Ordered phylogenomic subsampling enables diagnosis of systematic errors in the placement of the enigmatic arachnid order Palpigradi

The miniaturized arachnid order Palpigradi has ambiguous phylogenetic
affinities, due to its odd combination of plesiomorphic and derived
morphological traits. This lineage has never been sampled in phylogenomic
datasets because of its small body size and fragility of most species, a
sampling gap of immediate concern to recent disputes over arachnid
monophyly. To redress this gap, we sampled a population of the
cave-inhabiting species Eukoenenia spelaea from Slovakia
and inferred its placement in the phylogeny of Chelicerata using dense
phylogenomic matrices of up to 1450 loci, drawn from high-quality
transcriptomic libraries and complete genomes. The complete matrix
included exemplars of all extant orders of Chelicerata. Analyses of the
complete matrix recovered palpigrades as the sister group of the
long-branch order Parasitiformes (ticks) with high support. However,
sequential deletion of long-branch taxa revealed that the position of
palpigrades is prone to topological instability. Phylogenomic subsampling
approaches that maximized taxon or dataset completeness recovered
palpigrades as the sister group of camel spiders (Solifugae), with modest
support. While this relationship is congruent with the location and
architecture of the coxal glands, a long-forgotten character system that
opens in the pedipalpal segments only in palpigrades and solifuges, we
show that nodal support values in concatenated supermatrices can mask high
levels of underlying topological conflict in the placement of the
enigmatic Palpigradi.