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Lue CH, Abram PK, Hrcek J, Buffington ML, Staniczenko PPA. Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research. Mol Ecol 2023; 32:6461-6473. [PMID: 36040418 DOI: 10.1111/mec.16677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio-economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.
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Affiliation(s)
- Chia-Hua Lue
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York, New York City, New York, USA
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2
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Graham NR, Krehenwinkel H, Lim JY, Staniczenko P, Callaghan J, Andersen JC, Gruner DS, Gillespie RG. Ecological network structure in response to community assembly processes over evolutionary time. Mol Ecol 2023; 32:6489-6506. [PMID: 36738159 DOI: 10.1111/mec.16873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
The dynamic structure of ecological communities results from interactions among taxa that change with shifts in species composition in space and time. However, our ability to study the interplay of ecological and evolutionary processes on community assembly remains relatively unexplored due to the difficulty of measuring community structure over long temporal scales. Here, we made use of a geological chronosequence across the Hawaiian Islands, representing 50 years to 4.15 million years of ecosystem development, to sample 11 communities of arthropods and their associated plant taxa using semiquantitative DNA metabarcoding. We then examined how ecological communities changed with community age by calculating quantitative network statistics for bipartite networks of arthropod-plant associations. The average number of interactions per species (linkage density), ratio of plant to arthropod species (vulnerability) and uniformity of energy flow (interaction evenness) increased significantly in concert with community age. The index of specializationH 2 ' has a curvilinear relationship with community age. Our analyses suggest that younger communities are characterized by fewer but stronger interactions, while biotic associations become more even and diverse as communities mature. These shifts in structure became especially prominent on East Maui (~0.5 million years old) and older volcanos, after enough time had elapsed for adaptation and specialization to act on populations in situ. Such natural progression of specialization during community assembly is probably impeded by the rapid infiltration of non-native species, with special risk to younger or more recently disturbed communities that are composed of fewer specialized relationships.
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Affiliation(s)
- Natalie R Graham
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Regional and Environmental Sciences, Trier University, Trier, Germany
| | - Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Phillip Staniczenko
- Department of Biology, Brooklyn College, City University of New York, New York, New York, USA
| | - Jackson Callaghan
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, San Diego, California, USA
| | - Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Daniel S Gruner
- Department of Entomology, University of Maryland, College Park, Maryland, USA
| | - Rosemary G Gillespie
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
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3
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Kolasa M, Kajtoch Ł, Michalik A, Maryańska-Nadachowska A, Łukasik P. Till evolution do us part: The diversity of symbiotic associations across populations of Philaenus spittlebugs. Environ Microbiol 2023; 25:2431-2446. [PMID: 37525959 DOI: 10.1111/1462-2920.16473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 07/15/2023] [Indexed: 08/02/2023]
Abstract
Symbiotic bacteria have played crucial roles in the evolution of sap-feeding insects and can strongly affect host function. However, their diversity and distribution within species are not well understood; we do not know to what extent environmental factors or associations with other species may affect microbial community profiles. We addressed this question in Philaenus spittlebugs by surveying both insect and bacterial marker gene amplicons across multiple host populations. Host mitochondrial sequence data confirmed morphology-based identification of six species and revealed two divergent clades of Philaenus spumarius. All of them hosted the primary symbiont Sulcia that was almost always accompanied by Sodalis. Interestingly, populations and individuals often differed in the presence of Sodalis sequence variants, suggestive of intra-genome 16S rRNA variant polymorphism combined with rapid genome evolution and/or recent additional infections or replacements of the co-primary symbiont. The prevalence of facultative endosymbionts, including Wolbachia, Rickettsia, and Spiroplasma, varied among populations. Notably, cytochrome I oxidase (COI) amplicon data also showed that nearly a quarter of P. spumarius were infected by parasitoid flies (Verralia aucta). One of the Wolbachia operational taxonomic units (OTUs) was exclusively present in Verralia-parasitized specimens, suggestive of parasitoids as their source and highlighting the utility of host gene amplicon sequencing in microbiome studies.
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Affiliation(s)
- Michał Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland
| | - Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | | | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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4
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Chen J, Lewis OT. Experimental heatwaves facilitate invasion and alter species interactions and composition in a tropical host-parasitoid community. GLOBAL CHANGE BIOLOGY 2023; 29:6261-6275. [PMID: 37733768 DOI: 10.1111/gcb.16937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/22/2023] [Accepted: 08/13/2023] [Indexed: 09/23/2023]
Abstract
As mean temperatures increase and heatwaves become more frequent, species are expanding their distributions to colonise new habitats. The resulting novel species interactions will simultaneously shape the temperature-driven reorganization of resident communities. The interactive effects of climate change and climate change-facilitated invasion have rarely been studied in multi-trophic communities, and are likely to differ depending on the nature of the climatic driver (i.e., climate extremes or constant warming). We re-created under laboratory conditions a host-parasitoid community typical of high-elevation rainforest sites in Queensland, Australia, comprising four Drosophila species and two associated parasitoid species. We subjected these communities to an equivalent increase in average temperature in the form of periodic heatwaves or constant warming, in combination with an invasion treatment involving a novel host species from lower-elevation habitats. The two parasitoid species were sensitive to both warming and heatwaves, while the demographic responses of Drosophila species were highly idiosyncratic, reflecting the combined effects of thermal tolerance, parasitism, competition, and facilitation. After multiple generations, our heatwave treatment promoted the establishment of low-elevation species in upland communities. Invasion of the low-elevation species correlated negatively with the abundance of one of the parasitoid species, leading to cascading effects on its hosts and their competitors. Our study, therefore, reveals differing, sometimes contrasting, impacts of extreme temperatures and constant warming on community composition. It also highlights how the scale and direction of climate impacts could be further modified by invading species within a bi-trophic community network.
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Affiliation(s)
- Jinlin Chen
- Department of Biology, University of Oxford, Oxford, UK
| | - Owen T Lewis
- Department of Biology, University of Oxford, Oxford, UK
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5
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Tomanović Ž, Kavallieratos NG, Ye Z, Nika EP, Petrović A, Vollhardt IMG, Vorburger C. Cereal Aphid Parasitoids in Europe (Hymenoptera: Braconidae: Aphidiinae): Taxonomy, Biodiversity, and Ecology. INSECTS 2022; 13:1142. [PMID: 36555052 PMCID: PMC9785021 DOI: 10.3390/insects13121142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Cereals are very common and widespread crops in Europe. Aphids are a diverse group of herbivorous pests on cereals and one of the most important limiting factors of cereal production. Here, we present an overview of knowledge about the taxonomy, biodiversity, and ecology of cereal aphid parasitoids in Europe, an important group of natural enemies contributing to cereal aphid control. We review the knowledge obtained from the integrative taxonomy of 26 cereal aphid primary parasitoid species, including two allochthonous species (Lysiphlebus testaceipes and Trioxys sunnysidensis) and two recently described species (Lipolexis labialis and Paralipsis brachycaudi). We further review 28 hyperparasitoid species belonging to three hymenopteran superfamilies and four families (Ceraphronoidea: Megaspillidae; Chalcidoidea: Pteromalidae, Encyrtidae; Cynipoidea: Figitidae). We also compile knowledge on the presence of secondary endosymbionts in cereal aphids, as these are expected to influence the community composition and biocontrol efficiency of cereal aphid parasitoids. To study aphid-parasitoid-hyperparasitoid food webs more effectively, we present two kinds of DNA-based approach: (i) diagnostic PCR (mainly multiplex PCR), and (ii) DNA sequence-based methods. Finally, we also review the effects of landscape complexity on the different trophic levels in the food webs of cereal aphids and their associated parasitoids, as well as the impacts of agricultural practices and environmental variation.
