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Diversification processes between monogenoids (Dactylogyridae) and their marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America. Parasitology 2023; 150:184-194. [PMID: 36444641 PMCID: PMC10106279 DOI: 10.1017/s0031182022001615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Due to their high specificity, monogenoids from fish provide an interesting model to study historical associations of hosts and parasites. High agreement between host and parasite phylogeny is often interpreted as evidence of cospeciation. However, cophylogenetic signal may also arise from other, either adaptive or non-adaptive, processes. We applied the recently developed Cophylospace Framework to better understand the evolutionary relationship between monogenoids and marine catfish from the Atlantic coast of South America. The associations between 12 marine catfish and 10 monogenoid species were assessed. Molecular data of host and parasite species were used for phylogenetic reconstruction. We used anchor morphology based on Procrustes coordinates to evaluate whether closely related hosts are associated with morphologically similar parasites. To assess the association between parasite phylogeny and host morphology, we produced a distance matrix based on morphological characters of catfishes. Agreement between phylogenies and between phylogeny and morphology was measured using Procrustes R2 computed with PACo. The parasite phylogeny obtained in this study represents the first complete phylogenetic hypothesis of monogenoids parasitizing ariids from South America. The Cophylospace analysis suggested that phylogenetic and morphological distance of monogenoids contributes similarly to explain the pattern of host–parasite associations, whereas parasite phylogeny is more strongly associated with the morphological traits of the hosts than with host phylogeny. This evidence suggests that cospeciation is not a major force accounting for diversification in the monogenoids studied. Rather host morphological traits seem to be a more important driver, which conforms with evidence from other host‒monogenoid systems.
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Rahmouni C, Vanhove MP, Koblmüller S, Šimková A. Molecular phylogeny and speciation patterns in host-specific monogeneans (Cichlidogyrus, Dactylogyridae) parasitizing cichlid fishes (Cichliformes, Cichlidae) in lake tanganyika. Int J Parasitol 2022; 52:359-375. [DOI: 10.1016/j.ijpara.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022]
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Schachat SR, Labandeira CC, Clapham ME, Payne JL. A Cretaceous peak in family-level insect diversity estimated with mark-recapture methodology. Proc Biol Sci 2019; 286:20192054. [PMID: 31847775 PMCID: PMC6939917 DOI: 10.1098/rspb.2019.2054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
The history of insects' taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the 'range through' method suggests a steady, nearly monotonic increase in family-level diversity, whereas 'shareholder quorum subsampling' suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture-mark-recapture (CMR) approach is used to estimate insects' family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.
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Affiliation(s)
- Sandra R. Schachat
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Conrad C. Labandeira
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USA
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
- College of Life Sciences, Capital Normal University, Beijing 100048, People’s Republic of China
| | - Matthew E. Clapham
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Jonathan L. Payne
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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Benovics M, Desdevises Y, Šanda R, Vukić J, Šimková A. Cophylogenetic relationships betweenDactylogyrus(Monogenea) ectoparasites and endemic cyprinoids of the north‐eastern European peri‐Mediterranean region. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michal Benovics
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Yves Desdevises
- CNRS Biologie Intégrative des Organismes Marins (BIOM) Observatoire Océanologique Sorbonne Université Banyuls/Mer France
| | | | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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Huber KT, Moulton V, Sagot MF, Sinaimeri B. Exploring and Visualizing Spaces of Tree Reconciliations. Syst Biol 2018; 68:607-618. [DOI: 10.1093/sysbio/syy075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Katharina T Huber
- School of Computing Sciences, University of East Anglia, Norwich, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, UK
| | - Marie-France Sagot
- Inria Grenoble - Rhône-Alpes; Inovallée 655, Avenue de l’Europe, Montbonnot, 38334 Saint Ismier Cedex, France
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, CNRS, UMR5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Blerina Sinaimeri
- Inria Grenoble - Rhône-Alpes; Inovallée 655, Avenue de l’Europe, Montbonnot, 38334 Saint Ismier Cedex, France
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, CNRS, UMR5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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Urbini L, Sinaimeri B, Matias C, Sagot MF. Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:738-748. [PMID: 29993554 DOI: 10.1109/tcbb.2018.2838667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aim of this paper is to explore the robustness of the parsimonious host-symbiont tree reconciliation method under editing or small perturbations of the input. The editing involves making different choices of unique symbiont mapping to a host in the case where multiple associations exist. This is made necessary by the fact that the tree reconciliation model is currently unable to handle such associations. The analysis performed could however also address the problem of errors. The perturbations are re-rootings of the symbiont tree to deal with a possibly wrong placement of the root specially in the case of fast-evolving species. In order to do this robustness analysis, we introduce a simulation scheme specifically designed for the host-symbiont cophylogeny context, as well as a measure to compare sets of tree reconciliations, both of which are of interest by themselves.
