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

Authors: CRUAUD, A. - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; DELVARE, GERARD - Cirad, France; NIDELET, SABINE - University Of Montpellier; SAUNE, LAURE - French National Institute For Agricultural Research; RATNASINGHAM, SUJEEVAN - University Of Guelph; CHARTOIS, M. - University Of Montpellier; BLAIMER, BONNIE - North Carolina State University; Gates, Michael; BRADY, S. - Smithsonian Institute; FAURE, S. - Rhodes University; VAN NOORT, SIMON - Iziko Museums Of Cape Town; ROSSI, J. - University Of Montpellier; RASPLUS, J. - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France

Submitted to: Cladistics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2020
Publication Date: 4/20/2020
Citation: Cruaud, A., Delvare, G., Nidelet, S., Saune, L., Ratnasingham, S., Chartois, M., Blaimer, B., Gates, M.W., Brady, S.J., Faure, S., Van Noort, S., Rossi, J.P., Rasplus, J.Y. 2020. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics. 1-35.
DOI: https://doi.org/10.1111/cla.12416

Interpretive Summary: Understanding the relationships of parasitic wasps to one another and any resulting reclassification is critical as a foundation for future applied research. This foundation provides a predictive and stable framework for ongoing research. This is especially important as parasitic wasps are used in biological control programs against agricultural pests, saving millions of dollars annually in control costs. Here we report on a family of wasps, as part of an international, large-scale study, presenting the first phylogenomic/morphological study proposing well supported relationships within this group. This information will be useful to entomologists, biocontrol workers, and evolutionary biologists.

Technical Abstract: Recent technical advances combined with novel computational approaches have the potential to revolutionize 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 hypothesis for the family Chalcididae an emblematic group of parasitoid wasps, with a representative sampling (144 ingroups and 7 outgroups) that covers all described subfamilies and tribes and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements 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 markers /taxa properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded on 40 taxa representative of the diversity). This joint analysis reveals that UCEs help to sort among 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 artefactual results. We highlight a GC-content bias for ML approaches, an artefactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and 10 tribes that lay the foundations for future studies on the evolutionary history of Chalcididae.