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Affiliation(s)
- Željko Tomanović
- Faculty of Biology, Institute of Zoology, University of Belgrade, 16 Studentski trg, 11000 Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000 Belgrade, Serbia
| | - Nickolas G. Kavallieratos
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece
| | - Zhengpei Ye
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China
| | - Erifili P. Nika
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece
| | - Andjeljko Petrović
- Faculty of Biology, Institute of Zoology, University of Belgrade, 16 Studentski trg, 11000 Belgrade, Serbia
| | - Ines M. G. Vollhardt
- Agroecology, Department of Crop Science, Georg-August University Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
| | - Christoph Vorburger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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6
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Toro-Delgado E, Hernández-Roldán J, Dincă V, Vicente JC, Shaw MR, Quicke DL, Vodă R, Albrecht M, Fernández-Triana J, Vidiella B, Valverde S, Dapporto L, Hebert PDN, Talavera G, Vila R. Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.
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Affiliation(s)
| | - Juan Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid , c/ Darwin, 2, ES - 28049 Madrid , Spain
| | - Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu , 90014 Oulu , Finland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest , Bucharest , Romania
| | | | - Mark R Shaw
- National Museums of Scotland , Edinburgh , UK
| | - Donald Lj Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University , Bangkok , Thailand
| | | | | | | | - Blai Vidiella
- Centre de Recerca Matemàtica , Edifici C , Campus de Bellaterra, Barcelona , Spain
| | - Sergi Valverde
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- European Centre for Living Technology , Venice , Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, University of Florence , 50019 Sesto Fiorentino , Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph , Guelph, ON N1G 2W1 , Canada
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona , Passeig del Migdia s/n, 08038 Barcelona , Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
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7
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Abstract
Hyperparasitoids are some of the most diverse members of insect food webs. True hyperparasitoids parasitize the larvae of other parasitoids, reaching these larvae with their ovipositor through the herbivore that hosts the parasitoid larva. During pupation, primary parasitoids also may be attacked by pseudohyperparasitoids that lay their eggs on the parasitoid (pre)pupae. By attacking primary parasitoids, hyperparasitoids may affect herbivore population dynamics, and they have been identified as a major challenge in biological control. Over the past decades, research, especially on aphid- and caterpillar-associated hyperparasitoids, has revealed that hyperparasitoids challenge rules on nutrient use efficiency in trophic chains, account for herbivore outbreaks, or stabilize competitive interactions in lower trophic levels, and they may use cues derived from complex interaction networks to locate their hosts. This review focuses on the fascinating ecology of hyperparasitoids related to how they exploit and locate their often inconspicuous hosts and the insect community processes in which hyperparasitoids are prominent players.
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Affiliation(s)
- Erik H Poelman
- Laboratory of Entomology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands;
| | - Antonino Cusumano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy;
| | - Jetske G de Boer
- Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands;
- Aeres University of Applied Sciences, 6708 PB Wageningen, The Netherlands
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8
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Ollivier M, Lesieur V, Tavoillot J, Bénetière F, Tixier M, Martin J. An innovative approach combining metabarcoding and ecological interaction networks for selecting candidate biological control agents. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mélodie Ollivier
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
| | - Vincent Lesieur
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
- CSIRO Health and Biosecurity European Laboratory Montferrier sur Lez France
| | - Johannes Tavoillot
- CBGP IRD CIRAD INRAE Montpellier SupAgro Univ Montpellier Montpellier France
| | - Fanny Bénetière
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
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9
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Lue CH, Buffington ML, Scheffer S, Lewis M, Elliott TA, Lindsey ARI, Driskell A, Jandova A, Kimura MT, Carton Y, Kula RR, Schlenke TA, Mateos M, Govind S, Varaldi J, Guerrieri E, Giorgini M, Wang X, Hoelmer K, Daane KM, Abram PK, Pardikes NA, Brown JJ, Thierry M, Poirié M, Goldstein P, Miller SE, Tracey WD, Davis JS, Jiggins FM, Wertheim B, Lewis OT, Leips J, Staniczenko PPA, Hrcek J. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol Ecol Resour 2021; 21:2437-2454. [PMID: 34051038 DOI: 10.1111/1755-0998.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.