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Berry V, Chevenet F, Doyon JP, Jousselin E. A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions. Mol Ecol Resour 2018; 18:1173-1184. [PMID: 29697894 DOI: 10.1111/1755-0998.12897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 11/30/2022]
Abstract
Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and are not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX to visualize ancestral character states on the phylogenetic trees and highlight parts of reconciliations that are geographically inconsistent when not accounting for geographic constraints. We suggest that the comparison of reconciliations obtained with and without such constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography, and the advent of next-generation sequencing that leads to better-resolved trees, a geography-aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.
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Affiliation(s)
- Vincent Berry
- Institut de Biologie Computationnelle, LIRMM, Université de Montpellier, CNRS, Montpellier, France
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - François Chevenet
- Institut de Biologie Computationnelle, LIRMM, Université de Montpellier, CNRS, Montpellier, France
- MIVEGEC, CNRS 5290, IRD 224, Université de Montpellier, Montpellier, France
| | - Jean-Philippe Doyon
- Institut de Biologie Computationnelle, LIRMM, Université de Montpellier, CNRS, Montpellier, France
| | - Emmanuelle Jousselin
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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Fusu L. An integrative taxonomic study of European Eupelmus (Macroneura) (Hymenoptera: Chalcidoidea: Eupelmidae), with a molecular and cytogenetic analysis of Eupelmus (Macroneura) vesicularis: several species hiding under one name for 240 years. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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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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Amouroux P, Crochard D, Germain JF, Correa M, Ampuero J, Groussier G, Kreiter P, Malausa T, Zaviezo T. Genetic diversity of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile. Sci Rep 2017; 7:2014. [PMID: 28515435 PMCID: PMC5435716 DOI: 10.1038/s41598-017-01997-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 04/05/2017] [Indexed: 11/12/2022] Open
Abstract
Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees. We sequenced the COI and 28S genes in each population. In total, 19 Diaspididae species and 11 Coccidae species were identified morphologically. From the 63 COI haplotypes and the 54 28S haplotypes uncovered, and using several DNA data analysis methods (Automatic Barcode Gap Discovery, K2P distance, NJ trees), up to 36 genetic clusters were detected. Morphological and DNA data were congruent, except for three species (Aspidiotus nerii, Hemiberlesia rapax and Coccus hesperidum) in which DNA data revealed highly differentiated lineages. More than 50% of the haplotypes obtained had no high-scoring matches with any of the sequences in the GenBank database. This study provides 63 COI and 54 28S barcode sequences for the identification of Coccoidea from Chile.
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Affiliation(s)
- P Amouroux
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - D Crochard
- INRA, Université Côte d'Azur, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia, Antipolis, France
| | - J-F Germain
- ANSES, Laboratoire de la Santé des Végétaux, unité Entomologie et Plantes Invasives, CBGP, 755 avenue du Campus Agropolis, 34988, Montferrier-sur-Lez, France
| | - M Correa
- INRA, Université Côte d'Azur, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia, Antipolis, France
| | - J Ampuero
- Xilema-ANASAC Control Biológico, San Pedro, Quillota, Chile
| | - G Groussier
- INRA, Université Côte d'Azur, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia, Antipolis, France
| | - P Kreiter
- INRA, Université Côte d'Azur, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia, Antipolis, France
| | - T Malausa
- INRA, Université Côte d'Azur, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia, Antipolis, France
| | - T Zaviezo
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
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Cruaud A, Rasplus JY. Testing cospeciation through large-scale cophylogenetic studies. CURRENT OPINION IN INSECT SCIENCE 2016; 18:53-59. [PMID: 27939711 DOI: 10.1016/j.cois.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Insects are involved in a multitude of interactions with other organisms, which make them ideal models for large-scale cophylogenetic studies. Once phylogenies of interacting lineages have been inferred, there are a number of questions we may wish to ask, such as what was the relationship between the partners in the past? Have they co-evolved for thousands or millions of years, or has one of the partners switched among different host species? To answer such questions, researchers may conduct cophylogenetic analysis, to explore the relationships between the phylogenies of interacting lineages and determine whether the match is significant or find explanations for observed differences. When combined with dating analyses, cophylogenetic analyses may support cospeciation of the partners or phylogenetic tracking. As they may reveal dynamics of host-pathogen coevolution, cophylogenetic studies may also help tackle global health issues (e.g. document the spread of disease causing pathogens). Cophylogenetic studies of parasitoids and their insect hosts may also help identify effective biocontrol agents. With the advent of next generation sequencing technologies and keeping in mind that systematic errors may occur, cophylogenetics will benefit from better-resolved trees, allowing more accurate reconciliation. However as trees become larger, current algorithms also become more computationally challenging. Nevertheless, both theoretical and methodological developments are leading to more accurate and powerful tests of cospeciation through cophylogenetic analysis.
