A comprehensive phylogenomic framework for brachiopod evolution among lophotrochozoans

Brachiopods appeared early in the Cambrian radiation and represent an important clade for understanding the origin of animal body plans and the evolution of biomineralized structures. A robust phylogenetic framework of the living representatives is needed to answer persistent questions about the evolution of brachiopod mineralogy, shell morphology, and identification of the brachiopod sister group among Lophotrochozoa. To the best of our knowledge, we present the first phylogenomic analysis of Brachiopoda and related lophotrochozoan lineages using a comprehensive dataset encompassing all five extant brachiopod orders and using a custom-developed data-refining strategy, compositionally heterogeneous substitution models, and a novel implementation of the parametric-bootstrap likelihood ratio test. We recover monophyly of Lophophorata, with strong support for Brachiopoda as sister to Bryozoa plus Phoronida. Within Brachiopoda, we recover the clade of inarticulated phosphatic Linguliformea sister to the inarticulated calcitic Craniiformea, with both sister to the articulated calcitic Rhynchonellata, with miniaturized Thecideida unexpectedly nested within Terebratulida. Our phylogeny implies that at least one evolutionary transition in primary mineralogy occurred in Brachiopoda, a phenomenon not recognized in any other metazoan group.