Project 3929: A. Cruaud, G. Delvare, S. Nidelet, L. Sauné, S. Ratnasingham, M. Chartois, B. B. Blaimer, M. Gates, S. G. Brady, S. Faure, S. Noort, J. Rossi, J. Rasplus. 2021. Ultra‐Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics. 37 (1):1-35.
Specimen: Brachymeria tibialis (unvouchered)
View: whole organism

Abstract

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


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Article DOI: 10.1111/cla.12416

Project DOI: 10.7934/P3929, http://dx.doi.org/10.7934/P3929
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 40 Taxa
  • 1 Specimen
  • 130 Characters
Total size of project's media files: 368.4k

Download Project SDD File
Total scored cells: 4515
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 130
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 313
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:130/0
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MorphoBank Project 3929

    Authors' Institutions

    • Iziko South African Museum, Cape Town

    • National Museum of Natural History, Smithsonian Institution

    • Institut National de Recherches Agronomiques (INRA)

    • North Carolina State University

    • Universite de Montpellier

    • University of Cape Town

    • University of Guelph

    • Rhodes University



    Members

    member name taxa specimens media chars character
    media
    labels
    cell scorings
    (scored, NPA, "-")
    cell
    medialabels
    rules
    MorphoBank Curator
    Project Administrator
    4011130004515
    (4475, 0, 40)
    000
    Jean-Yves Rasplus
    Full membership
    0000000
    (0, 0, 0)
    000


    Taxonomic Overview for Matrix 'M27233' (40 Taxa)

    taxon unscored
    cells
    scored
    cells
    no cell
    support
    NPA
    cells
    "-" cellscell images labels on
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    member
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    [1] Tetramesa sp
    Last Modified in 02/17/21
    2010610604002
    [2] Rileya jras07552
    Last Modified in 02/17/21
    2110610603002
    [3] Macrorileya inopinata
    Last Modified in 02/17/21
    112512504002
    [4] Acanthochalcis nigricans
    Last Modified in 02/17/21
    2010810802002
    [5] Cratocentrus aff decoratus
    Last Modified in 02/17/21
    112412405002
    [6] Cratocentrus gdel00534
    Last Modified in 02/17/21
    34959501002
    [7] Trigonura sp
    Last Modified in 02/17/21
    212812800002
    [8] Trigonura gdel00437
    Last Modified in 02/17/21
    31999900002
    [9] Stypiura sp
    Last Modified in 02/17/21
    212812800002
    [10] Stypiura gdel00580
    Last Modified in 02/17/21
    32989800002
    [11] Brachymeria minuta
    Last Modified in 02/17/21
    112912900002
    [12] Brachymeria podagrica
    Last Modified in 02/17/21
    32989800002
    [13] Brachymeria tibialis
    Last Modified in 02/17/21
    112912900002
    [14] Brachymeria gdel00453
    Last Modified in 02/17/21
    34969600002
    [15] Chalcis myrifex
    Last Modified in 02/17/21
    013013000002
    [16] Melanosmicra variventris
    Last Modified in 02/17/21
    112912900002
    [17] Conura immaculata
    Last Modified in 02/17/21
    013013000002
    [18] Conura marcosensis
    Last Modified in 02/17/21
    3010010000002
    [19] Conura decisa
    Last Modified in 02/17/21
    112912900002
    [20] Conura aff xanthostigma
    Last Modified in 02/17/21
    32989800002
    [21] Dirhinus anthracia
    Last Modified in 02/17/21
    112812801002
    [22] Hontalia aff caerulea
    Last Modified in 02/17/21
    38929200002
    [23] Epitranus observator
    Last Modified in 02/17/21
    212612602002
    [24] Epitranus gdel00570
    Last Modified in 02/17/21
    3010010000002
    [25] Smicromorpha doddi
    Last Modified in 02/17/21
    1710710706002
    [26] Smicromorpha malaica
    Last Modified in 02/17/21
    40868604002
    [27] Belaspidia nigra
    Last Modified in 02/17/21
    1611411400002
    [28] Tropimeris gdel00333
    Last Modified in 02/17/21
    32989800002
    [29] Neochalcis fertoni
    Last Modified in 02/17/21
    1611411400002
    [30] Hockeria bifasciata
    Last Modified in 02/17/21
    013013000002
    [31] Haltichella gdel00144
    Last Modified in 02/17/21
    1911011001002
    [32] Antrocephalus sp
    Last Modified in 02/17/21
    012912901002
    [33] Antrocephalus gdel00481
    Last Modified in 02/17/21
    33969601002
    [34] Notaspidium sp
    Last Modified in 02/17/21
    712112102002
    [35] Notaspidium gdel00469
    Last Modified in 02/17/21
    37929201002
    [36] Zavoya cooperi
    Last Modified in 02/17/21
    1910910902002
    [37] Irichohalticella sp
    Last Modified in 02/17/21
    34969600002
    [38] Lasiochalcidia dargelasii
    Last Modified in 02/17/21
    1511511500002
    [39] Psilochalcis immaculata
    Last Modified in 02/17/21
    33979700002
    [40] Invreia subaenea
    Last Modified in 02/17/21
    013013000002


    Project views

    type number of views Individual items viewed (where applicable)
    Total project views390
    Project overview48
    Matrix views47Morphological data matrix (14 views); Matrix landing page (33 views);
    Specimen list40
    Media views99Media search (85 views); M739114 (14 views);
    Views for media list29
    Taxon list112
    Bibliography15




    Project downloads

    type number of downloads Individual items downloaded (where applicable)
    Total downloads from project19
    Media downloads2M739114 (2 downloads);
    Matrix downloads4Morphological data matrix (4 downloads);
    Project downloads13