systematic Entomology Laboratory; USDA; ARS; PSI; c/o National Museum of Natural History; Washington; DC; 20013; USA
| | - Jason Mottern
- Department of Entomology; University of California; Riverside; CA; 92521; USA
| | - Elizabeth Murray
- Department of Entomology; University of California; Riverside; CA; 92521; USA
| | - Ana Dal Molin
- Department of Entomology; Texas A&M University; College Station; TX; 77843; USA
| | - Serguei Triapitsyn
- Department of Entomology; University of California; Riverside; CA; 92521; USA
| | - Hannes Baur
- Abt. Wirbellose Tiere; Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15; 3005; Bern; Switzerland
| | | | | | - Jeremiah George
- Department of Entomology; University of California; Riverside; CA; 92521; USA
| | - Matthew Yoder
- Illinois Natural History Survey; University of Illinois; Champaign; IL; 61820; USA
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Munro JB, Heraty JM, Burks RA, Hawks D, Mottern J, Cruaud A, Rasplus JY, Jansta P. A molecular phylogeny of the Chalcidoidea (Hymenoptera). PLoS One 2011; 6:e27023. [PMID: 22087244 PMCID: PMC3207832 DOI: 10.1371/journal.pone.0027023] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 10/07/2011] [Indexed: 11/19/2022] Open
Abstract
Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy.
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Affiliation(s)
- James B. Munro
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - John M. Heraty
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Roger A. Burks
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - David Hawks
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Jason Mottern
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Astrid Cruaud
- Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Jean-Yves Rasplus
- INRA, Centre de Biologie et de Gestion des Populations, Montferrier-sur-Lez, France
| | - Petr Jansta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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