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

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 LBA 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 datasets. Pseudoscorpion placement
is particularly variable across datasets and analytical frameworks, with
this group either clustering with other long-branch orders or with
Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, 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.