Phoronid genome supports a monophyletic Lophophorata

Resolving deep branches of the animal tree of life remains a major challenge in evolutionary biology. One long-standing debate concerns the putative clade Lophophorata, which includes brachiopods, phoronids, and bryozoans, united by a ciliated feeding organ known as the lophophore. While some phylogenomic studies support lophophorate monophyly,^1,2 others group bryozoans with entoprocts and cycliophorans as Polyzoa.^3,4 Here, we show that shared chromosome fusion events provide sequence-independent evidence for a close relationship between phoronids and bryozoans. Using a new chromosome-level genome of a phoronid, we identify seven irreversible fusion-with-mixing events shared with bryozoans, one of which is also found in brachiopods. These fusions are absent from other lophotrochozoans, including molluscs, annelids, and nemerteans, supporting a grouping of the three lophophorates. Phylogenomic analyses utilizing chromosome-level genomes and ortholog sets curated to reduce systematic errors also consistently recover Lophophorata as monophyletic. Finally, transcriptomic profiling of lophophores across the three lophophorate phyla reveals a shared co-option of vertebrate head genes together with the shared expression of lineage-specific genes. This integration of ancestral and derived components provides molecular evidence that lophophores are homologous organs rather than convergent filter-feeding adaptations. Together, these findings resolve a century-old debate in metazoan phylogeny, robustly placing phoronids as the sister phylum to bryozoans and highlighting the potential of genome structure analyses in reconstructing deep evolutionary relationships.