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Affiliation(s)
- Astrid Cruaud
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
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Hamerlinck G, Hulbert D, Hood GR, Smith JJ, Forbes AA. Histories of host shifts and cospeciation among free‐living parasitoids of
Rhagoletis
flies. J Evol Biol 2016; 29:1766-79. [DOI: 10.1111/jeb.12909] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 02/05/2023]
Affiliation(s)
- G. Hamerlinck
- Department of Biology University of Iowa Iowa City IA USA
| | - D. Hulbert
- Department of Entomology Michigan State University East Lansing MI USA
| | - G. R. Hood
- Department of Biological Sciences University of Notre Dame South Bend IN USA
| | - J. J. Smith
- Department of Entomology Michigan State University East Lansing MI USA
| | - A. A. Forbes
- Department of Biology University of Iowa Iowa City IA USA
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Gebiola M, Bernardo U, Ribes A, Gibson GAP. An integrative study of Necremnus Thomson (Hymenoptera: Eulophidae) associated with invasive pests in Europe and North America: taxonomic and ecological implications. Zool J Linn Soc 2015; 173:352-423. [PMID: 25745268 PMCID: PMC4328149 DOI: 10.1111/zoj.12210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 02/05/2023]
Abstract
The species of Necremnus attacking two invasive pests of tomato and canola in Europe and North America, respectively, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) and Ceutorhynchus obstrictus (Marsham) (Coleoptera: Curculionidae), have been revised using an integrative taxonomy approach. Molecular data from the mitochondrial cytochrome oxidase c subunit I and the nuclear D2 expansion region of the 28S ribosomal subunit and internal transcribed spacer 2, the discovery of new morphological features, and study of type material resulted in the delineation of three species groups, the Necremnus artynes, Necremnus cosconius, and Necremnus tidius groups, the discovery of four new species, and the resurrection of three taxa from synonymy. Lectotypes have been designated for 13 species originally described in Eulophus by Walker. Although Necremnus has not been revised, an illustrated key is given to differentiate 23 recognized European species. The key, type images, and treatments of the three species groups will enable more accurate identification of the valid species of Necremnus in the future. They will also benefit biological control practitioners of pest species. The ecological consequences of the new taxonomic concepts are discussed.
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Affiliation(s)
- Marco Gebiola
- CNR - Istituto per la Protezione Sostenibile delle Plante UOS di Portici - Via Università 133, 80055, Portici, NA, Italy ; Department of Entomology, The University of Arizona 410 Forbes Bldg., Tucson, AZ, 85721, USA
| | - Umberto Bernardo
- CNR - Istituto per la Protezione Sostenibile delle Plante UOS di Portici - Via Università 133, 80055, Portici, NA, Italy
| | - Antoni Ribes
- C/Lleida 36 25170 Torres de Segre, Lleida, Spain
| | - Gary A P Gibson
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes K. W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, Canada, K1A 0C6
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Abstract
Background Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tree using event-based maximum parsimony. Given a cost model for the events, many optimal reconciliations are however possible. Any further biological interpretation of them must therefore take this into account, making the capacity to enumerate all optimal solutions a crucial point. Only two algorithms currently exist that attempt such enumeration; in one case not all possible solutions are produced while in the other not all cost vectors are currently handled. The objective of this paper is two-fold. The first is to fill this gap, and the second is to test whether the number of solutions generally observed can be an issue in terms of interpretation. Results We present a polynomial-delay algorithm for enumerating all optimal reconciliations. We show that in general many solutions exist. We give an example where, for two pairs of host-parasite trees having each less than 41 leaves, the number of solutions is 5120, even when only time-feasible ones are kept. To facilitate their interpretation, those solutions are also classified in terms of how many of each event they contain. The number of different classes of solutions may thus be notably smaller than the number of solutions, yet they may remain high enough, in particular for the cases where losses have cost 0. In fact, depending on the cost vector, both numbers of solutions and of classes thereof may increase considerably. To further deal with this problem, we introduce and analyse a restricted version where host switches are allowed to happen only between species that are within some fixed distance along the host tree. This restriction allows us to reduce the number of time-feasible solutions while preserving the same optimal cost, as well as to find time-feasible solutions with a cost close to the optimal in the cases where no time-feasible solution is found. Conclusions We present Eucalypt, a polynomial-delay algorithm for enumerating all optimal reconciliations which is freely available at http://eucalypt.gforge.inria.fr/. Electronic supplementary material The online version of this article (doi:10.1186/s13015-014-0031-3) contains supplementary material, which is available to authorized users.
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Kapranas A, Tena A. Encyrtid parasitoids of soft scale insects: biology, behavior, and their use in biological control. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:195-211. [PMID: 25341100 DOI: 10.1146/annurev-ento-010814-021053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Parasitoids of the hymenopterous family Encyrtidae are one of the most important groups of natural enemies of soft scale insects and have been used extensively in biological control. We summarize existing knowledge of the biology, ecology, and behavior of these parasitoids and how it relates to biological control. Soft scale stage/size and phenology are important determinants of host range and host utilization, which are key aspects in understanding how control by these parasitoids is exerted. Furthermore, the nutritional ecology of encyrtids and their physiological interactions with their hosts affect soft scale insect population dynamics. Lastly, the interactions among encyrtids, heteronomous parasitoids, and ants shape parasitoid species complexes and consequently have a direct impact on the biological control of soft scale insects.
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Affiliation(s)
- Apostolos Kapranas
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland;
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