Shared derived chromosome features between bryozoans and brachiopods support the Lophophorata hypothesis. (A) Chromosome-scale gene linkage between the bryozoan M. membranacea and the brachiopod L. anatina. Horizontal bars represent chromosomes. Vertical lines connect the genomic position of orthologous genes in each genome. Lines are colored by bilaterian ALGs. (B) Oxford dot plot showing shared ALG fusion events between L. anatina and M. membranacea. Each point represents a pair of orthologs placed by their ordinal position in each genome, colored by their bilaterian ALG. Black boxes highlight shared fusion-with-mixing events, in which two ALGs appear together on the same chromosome in both species. (C) Representation of the nine ALG fusion-with-mixing events shared between L. anatina and M. membranacea. Colored squares represent ALGs; black lines represent chromosomes; and ⊗ marks ALG fusion-with-mixing events. ALGs J2, L, O1, R, C1, G, I, O2, and K are colocated on Chr 1 in L. anatina. ALGs J2, L, O1, R, C1, G, and I (Chrs 1, 2, 3, 4) and O2 and K (Chrs 9, 10) are also colocated in M. membranacea. Thus, J2 ⊗ L ⊗ O1 ⊗ R ⊗ C1 ⊗ G ⊗ I and O2 ⊗ K represent seven fusion-with-mixing events shared by both species. ALGs H, Q, A1, and C2 are colocated on Chr 2 in L. anatina. H and Q (Chrs 1, 2, 4) and A1 and C2 (Chrs 6, 8) are also colocated in M. membranacea. Accordingly, H ⊗ Q and A1 ⊗ C2 represent two additional fusion-with-mixing events shared by both species, for a total of nine. We note that several spiralian phyla share four of these events (“lophotrochozoan ancestral fusions”), represented by ⊗ within parentheses, although their timing remains uncertain. If these events are present in all spiralians, for instance, they may not be useful phylogenetic markers for the position of bryozoans. This leaves five confirmed derived fusion-with-mixing events (highlighted in bold) shared between bryozoans and brachiopods but not present in molluscs and annelids. These events suggest a close evolutionary relationship between bryozoans and brachiopods and are marked by ⊗ occurring outside of parentheses: (J2 ⊗ L) ⊗ (O1 ⊗ R) ⊗ C1 ⊗ G⊗I and A1 ⊗ C2. (D–G) Visual representation of four possible evolutionary scenarios that could give rise to the five derived fusion-with-mixing events shared between bryozoans and brachiopods (types A, B, and C). An open circle marks the base of the Lophotrochozoa. Black circles mark chromosome fusion-with-mixing events. (D) Scenario type A: Brachiopods, phoronids, and bryozoans are closely related, forming the Lophophorata. The five fusion-with-mixing events shared between bryozoans and L. anatina occurred in the ancestor of the Lophophorata. Total number of fusions required: five. (E) Scenario type B-1: Bryozoans, Cycliophora, and Entoprocta are closely related, forming the Polyzoa. Bryozoans are distantly related to brachiopods. The five fusion-with-mixing events shared between bryozoans and L. anatina occurred independently in bryozoans and brachiopods. Total number of fusions required: 10. (F) Scenario type B-2: Brachiopods, phoronids, and bryozoans are closely related, forming the Lophophorata. The five fusion-with-mixing events shared between bryozoans and L. anatina occurred independently in bryozoans and brachiopods. Total number of fusions required: 10. (G) Scenario type C: Brachiopods, phoronids, and bryozoans are closely related, forming the Lophophorata. Some of the five fusion-with-mixing events shared between bryozoans and L. anatina occurred in the ancestor of Lophophorata, whereas some occurred independently in bryozoans and brachiopods. Total number of fusions required: six to nine.
