Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Andrew Z. Ontano, Guilherme Gainett, Shlomi Aharon, Jesus A. Ballesteros, Ligia R. Benavides, Kevin F. Corbett, Efrat Gavish-Regev, Mark S. Harvey, Scott Monsma, Carlos E. Santibañez-Lopez, Emily V.W. Setton, Jakob T. Zehms, Jeanne A. Zeh, David W. Zeh, Prashant P. Sharma*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

42 Scopus citations

Abstract

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Original languageAmerican English
Pages (from-to)2446-2467
Number of pages22
JournalMolecular Biology and Evolution
Volume38
Issue number6
DOIs
StatePublished - 1 Jun 2021

Bibliographical note

Publisher Copyright:
© The Author(s) 2021.

Keywords

  • Arachnids
  • MicroRNA
  • Ohnologs
  • Species tree reconciliation
  • Supermatrix

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