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Affiliation(s)
- Chia-Hua Lue
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sonja Scheffer
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Matthew Lewis
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Amy Driskell
- Laboratories of Analytical Biology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Anna Jandova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | | | - Yves Carton
- "Évolution, Génomes, Comportement, Écologie", CNRS et Université Paris-Saclay, Paris, France
| | - Robert R Kula
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Mariana Mateos
- Wildlife and Fisheries Sciences Department, Texas A&M University, College Station, TX, USA
| | - Shubha Govind
- The Graduate Center of the City University of New York, New York, NY, USA
| | - Julien Varaldi
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Emilio Guerrieri
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Massimo Giorgini
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kim Hoelmer
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Nicholas A Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Joel J Brown
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Melanie Thierry
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Marylène Poirié
- INRAE, CNRS. and Evolution and Specificity of Multitrophic Interactions (ESIM) Sophia Agrobiotech Institute, Université "Côte d'Azur", Sophia Antipolis, France
| | - Paul Goldstein
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Scott E Miller
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - W Daniel Tracey
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Gill Center for Biomolecular Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jeremy S Davis
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Biology Department, University of Kentucky, Lexington, KY, USA
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
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10
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Deng X, Chen L, Tian E, Zhang D, Wattana T, Yu H, Kjellberg F, Segar ST. Low host specificity and broad geographical ranges in a community of parasitic non-pollinating fig wasps (Sycoryctinae; Chalcidoidea). J Anim Ecol 2021; 90:1678-1690. [PMID: 33738802 DOI: 10.1111/1365-2656.13483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022]
Abstract
Plants, phytophagous insects and their parasitoids form the most diverse assemblages of macroscopic organisms on earth. Enclosed assemblages in particular represent a tractable system for studying community assembly and diversification. Communities associated with widespread plant species are especially suitable as they facilitate a comparative approach. Pantropical fig-wasp communities represent a remarkably well-replicated system, ideal for studying these historical processes. We expect high dispersal ability in non-pollinating fig wasps to result in lower geographical turnover in comparison to pollinating fig wasps. The ability of non-pollinating wasps to utilise a number of hosts (low host specificity) is a key determinant of overall geographical range, with intraspecific competition becoming a constraining factor should diet breadth overlap among species. Finally, we expect conserved community structure throughout the host range. We aim to test these expectations, derived from population genetic and community studies, using the multi-trophic insect community associated with Ficus hirta throughout its 3,500 km range across continental and insular Asia. We collect molecular evidence from one coding mitochondrial gene, one non-coding nuclear gene and multiple microsatellites across 25 geographical sites. Using these data, we establish species boundaries, determine levels of host specificity among non-pollinating fig wasps and quantify geographical variation in community composition. We find low host specificity in two genera of non-pollinating fig wasps. Functional community structure is largely conserved across the range of the host fig, despite limited correspondence between the ranges of non-pollinator and pollinator species. While nine pollinators are associated with Ficus hirta, the two non-pollinator tribes developing in its figs each contained only four species. Contrary to predictions, we find stronger isolation by distance in non-pollinators than pollinators. Long-lived non-pollinators may disperse more gradually and be less reliant on infrequent long-distance dispersal by wind currents. Segregation among non-pollinating species across their range is suggestive of competitive exclusion and we propose that this may be a result of increased levels of local adaptation and moderate, but regular, rates of dispersal. Our findings provide one more example of lack of strict codiversification in the geographical diversification of plant-associated insect communities.
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Affiliation(s)
- Xiaoxia Deng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Lianfu Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Enwei Tian
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China
| | - Dayong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | | | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Finn Kjellberg
- CEFE, University of Montpellier, CNRS, University of Paul Valéry Montpellier, EPHE, IRD, Montpellier Cedex 5, France
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
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11
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Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring project. ADV ECOL RES 2021. [DOI: 10.1016/bs.aecr.2021.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Wang MQ, Li Y, Chesters D, Bruelheide H, Ma K, Guo PF, Zhou QS, Staab M, Zhu CD, Schuldt A. Host functional and phylogenetic composition rather than host diversity structure plant-herbivore networks. Mol Ecol 2020; 29:2747-2762. [PMID: 32564434 DOI: 10.1111/mec.15518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/10/2020] [Indexed: 12/18/2022]
Abstract
Declining plant diversity alters ecological networks, such as plant-herbivore interactions. However, our knowledge of the potential mechanisms underlying effects of plant species loss on plant-herbivore network structure is still limited. We used DNA barcoding to identify herbivore-host plant associations along declining levels of tree diversity in a large-scale, subtropical biodiversity experiment. We tested for effects of tree species richness, host functional and phylogenetic diversity, and host functional (leaf trait) and phylogenetic composition on species, phylogenetic and network composition of herbivore communities. We found that phylogenetic host composition and related palatability/defence traits but not tree species richness significantly affected herbivore communities and interaction network complexity at both the species and community levels. Our study indicates that evolutionary dependencies and functional traits of host plants determine the composition of higher trophic levels and corresponding interaction networks in species-rich ecosystems. Our findings highlight that characteristics of the species lost have effects on ecosystem structure and functioning across trophic levels that cannot be predicted from mere reductions in species richness.
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Affiliation(s)
- Ming-Qiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Forest Nature Conservation, Georg-August-University Goettingen, Goettingen, Germany
| | - Yi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Keping Ma
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Peng-Fei Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Staab
- Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg, Germany
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Andreas Schuldt
- Forest Nature Conservation, Georg-August-University Goettingen, Goettingen, Germany
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13
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Dong Y, Xi X, Chen H, Yang Y, Sun S. A Protocol to Identify the Host of Parasitoids by DNA Barcoding of Vestigial Tissues. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Yuran Dong
- Department of Ecology, School of Life Science, Nanjing University, CN-210046 Nanjing, Jiangsu Province, China
| | - Xinqiang Xi
- Department of Ecology, School of Life Science, Nanjing University, CN-210046 Nanjing, Jiangsu Province, China
| | - Hanxiang Chen
- Department of Ecology, School of Life Science, Nanjing University, CN-210046 Nanjing, Jiangsu Province, China
| | - Yangheshan Yang
- Department of Ecology, School of Life Science, Nanjing University, CN-210046 Nanjing, Jiangsu Province, China
| | - Shucun Sun
- Department of Ecology, School of Life Science, Nanjing University, CN-210046 Nanjing, Jiangsu Province, China
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14
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Evans DM, Kitson JJ. Molecular ecology as a tool for understanding pollination and other plant-insect interactions. CURRENT OPINION IN INSECT SCIENCE 2020; 38:26-33. [PMID: 32087411 DOI: 10.1016/j.cois.2020.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Advances in molecular ecology offer unprecedented opportunities to understand the ecology and evolution of insects, the complex ways in which they interact and their role in ecosystem functioning. Rapidly developing DNA sequencing technologies are resolving previously intractable questions in taxonomic and functional biodiversity and provide significant potential to determine formerly difficult to observe plant-insect interactions. We provide an overview of the state-of-the-art and critically appraise the range of molecular approaches currently available for the study of insect pollination, host-parasitoid interactions and/or wider food-web studies. Species-interaction data are increasingly being incorporated into ecological network analyses. DNA metabarcoding offers opportunities to scale-up efforts to create large, highly resolved, phylogenetically structured networks within an exciting framework to study pressing questions in ecology and evolution.
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Affiliation(s)
- Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom.
| | - James Jn Kitson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
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15
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Ollivier M, Lesieur V, Raghu S, Martin JF. Characterizing ecological interaction networks to support risk assessment in classical biological control of weeds. CURRENT OPINION IN INSECT SCIENCE 2020; 38:40-47. [PMID: 32088650 DOI: 10.1016/j.cois.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
A key element in weed biological control is the selection of a biological control agent that minimizes the risks of non-target attack and indirect effects on the recipient community. Network ecology is a promising approach that could help decipher tritrophic interactions in both the native and the invaded ranges, to complement quarantine-based host-specificity tests and gain insights on potential interactions of biological control agents. This review highlights practical questions addressed by networks, including 1) biological control agent selection, based on specialization indices, 2) risk assessment of biological control agent release into a novel environment, via particular patterns of association such as apparent competition between agent(s) and native herbivore(s), 3) network comparisons through structural metrics, 4) potential of network modelling and 5) limits of network construction methods.
