A genome-scale phylogeny of scorpions: model comparison and modeling among-site compositional heterogeneity

The evolutionary history of scorpions, one of the most charismatic groups of arthropods with over 2,500 described species, is a subject of great interest. Given their unique body plan and ancient fossil record, understanding their phylogeny is crucial. Recent genome-scale data have shown potential in elucidating interfamilial relationships within the scorpion tree of life; however, discrepancies between molecular datasets have also been observed. To address this, we explored the phylogenetic relationships of scorpions by synthesizing three previous phylogenomic studies using model comparison methods that account for among-site compositional heterogeneity. Our analyses indicate that under the infinite site-heterogeneous CAT and finite mixture models, the relationships within Scorpiones differ significantly from prevailing conclusions, particularly regarding the interfamilial relationships within Buthida. Our results show the following relationships: [Pseudochactoidea + [Buthoidea + Chaeriloidea]]. Our leave-one-out cross-validation analysis shows that the site-heterogeneous CAT-GTR+G model fits significantly better than the site-homogeneous model (LG) and finite mixture models (LG+C20, LG+C60), and it identifies contentious nodes in scorpion phylogeny. These analyses resolve a longstanding controversy in deep scorpion phylogeny and emphasize the significance of adequate modeling of compositional heterogeneity in reconstructing the deep phylogeny of scorpions.