Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps

Junxia Zhang, Amelia R.I. Lindsey, Ralph S. Peters, John M. Heraty, Keith R. Hopper, John H. Werren, Ellen O. Martinson, James B. Woolley, Matt J. Yoder, Lars Krogmann

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we present a transcriptome-based phylogeny of Chalcidoidea; we found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data. Concatenation analyses consistently place Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However, our coalescent analyses provide a different hypothesis with a grouping of (Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)), remaining Chalcidoidea)). This hypothesis complicates our hypothesis of egg parasitism as being the ancestral state in Chalcidoidea. At the deeper nodes, the results uncovered a wide spectrum of gene discordance in the transcriptomic markers and identified a strong signal of functional bias in genes supporting alternative phylogenies. These deeper nodes of the phylogeny are thus strongly influenced by biased support from different functional gene complexes. Shallower nodes showed similar gene discordance, but without strong functional bias. Understanding and identifying mechanisms that result in gene tree discordance may be beneficial and even essential for elucidating deeper relationships, especially for groups that have undergone extremely rapid radiation.

Original languageEnglish (US)
Pages (from-to)783-802
Number of pages20
JournalSystematic Entomology
Issue number4
StatePublished - Oct 1 2020

Bibliographical note

Funding Information:
This work was funded by the NSF DEB-1555808 to JMH, JBW and MY, NSF DEB-1257601 to KRH and JBW, the NIH RO1GM098667 and Nathaniel and Helen Wisch Chair to JHW, and the Advanced Talents Incubation Program of the Hebei University to JZ (grant no. 521000981324). We would like to express our gratitude to Mark Hibbins, Mark S. Springer, Richard Stouthamer, Roger Burks, Alexander Knyshov, Austin Baker, Ryan Perry, Robert Kresslein, Krissy Dominguez and Samantha Smith for valuable discussions and comments on this project, and to Mike Lewis (Centre for Invasive Species Research, UC Riverside), Nina Fatouros, Hana K???eneck?, Libor Kub?tl, Piotr Nasrecki, and Alex Wild for permission to use their photographs in this publication. We thank Irene Newton for running phybin. Petr Jan?ta is acknowledged for providing specimens of G. stigma and Podagrionini sp. Alex Donath submitted the Glyphomerus and Podagrionini sp. data to GenBank. The Supercomputer Centre at Hebei University provided computational resources for part of the analyses. The authors declare that there is no conflict of interest.

Publisher Copyright:
© 2020 The Royal Entomological Society


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