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Affiliation(s)
- Melodie Ollivier
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France.
| | - Vincent Lesieur
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France; CSIRO Health and Biosecurity, European Laboratory, Montferrier sur Lez, 34980, France
| | | | - Jean-François Martin
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France
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16
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Abdala‐Roberts L, Puentes A, Finke DL, Marquis RJ, Montserrat M, Poelman EH, Rasmann S, Sentis A, van Dam NM, Wimp G, Mooney K, Björkman C. Tri-trophic interactions: bridging species, communities and ecosystems. Ecol Lett 2019; 22:2151-2167. [PMID: 31631502 PMCID: PMC6899832 DOI: 10.1111/ele.13392] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/18/2019] [Accepted: 09/05/2019] [Indexed: 01/12/2023]
Abstract
A vast body of research demonstrates that many ecological and evolutionary processes can only be understood from a tri-trophic viewpoint, that is, one that moves beyond the pairwise interactions of neighbouring trophic levels to consider the emergent features of interactions among multiple trophic levels. Despite its unifying potential, tri-trophic research has been fragmented, following two distinct paths. One has focused on the population biology and evolutionary ecology of simple food chains of interacting species. The other has focused on bottom-up and top-down controls over the distribution of biomass across trophic levels and other ecosystem-level variables. Here, we propose pathways to bridge these two long-standing perspectives. We argue that an expanded theory of tri-trophic interactions (TTIs) can unify our understanding of biological processes across scales and levels of organisation, ranging from species evolution and pairwise interactions to community structure and ecosystem function. To do so requires addressing how community structure and ecosystem function arise as emergent properties of component TTIs, and, in turn, how species traits and TTIs are shaped by the ecosystem processes and the abiotic environment in which they are embedded. We conclude that novel insights will come from applying tri-trophic theory systematically across all levels of biological organisation.
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Affiliation(s)
- Luis Abdala‐Roberts
- Departamento de Ecología TropicalCampus de Ciencias Biológicas y AgropecuariasUniversidad Autónoma de YucatánKm. 15.5 Carretera Mérida‐XmatkuilMX‐97000MéridaYucatánMéxico
| | - Adriana Puentes
- Department of EcologySwedish University of Agricultural SciencesBox 7044SE‐750 07UppsalaSweden
| | - Deborah L. Finke
- Division of Plant SciencesUniversity of Missouri1‐33 Agriculture BuildingUS‐65211ColumbiaMOUSA
| | - Robert J. Marquis
- Department of Biology and the Whitney R. Harris World Ecology CenterUniversity of Missouri–St. Louis1 University BoulevardUS‐63121St. LouisMOUSA
| | - Marta Montserrat
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM‐UMA‐CSIC)Consejo Superior de Investigaciones CientíficasE‐29750Algarrobo‐Costa (Málaga)Spain
| | - Erik H. Poelman
- Laboratory of EntomologyWageningen UniversityP.O. Box 166700 AAWageningenThe Netherlands
| | - Sergio Rasmann
- Institute of BiologyUniversity of NeuchâtelRue Emile‐Argand 11CH‐2000NeuchâtelSwitzerland
| | - Arnaud Sentis
- UMR RECOVERIRSTEAAix Marseille University3275 route Cézanne13182Aix‐en‐ProvenceFrance
| | - Nicole M. van Dam
- Molecular Interaction EcologyFriedrich‐Schiller‐University Jena & German Centre for Integrative Biodiversity Research (iDiv)Halle‐Jena‐LeipzigDeutscher Platz 5eDE‐04103LeipzigGermany
| | - Gina Wimp
- Department of BiologyGeorgetown University406 Reiss Science BuildingUS‐20057WashingtonDCUSA
| | - Kailen Mooney
- Department of Ecology and Evolutionary BiologyUniversity of California Irvine321 Steinhaus HallUS‐92697IrvineCAUSA
| | - Christer Björkman
- Department of EcologySwedish University of Agricultural SciencesBox 7044SE‐750 07UppsalaSweden
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17
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Derocles SAP, Lunt DH, Berthe SCF, Nichols PC, Moss ED, Evans DM. Climate warming alters the structure of farmland tritrophic ecological networks and reduces crop yield. Mol Ecol 2018; 27:4931-4946. [DOI: 10.1111/mec.14903] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/21/2018] [Accepted: 10/03/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Stephane A. P. Derocles
- INRA; UMR 1347 Agroécologie; Dijon France
- School of Environmental Sciences; University of Hull; Hull UK
| | - David H. Lunt
- School of Environmental Sciences; University of Hull; Hull UK
| | | | - Paul C. Nichols
- School of Environmental Sciences; University of Hull; Hull UK
| | - Ellen D. Moss
- School of Environmental Sciences; University of Hull; Hull UK
- School of Natural and Environmental Sciences; Newcastle University; Newcastle upon Tyne UK
| | - Darren M. Evans
- School of Environmental Sciences; University of Hull; Hull UK
- School of Natural and Environmental Sciences; Newcastle University; Newcastle upon Tyne UK
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18
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Gariepy TD, Bruin A, Konopka J, Scott‐Dupree C, Fraser H, Bon M, Talamas E. A modified
DNA
barcode approach to define trophic interactions between native and exotic pentatomids and their parasitoids. Mol Ecol 2018; 28:456-470. [DOI: 10.1111/mec.14868] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Tara D. Gariepy
- Agriculture and Agri‐Food Canada London Research and Development Centre London Ontario Canada
| | - Allison Bruin
- Agriculture and Agri‐Food Canada London Research and Development Centre London Ontario Canada
| | - Joanna Konopka
- Agriculture and Agri‐Food Canada London Research and Development Centre London Ontario Canada
| | | | - Hannah Fraser
- Ontario Ministry of Agriculture, Food and Rural Affairs Guelph Ontario Canada
| | - Marie‐Claude Bon
- USDA‐ARS European Biological Control Lab Campus International de Baillarguet St. Gely du Fesc France
| | - Elijah Talamas
- Florida Department of Agriculture and Consumer Services Division of Plant Industry Gainsville Florida
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19
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Qin Y, Zhou Q, Yu F, Wang X, Wei J, Zhu C, Zhang Y, Vogler AP. Host specificity of parasitoids (Encyrtidae) toward armored scale insects (Diaspididae): Untangling the effect of cryptic species on quantitative food webs. Ecol Evol 2018; 8:7879-7893. [PMID: 30250670 PMCID: PMC6144978 DOI: 10.1002/ece3.4344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 01/04/2023] Open
Abstract
Host specificity of parasitoids may be measured by various specialization indices to assess the variation of interaction strength among species and the structure of the wider interaction network. However, the conclusions from analyses at the species and network levels may differ, which remains poorly explored. In addition, the recovery of cryptic species of hosts and parasitoids with molecular data may affect the structure of inferred interaction links. We quantified host specificity of hymenopteran parasitoids (family Encyrtidae) on armored scale insects (Hemiptera: Diaspididae) from a wide geographic sampling range across the Chinese Mainland based on both morphological and molecular species delimitation. Mitochondrial COI and nuclear 28S markers detected high cryptic species diversity in the encyrtids and to a lesser degree in the diaspidids, which divided generalist morphospecies into complexes of specialists and generalists. One-to-one reciprocal host-parasite links were increased in the molecular data set, but different quantitative species-level indices produced contrasting estimates of specificity from various one-to-multiple and multiple-to-multiple host-parasite links. Network indices calculated from DNA-based species, compared to morphology-based species definitions, showed lower connectance and generality, but greater specialization and compartmentalization of the interaction network. We conclude that a high degree of cryptic species in host-parasitoid systems refines the true network structure and may cause us overestimating the stability of these interaction webs.
