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Ultra-conserved elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

Cruaud Astrid, Delvare Gérard, Nidelet Sabine, Sauné Laure, Ratnasingham Sujeevan, Chartois Marguerite, Blaimer Bonnie B., Gates Michael W., Brady Seán G., Faure Sariana, Van Noort Simon, Rossi Jean-Pierre, Rasplus Jean-Yves. 2020. Ultra-conserved elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics, 35 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Abstract : Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAXML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

Mots-clés Agrovoc : Chalcididae, Phylogénie, morphologie

Mots-clés complémentaires : élément ultra-conservé

Mots-clés libres : Hymenoptera, Chalcidoidea, Chalcididae, Phylogenetic analysis, Ultra Conserved elements, Morphology

Classification Agris : L10 - Animal genetics and breeding

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Cruaud Astrid, INRAE (FRA)
  • Delvare Gérard, CIRAD-BIOS-UMR CBGP (FRA)
  • Nidelet Sabine, Université de Montpellier (FRA)
  • Sauné Laure, INRAE (FRA)
  • Ratnasingham Sujeevan, University of Guelph (CAN)
  • Chartois Marguerite, INRAE (FRA)
  • Blaimer Bonnie B., North Carolina State University (USA)
  • Gates Michael W., USDA (USA)
  • Brady Seán G., National Museum of Natural History (USA)
  • Faure Sariana, Rhodes University (ZAF)
  • Van Noort Simon, Iziko South African Museum (ZAF)
  • Rossi Jean-Pierre, INRAE (FRA)
  • Rasplus Jean-Yves, INRAE (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/596136/)

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