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.
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.Read the article »
Article DOI: 10.1111/cla.12416
Project DOI: 10.7934/P3929, http://dx.doi.org/10.7934/P3929
This project contains | Matrices |
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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 |
Currently Viewing:
MorphoBank Project 3929
MorphoBank Project 3929
- Creation Date:
17 February 2021 - Publication Date:
17 February 2021 - Project views: 10548
- Media downloads: 2
- Matrix downloads: 15
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
| cell scorings (scored, NPA, "-") | cell
| rules | ||||||
MorphoBank Curator Project Administrator | 40 | 1 | 1 | 130 | 0 | 0 | 4515 (4475, 0, 40) | 0 | 0 | 0 | ||||
Jean-Yves Rasplus Full membership | 0 | 0 | 0 | 0 | 0 | 0 | 0 (0, 0, 0) | 0 | 0 | 0 |
Taxonomic Overview for Matrix 'M27233' (40 Taxa)
taxon | unscored cells |
scored cells |
no cell support |
NPA cells |
"-" cells | cell images | labels on cell images |
member access |
[1] Tetramesa sp Last Modified in 02/17/21 | 20 | 106 | 106 | 0 | 4 | 0 | 0 | 2 |
[2] Rileya jras07552 Last Modified in 02/17/21 | 21 | 106 | 106 | 0 | 3 | 0 | 0 | 2 |
[3] Macrorileya inopinata Last Modified in 02/17/21 | 1 | 125 | 125 | 0 | 4 | 0 | 0 | 2 |
[4] Acanthochalcis nigricans Last Modified in 02/17/21 | 20 | 108 | 108 | 0 | 2 | 0 | 0 | 2 |
[5] Cratocentrus aff decoratus Last Modified in 02/17/21 | 1 | 124 | 124 | 0 | 5 | 0 | 0 | 2 |
[6] Cratocentrus gdel00534 Last Modified in 02/17/21 | 34 | 95 | 95 | 0 | 1 | 0 | 0 | 2 |
[7] Trigonura sp Last Modified in 02/17/21 | 2 | 128 | 128 | 0 | 0 | 0 | 0 | 2 |
[8] Trigonura gdel00437 Last Modified in 02/17/21 | 31 | 99 | 99 | 0 | 0 | 0 | 0 | 2 |
[9] Stypiura sp Last Modified in 02/17/21 | 2 | 128 | 128 | 0 | 0 | 0 | 0 | 2 |
[10] Stypiura gdel00580 Last Modified in 02/17/21 | 32 | 98 | 98 | 0 | 0 | 0 | 0 | 2 |
[11] Brachymeria minuta Last Modified in 02/17/21 | 1 | 129 | 129 | 0 | 0 | 0 | 0 | 2 |
[12] Brachymeria podagrica Last Modified in 02/17/21 | 32 | 98 | 98 | 0 | 0 | 0 | 0 | 2 |
[13] Brachymeria tibialis Last Modified in 02/17/21 | 1 | 129 | 129 | 0 | 0 | 0 | 0 | 2 |
[14] Brachymeria gdel00453 Last Modified in 02/17/21 | 34 | 96 | 96 | 0 | 0 | 0 | 0 | 2 |
[15] Chalcis myrifex Last Modified in 02/17/21 | 0 | 130 | 130 | 0 | 0 | 0 | 0 | 2 |
[16] Melanosmicra variventris Last Modified in 02/17/21 | 1 | 129 | 129 | 0 | 0 | 0 | 0 | 2 |
[17] Conura immaculata Last Modified in 02/17/21 | 0 | 130 | 130 | 0 | 0 | 0 | 0 | 2 |
[18] Conura marcosensis Last Modified in 02/17/21 | 30 | 100 | 100 | 0 | 0 | 0 | 0 | 2 |