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Affiliation(s)
- Yao‐Guang Qin
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of Sciences (UCAS)BeijingChina
| | - Qing‐Song Zhou
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of Sciences (UCAS)BeijingChina
| | - Fang Yu
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of Sciences (UCAS)BeijingChina
| | - Xu‐Bo Wang
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
| | - Jiu‐Feng Wei
- College of AgricultureShanxi Agricultural UniversityShanxiChina
| | - Chao‐Dong Zhu
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of Sciences (UCAS)BeijingChina
| | - Yan‐Zhou Zhang
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of Sciences (UCAS)BeijingChina
| | - Alfried P. Vogler
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
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20
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Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience 2018; 7:1-31. [PMID: 29648623 PMCID: PMC6333914 DOI: 10.1093/gigascience/giy014] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/15/2018] [Accepted: 02/13/2018] [Indexed: 11/14/2022] Open
Abstract
The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.
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Affiliation(s)
- Georgios A Pavlopoulos
- Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Panagiota I Kontou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
| | - Costas Bouyioukos
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
| | - Evripides Markou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Pantelis G Bagos
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
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21
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Bonato KO, Silva PC, Malabarba LR. Unrevealing Parasitic Trophic Interactions—A Molecular Approach for Fluid-Feeding Fishes. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Kitson JJN, Hahn C, Sands RJ, Straw NA, Evans DM, Lunt DH. Detecting host–parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding. Mol Ecol 2018; 28:471-483. [DOI: 10.1111/mec.14518] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 12/26/2022]
Affiliation(s)
- James J. N. Kitson
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Evolutionary and Environmental Genomics Group School of Environmental Sciences University of Hull Hull UK
| | - Christoph Hahn
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Institute of Zoology Karl‐Franzens‐Universität Graz Austria
| | - Richard J. Sands
- Forest Research Centre for Ecosystems, Society and Biosecurity Farnham UK
- Centre for Biological Sciences Highfield Campus The University of Southampton Southampton UK
| | - Nigel A. Straw
- Forest Research Centre for Ecosystems, Society and Biosecurity Farnham UK
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - David H. Lunt
- Evolutionary and Environmental Genomics Group School of Environmental Sciences University of Hull Hull UK
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23
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Toju H, Baba YG. DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs. ZOOLOGICAL LETTERS 2018; 4:4. [PMID: 29468086 PMCID: PMC5815251 DOI: 10.1186/s40851-018-0088-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Understanding feedback between above- and below-ground processes of biological communities is a key to the effective management of natural and agricultural ecosystems. However, as above- and below-ground food webs are often studied separately, our knowledge of material flow and community dynamics in terrestrial ecosystems remains limited. RESULTS We developed a high-throughput sequencing method for examining how spiders link above- and below-ground food webs as generalist predators. To overcome problems related to DNA-barcoding-based analyses of arthropod-arthropod interactions, we designed spider-specific blocking primers and Hexapoda-specific primers for the selective PCR amplification of Hexapoda prey sequences from spider samples. By applying the new DNA metabarcoding framework to spider samples collected in a temperate secondary forest in Japan, we explored the structure of a food web involving 15 spider species and various taxonomic groups of Hexapoda prey. These results support the hypothesis that multiple spider species in a community can prey on both above- and below-ground prey species, potentially coupling above- and below-ground food-web dynamics. CONCLUSIONS The PCR primers and metabarcoding pipeline described in this study are expected to accelerate nuclear marker-based analyses of food webs, illuminating poorly understood trophic interactions in ecosystems.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113 Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Honcho 4-1-8, Kawaguchi, Saitama 332-0012 Japan
| | - Yuki G. Baba
- Institute for Agro-Environmental Sciences, NARO, Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604 Japan
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24
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Berger JS, Birkhofer K, Hanson HI, Hedlund K. Landscape configuration affects herbivore-parasitoid communities in oilseed rape. JOURNAL OF PEST SCIENCE 2018; 91:1093-1105. [PMID: 29937705 PMCID: PMC5978837 DOI: 10.1007/s10340-018-0965-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 12/29/2017] [Accepted: 02/19/2018] [Indexed: 05/12/2023]
Abstract
It is crucial to consider the effects of large-scale drivers on species presences and ecological interactions to understand what structures communities. In our study, we investigated how the species composition and the potential interaction networks of herbivore and parasitoid communities in oilseed rape fields are affected by agricultural landscape characteristics. Insect communities of 26 winter oilseed rape fields in southern Sweden were captured in water traps over a continuous time span of 30 ± 2 days. In total, 31% of the variation in the composition of herbivore host communities was explained by a combination of the surrounding oilseed rape area in the study year and the previous year and distance to the nearest forest. The oilseed rape area in the study year and distance to forest also explained 14% of the variation in the composition of parasitoid communities. Distance to the nearest forest together with the area of oilseed rape in the previous year explained 45% of the variation in asymmetry of interaction webs. These results indicate that several measures of landscape configuration are important both for the composition of host and parasitoid communities and also for the structure of interaction networks. Our results support the view that it is an appropriate strategy to cultivate oilseed rape in landscapes that are far away from forests, in order to minimize recolonization by pest species and at the same time to attract parasitoid species from the open landscape.
