Phylogenomic analysis of ultraconserved elements clarifies relationships and morphological evolution in...

Targeted enrichment of ultraconserved elements (UCEs) is a powerful tool for resolving phylogeny in groups with limited morphological or molecular data. Here, we use UCEs to reconstruct the first comprehensive phylogeny of the chiton superfamily Cryptoplacoidea, including museum material up to 133 years old. Phylogenomic analyses based on maximum likelihood, ASTRAL, and maximum parsimony demonstrate that Acanthochitonidae, as it was traditionally defined, is paraphyletic, comprising three distinct, well-supported families. We restrict Acanthochitonidae sensu stricto to Acanthochitona and the reinstated genus Meturoplax, reinstate a family Cryptoconchidae, and establish a new family Sulcichitonidae. Nuttallochitonidae is elevated to superfamily rank based on its consistent phylogenetic position and distinctive morphology. The genus Choneplax is polyphyletic, with its species distributed across three genera in two families, possibly resulting from habitat-driven convergent evolution. Ancestral state reconstructions reveal that there is no stepwise reduction in slit number but independent shifts correlating with tegmentum reduction and ecological specialization in multiple lineages. Reconstruction of historical biogeography suggests an Indo-Pacific origin for Cryptoplacoidea, with strong geographic structuring within Acanthochitona. Our results demonstrate the power of UCEs to capture data from historical specimens and for resolving complex phylogenetic problems. This study provides a robust framework for understanding morphological evolution and diversification in difficult groups.