[19] Conura decisa Last Modified in 02/17/21 | 1 | 129 | 129 | 0 | 0 | 0 | 0 | 2 |
[20] Conura aff xanthostigma Last Modified in 02/17/21 | 32 | 98 | 98 | 0 | 0 | 0 | 0 | 2 |
[21] Dirhinus anthracia Last Modified in 02/17/21 | 1 | 128 | 128 | 0 | 1 | 0 | 0 | 2 |
[22] Hontalia aff caerulea Last Modified in 02/17/21 | 38 | 92 | 92 | 0 | 0 | 0 | 0 | 2 |
[23] Epitranus observator Last Modified in 02/17/21 | 2 | 126 | 126 | 0 | 2 | 0 | 0 | 2 |
[24] Epitranus gdel00570 Last Modified in 02/17/21 | 30 | 100 | 100 | 0 | 0 | 0 | 0 | 2 |
[25] Smicromorpha doddi Last Modified in 02/17/21 | 17 | 107 | 107 | 0 | 6 | 0 | 0 | 2 |
[26] Smicromorpha malaica Last Modified in 02/17/21 | 40 | 86 | 86 | 0 | 4 | 0 | 0 | 2 |
[27] Belaspidia nigra Last Modified in 02/17/21 | 16 | 114 | 114 | 0 | 0 | 0 | 0 | 2 |
[28] Tropimeris gdel00333 Last Modified in 02/17/21 | 32 | 98 | 98 | 0 | 0 | 0 | 0 | 2 |
[29] Neochalcis fertoni Last Modified in 02/17/21 | 16 | 114 | 114 | 0 | 0 | 0 | 0 | 2 |
[30] Hockeria bifasciata Last Modified in 02/17/21 | 0 | 130 | 130 | 0 | 0 | 0 | 0 | 2 |
[31] Haltichella gdel00144 Last Modified in 02/17/21 | 19 | 110 | 110 | 0 | 1 | 0 | 0 | 2 |
[32] Antrocephalus sp Last Modified in 02/17/21 | 0 | 129 | 129 | 0 | 1 | 0 | 0 | 2 |
[33] Antrocephalus gdel00481 Last Modified in 02/17/21 | 33 | 96 | 96 | 0 | 1 | 0 | 0 | 2 |
[34] Notaspidium sp Last Modified in 02/17/21 | 7 | 121 | 121 | 0 | 2 | 0 | 0 | 2 |
[35] Notaspidium gdel00469 Last Modified in 02/17/21 | 37 | 92 | 92 | 0 | 1 | 0 | 0 | 2 |
[36] Zavoya cooperi Last Modified in 02/17/21 | 19 | 109 | 109 | 0 | 2 | 0 | 0 | 2 |
[37] Irichohalticella sp Last Modified in 02/17/21 | 34 | 96 | 96 | 0 | 0 | 0 | 0 | 2 |
[38] Lasiochalcidia dargelasii Last Modified in 02/17/21 | 15 | 115 | 115 | 0 | 0 | 0 | 0 | 2 |
[39] Psilochalcis immaculata Last Modified in 02/17/21 | 33 | 97 | 97 | 0 | 0 | 0 | 0 | 2 |
[40] Invreia subaenea Last Modified in 02/17/21 | 0 | 130 | 130 | 0 | 0 | 0 | 0 | 2 |
Project views
type | number of views | Individual items viewed (where applicable) |
Total project views | 10548 | |
Project overview | 773 | |
Matrix views | 687 | Morphological data matrix (79 views); Matrix landing page (608 views); |
Specimen list | 1000 | |
Media views | 2024 | Media search (1720 views); M739114 (304 views); |
Views for media list | 618 | |
Taxon list | 5069 | |
Bibliography | 371 | |
Documents list | 6 |
Project downloads
type | number of downloads | Individual items downloaded (where applicable) |
Total downloads from project | 91 | |
Media downloads | 2 | M739114 (2 downloads); |
Matrix downloads | 15 | Morphological data matrix (15 downloads); |
Project downloads | 74 |