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Affiliation(s)
- Josef S. Berger
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - Klaus Birkhofer
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Helena I. Hanson
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - Katarina Hedlund
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
- Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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25
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Šigut M, Kostovčík M, Šigutová H, Hulcr J, Drozd P, Hrček J. Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host-parasitoid interactions. PLoS One 2017; 12:e0187803. [PMID: 29236697 PMCID: PMC5728528 DOI: 10.1371/journal.pone.0187803] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/26/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding interactions between herbivores and parasitoids is essential for successful biodiversity protection and monitoring and for biological pest control. Morphological identifications employ insect rearing and are complicated by insects’ high diversity and crypsis. DNA barcoding has been successfully used in studies of host–parasitoid interactions as it can substantially increase the recovered real host–parasitoid diversity distorted by overlooked species complexes, or by species with slight morphological differences. However, this approach does not allow the simultaneous detection and identification of host(s) and parasitoid(s). Recently, high-throughput sequencing has shown high potential for surveying ecological communities and trophic interactions. Using mock samples comprising insect larvae and their parasitoids, we tested the potential of DNA metabarcoding for identifying individuals involved in host–parasitoid interactions to different taxonomic levels, and compared it to standard DNA barcoding and morphological approaches. For DNA metabarcoding, we targeted the standard barcoding marker cytochrome oxidase subunit I using highly degenerate primers, 2*300 bp sequencing on a MiSeq platform, and RTAX classification using paired-end reads. Additionally, using a large host–parasitoid dataset from a Central European floodplain forest, we assess the completeness and usability of a local reference library by confronting the number of Barcoding Index Numbers obtained by standard barcoding with the number of morphotypes. Overall, metabarcoding recovery was high, identifying 92.8% of the taxa present in mock samples, and identification success within individual taxonomic levels did not significantly differ among metabarcoding, standard barcoding, and morphology. Based on the current local reference library, 39.4% parasitoid and 90.7% host taxa were identified to the species level. DNA barcoding estimated higher parasitoid diversity than morphotyping, especially in groups with high level of crypsis. This study suggests the potential of metabarcoding for effectively recovering host–parasitoid diversity, together with more accurate identifications obtained from building reliable and comprehensive reference libraries, especially for parasitoids.
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Affiliation(s)
- Martin Šigut
- Department of Biology and Ecology/Institute of Environmental Technologies, University of Ostrava, Ostrava, Czech Republic
| | - Martin Kostovčík
- Department of Genetics and Microbiology, Charles University in Prague, Praha, Czech Republic
- BIOCEV, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Hana Šigutová
- Department of Biology and Ecology/Institute of Environmental Technologies, University of Ostrava, Ostrava, Czech Republic
- * E-mail: (HŠ); (PD)
| | - Jiří Hulcr
- School of Forest Resources and Conservation, University of Florida-IFAS, Gainesville, Florida, United States of America
- Entomology and Nematology Department, University of Florida-IFAS, Gainesville, Florida, United States of America
| | - Pavel Drozd
- Department of Biology and Ecology/Institute of Environmental Technologies, University of Ostrava, Ostrava, Czech Republic
- * E-mail: (HŠ); (PD)
| | - Jan Hrček
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
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McLean AHC, Parker BJ, Hrček J, Henry LM, Godfray HCJ. Insect symbionts in food webs. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0325. [PMID: 27481779 PMCID: PMC4971179 DOI: 10.1098/rstb.2015.0325] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 12/22/2022] Open
Abstract
Recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. Here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. Using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. Many symbionts are now known to help their hosts escape or resist natural enemy attack, and others can allow their hosts to withstand abiotic stress or affect host plant use. In addition to the direct effect of symbionts on aphid phenotypes there may be indirect effects mediated through trophic and non-trophic community interactions. We believe that by using data from barcoding studies to identify bacterial symbionts, this extra, microbial dimension to insect food webs can be better elucidated. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Ailsa H C McLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Benjamin J Parker
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Jan Hrček
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Lee M Henry
- Faculty of Earth and Life Sciences, University of Amsterdam, De Boelelaan 1085-1087, 1081 HV Amsterdam, The Netherlands
| | - H Charles J Godfray
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Tylianakis JM, Morris RJ. Ecological Networks Across Environmental Gradients. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022821] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jason M. Tylianakis
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Rebecca J. Morris
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
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Species composition and seasonal dynamics of aphid parasitoids and hyperparasitoids in wheat fields in northern China. Sci Rep 2017; 7:13989. [PMID: 29070808 PMCID: PMC5656665 DOI: 10.1038/s41598-017-14441-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/10/2017] [Indexed: 11/08/2022] Open
Abstract
Parasitoids are important natural enemies of aphids in wheat fields of northern China, and interest in them has increased in recent years. However, little is known regarding parasitoids of wheat aphids, which has hindered the study and understanding of aphid-parasitoid interactions. In the present study, three primary parasitoids and 15 hyperparasitoids were collected in wheat fields during a 2-year survey in northern China (2014, 2015) and a 2-year investigation at Langfang, Hebei Province (2015, 2016). Among them, Aphidius uzbekistanicus Luzhetski was found most frequently among the primary parasitoids, while Pachyneuron aphidis (Bouché) dominated the hyperparasitoid community. Investigation of the dynamics of wheat aphids and parasitoids revealed that the primary parasitoids appeared early in the growing period and that the hyperparasitoids appeared later. Analysis of the seasonal dynamics revealed that growth of the parasitoid population followed that of the aphid population and that the parasitism rates were highest in the late growing period.
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Molecular Tools for the Detection and the Identification of Hymenoptera Parasitoids in Tortricid Fruit Pests. Int J Mol Sci 2017; 18:ijms18102031. [PMID: 28937594 PMCID: PMC5666713 DOI: 10.3390/ijms18102031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/30/2022] Open
Abstract
Biological control requires specific tools for the accurate detection and identification of natural enemies in order to estimate variations in their abundance and their impact according to changes in environmental conditions or agricultural practices. Here, we developed two molecular methods of detection based on PCR-RFLP with universal primers and on PCR with specific primers to identify commonly occurring larval parasitoids of the tortricid fruit pests and to estimate parasitism in the codling moth. Both methods were designed based on DNA sequences of the COI mitochondrial gene for a range of parasitoids that emerged from Cydia pomonella and Grapholitamolesta caterpillars (102 parasitoids; nine species) and a range of potential tortricid hosts (40 moths; five species) damaging fruits. The PCR-RFLP method (digestion by AluI of a 482 bp COI fragment) was very powerful to identify parasitoid adults and their hosts, but failed to detect parasitoid larvae within eggs or within young C. pomonella caterpillars. The PCR method based on specific primers amplified COI fragments of different lengths (131 to 463 bp) for Ascogaster quadridentata (Braconidae); Pristomerusvulnerator (Ichneumonidae); Trichomma enecator (Ichneumonidae); and Perilampus tristis (Perilampidae), and demonstrated a higher level of sensibility than the PCR-RFLP method. Molecular estimations of parasitism levels in a natural C. pomonella population with the specific primers did not differ from traditional estimations based on caterpillar rearing (about 60% parasitism in a non-treated apple orchard). These PCR-based techniques provide information about within-host parasitoid assemblage in the codling moth and preliminary results on the larval parasitism of major tortricid fruit pests.
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Ye Z, Vollhardt IMG, Girtler S, Wallinger C, Tomanovic Z, Traugott M. An effective molecular approach for assessing cereal aphid-parasitoid-endosymbiont networks. Sci Rep 2017; 7:3138. [PMID: 28600542 PMCID: PMC5466676 DOI: 10.1038/s41598-017-02226-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/10/2017] [Indexed: 01/08/2023] Open
Abstract
Molecular approaches are increasingly being used to analyse host-parasitoid food webs as they overcome several hurdles inherent to conventional approaches. However, such studies have focused primarily on the detection and identification of aphids and their aphidiid primary parasitoids, largely ignoring primary parasitoid-hyperparasitoid interactions or limiting these to a few common species within a small geographical area. Furthermore, the detection of bacterial secondary endosymbionts has not been considered in such assays despite the fact that endosymbionts may alter aphid-parasitoid interactions, as they can confer protection against parasitoids. Here we present a novel two-step multiplex PCR (MP-PCR) protocol to assess cereal aphid-primary parasitoid-hyperparasitoid-endosymbiont interactions. The first step of the assay allows detection of parasitoid DNA at a general level (24 primary and 16 hyperparasitoid species) as well as the species-specific detection of endosymbionts (3 species) and cereal aphids (3 species). The second step of the MP-PCR assay targets seven primary and six hyperparasitoid species that commonly occur in Central Europe. Additional parasitoid species not covered by the second-step of the assay can be identified via sequencing 16S rRNA amplicons generated in the first step of the assay. The approach presented here provides an efficient, highly sensitive, and cost-effective (~consumable costs of 1.3 € per sample) tool for assessing cereal aphid-parasitoid-endosymbiont interactions.
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Affiliation(s)
- Zhengpei Ye
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
| | - Ines M G Vollhardt
- Agroecology, Department of Crop Sciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Susanne Girtler
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Corinna Wallinger
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Zeljko Tomanovic
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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Hall AAG, Steinbauer MJ, Taylor GS, Johnson SN, Cook JM, Riegler M. Unravelling mummies: cryptic diversity, host specificity, trophic and coevolutionary interactions in psyllid - parasitoid food webs. BMC Evol Biol 2017; 17:127. [PMID: 28587639 PMCID: PMC5461677 DOI: 10.1186/s12862-017-0959-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parasitoids are hyperdiverse and can contain morphologically and functionally cryptic species, making them challenging to study. Parasitoid speciation can arise from specialisation on niches or diverging hosts. However, which process dominates is unclear because cospeciation across multiple parasitoid and host species has rarely been tested. Host specificity and trophic interactions of the parasitoids of psyllids (Hemiptera) remain mostly unknown, but these factors are fundamentally important for understanding of species diversity, and have important applied implications for biological control. RESULTS We sampled diverse parasitoid communities from eight Eucalyptus-feeding psyllid species in the genera Cardiaspina and Spondyliaspis, and characterised their phylogenetic and trophic relationships using a novel approach that forensically linked emerging parasitoids with the presence of their DNA in post-emergence insect mummies. We also tested whether parasitoids have cospeciated with their psyllid hosts. The parasitoid communities included three Psyllaephagus morphospecies (two primary and, unexpectedly, one heteronomous hyperparasitoid that uses different host species for male and female development), and the hyperparasitoid, Coccidoctonus psyllae. However, the number of genetically delimited Psyllaephagus species was three times higher than the number of recognisable morphospecies, while the hyperparasitoid formed a single generalist species. In spite of this, cophylogenetic analysis revealed unprecedented codivergence of this hyperparasitoid with its primary parasitoid host, suggesting that this single hyperparasitoid species is possibly diverging into host-specific species. Overall, parasitoid and hyperparasitoid diversification was characterised by functional conservation of morphospecies, high host specificity and some host switching between sympatric psyllid hosts. CONCLUSIONS We conclude that host specialisation, host codivergence and host switching are important factors driving the species diversity of endoparasitoid communities of specialist host herbivores. Specialisation in parasitoids can also result in heteronomous life histories that may be more common than appreciated. A host generalist strategy may be rare in endoparasitoids of specialist herbivores despite the high conservation of morphology and trophic roles, and endoparasitoid species richness is likely to be much higher than previously estimated. This also implies that the success of biological control requires detailed investigation to enable accurate identification of parasitoid-host interactions before candidate parasitoid species are selected as biological control agents for target pests.
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Affiliation(s)
- Aidan A G Hall
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Martin J Steinbauer
- Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, VIC 3086, Australia
| | - Gary S Taylor
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Scott N Johnson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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33
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González-Chang M, Wratten SD, Lefort MC, Boyer S. Food webs and biological control: A review of molecular tools used to reveal trophic interactions in agricultural systems. FOOD WEBS 2016. [DOI: 10.1016/j.fooweb.2016.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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34
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Littlefair JE, Clare EL. Barcoding the food chain: from Sanger to high-throughput sequencing. Genome 2016; 59:946-958. [DOI: 10.1139/gen-2016-0028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
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Affiliation(s)
- Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
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Sint D, Sporleder M, Wallinger C, Zegarra O, Oehm J, Dangi N, Giri YP, Kroschel J, Traugott M. A two‐dimensional pooling approach towards efficient detection of parasitoid and pathogen
DNA
at low infestation rates. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12621] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Sint
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Marc Sporleder
- The International Potato Center (CIP) DCE Crop Systems Intensification and Climate Change (CSI‐CC) Apartado 1558 Lima 12 Peru
| | - Corinna Wallinger
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Octavio Zegarra
- The International Potato Center (CIP) DCE Crop Systems Intensification and Climate Change (CSI‐CC) Apartado 1558 Lima 12 Peru
| | - Johannes Oehm
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Naresh Dangi
- Entomology Division Nepal Agricultural Research Council (NARC) Khumaltar 44700 Lalitpur Nepal
| | - Yagya P. Giri
- Entomology Division Nepal Agricultural Research Council (NARC) Khumaltar 44700 Lalitpur Nepal
| | - Jürgen Kroschel
- The International Potato Center (CIP) DCE Crop Systems Intensification and Climate Change (CSI‐CC) Apartado 1558 Lima 12 Peru
| | - Michael Traugott
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
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Evans DM, Kitson JJN, Lunt DH, Straw NA, Pocock MJO. Merging
DNA
metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12659] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Darren M. Evans
- School of Biology Newcastle University Newcastle upon Tyne NE1 7RU UK
- School of Biological, Biomedical and Environmental Sciences University of Hull Hull HU6 7RX UK
| | - James J. N. Kitson
- School of Biological, Biomedical and Environmental Sciences University of Hull Hull HU6 7RX UK
| | - David H. Lunt
- School of Biological, Biomedical and Environmental Sciences University of Hull Hull HU6 7RX UK
| | - Nigel A. Straw
- Forest Research Alice Holt Lodge Farnham, Surrey GU10 4LH UK
| | - Michael J. O. Pocock
- Centre for Ecology & Hydrology Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB UK
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Roslin T, Majaneva S. The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite! Genome 2016; 59:603-28. [PMID: 27484156 DOI: 10.1139/gen-2015-0229] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.
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Affiliation(s)
- Tomas Roslin
- a Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden.,b Spatial Foodweb Ecology Group, Department of Agricultural Sciences, PO Box 27, (Latokartanonkaari 5), FI-00014 University of Helsinki, Finland
| | - Sanna Majaneva
- c Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden
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Stireman JO. Community ecology of the 'other' parasitoids. CURRENT OPINION IN INSECT SCIENCE 2016; 14:87-93. [PMID: 27436652 DOI: 10.1016/j.cois.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/03/2016] [Indexed: 06/06/2023]
Abstract
The study of parasitoid communities is an active and dynamic field. Most studies, however, are focused primarily on parasitic wasps, despite the thousands of other insect parasitoids distributed across many lineages. Although questions in parasitoid community ecology are much the same for different groups, answers to these questions may not be due to differing biological traits. The ecology of non-hymenopteran ('NH') parasitoid communities is poorly known, but recent work indicates that habitat and host traits have strong impacts on the size and composition of these parasitoid assemblages. Recent food-web analyses indicate that host ranges vary widely within and among taxa and associations are shaped by host ecology and defenses. Evidence is also accumulating for strong 'bottom-up' and 'top-down' multi-trophic interactions between NH-parasitoids and nonadjacent trophic levels, as well as trait-mediated indirect effects on communities. Recent technical and conceptual advances in characterizing and comparing food webs, consideration of phylogenetic history, and increasing anthropogenic impacts provide many new and stimulating areas of research on parasitoid communities.
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Affiliation(s)
- John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH, USA.
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39
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Frago E. Interactions between parasitoids and higher order natural enemies: intraguild predation and hyperparasitoids. CURRENT OPINION IN INSECT SCIENCE 2016; 14:81-86. [PMID: 27436651 DOI: 10.1016/j.cois.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 05/26/2023]
Abstract
Parasitoids kill and live at the expense of their hosts, but they also serve as food for intraguild predators and hyperparasitoids. Natural enemy diversity can thus challenge herbivore suppression by parasitoids, but this depends on the ecological niches of the species involved and their functional diversity. The spatial context is another important layer of complexity, particularly in areas with reduced habitat complexity and increased fragmentation. Parasitoids have evolved strategies to locate their host, but this can be affected by risk of intraguild predation or hyperparasitism. To better understand these interactions we need more long-term experiments and trophic-web studies. This will provide fundamental knowledge, improve pest control, and allow ecologists to better predict the impact of human activities on species extinctions.
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Affiliation(s)
- Enric Frago
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion, France; Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, Building 107, PO Box 16, 6700AA Wageningen, The Netherlands.
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van Nouhuys S. Diversity, population structure, and individual behaviour of parasitoids as seen using molecular markers. CURRENT OPINION IN INSECT SCIENCE 2016; 14:94-99. [PMID: 27436653 DOI: 10.1016/j.cois.2016.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 06/06/2023]
Abstract
Parasitoids have long been models for host-parasite interactions, and are important in biological control. Neutral molecular markers have become increasingly accessible tools, revealing previously unknown parasitoid diversity. Thus, insect communities are now seen as more speciose. They have also been found to be more complex, based on trophic links detected using bits of parasitoid DNA in hosts, and host DNA in adult parasitoids. At the population level molecular markers are used to determine the influence of factors such as host dynamics on parasitoid population structure. Finally, at the individual level, they are used to identify movement of individuals. Overall molecular markers greatly increase the value of parasitoid samples collected, for both basic and applied research, at all levels of study.
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Affiliation(s)
- Saskya van Nouhuys
- Department of Biosciences, University of Helsinki, PO box 65, Helsinki 00014, Finland; Department of Entomology, Cornell University, Comstock Hall, Cornell University, Ithaca, NY 14853, USA.
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41
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Affiliation(s)
- Sven Buerki
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
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42
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Wirta HK, Vesterinen EJ, Hambäck PA, Weingartner E, Rasmussen C, Reneerkens J, Schmidt NM, Gilg O, Roslin T. Exposing the structure of an Arctic food web. Ecol Evol 2015; 5:3842-56. [PMID: 26380710 PMCID: PMC4567885 DOI: 10.1002/ece3.1647] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/16/2015] [Accepted: 07/09/2015] [Indexed: 02/06/2023] Open
Abstract
How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure for a large part of a high-arctic food web. For this purpose, we apply a combination of recent techniques to describing the links between three predator guilds (insectivorous birds, spiders, and lepidopteran parasitoids) and their two dominant prey orders (Diptera and Lepidoptera). The resultant web shows a dense link structure and no compartmentalization or modularity across the three predator guilds. Thus, both individual predators and predator guilds tap heavily into the prey community of each other, offering versatile scope for indirect interactions across different parts of the web. The current description of a first but single arctic web may serve as a benchmark toward which to gauge future webs resolved by similar techniques. Targeting an unusual breadth of predator guilds, and relying on techniques with a high resolution, it suggests that species in this web are closely connected. Thus, our findings call for similar explorations of link structure across multiple guilds in both arctic and other webs. From an applied perspective, our description of an arctic web suggests new avenues for understanding how arctic food webs are built and function and of how they respond to current climate change. It suggests that to comprehend the community-level consequences of rapid arctic warming, we should turn from analyses of populations, population pairs, and isolated predator-prey interactions to considering the full set of interacting species.
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Affiliation(s)
- Helena K Wirta
- Department of Agricultural Sciences, University of Helsinki Latokartanonkaari 5, FI-00014, Helsinki, Finland
| | - Eero J Vesterinen
- Department of Biology, University of Turku Vesilinnantie 5, FI-20014, Turku, Finland
| | - Peter A Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University SE-106 91, Stockholm, Sweden
| | - Elisabeth Weingartner
- Department of Ecology, Environment and Plant Sciences, Stockholm University SE-106 91, Stockholm, Sweden
| | - Claus Rasmussen
- Department of Bioscience, Aarhus University Ny Munkegade 114, DK-8000, Aarhus, Denmark
| | - Jeroen Reneerkens
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen P.O. Box 11103, 9700 CC, Groningen, The Netherlands ; Arctic Research Centre, Department of Bioscience, Aarhus University Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Niels M Schmidt
- Arctic Research Centre, Department of Bioscience, Aarhus University Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Olivier Gilg
- Laboratoire Biogéosciences, UMR CNRS 6282, Université de Bourgogne 6 Boulevard Gabriel, 21000, Dijon, France ; Groupe de Recherche en Ecologie Arctique 16 rue de Vernot, 21440, Francheville, France
| | - Tomas Roslin
- Department of Agricultural Sciences, University of Helsinki Latokartanonkaari 5, FI-00014, Helsinki, Finland
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