(a) Three scenarios of phylogenetic relationships among bilaterians can be postulated. In the first scenario (monophyletic deuterostome), 2 deuterostome branches, chordates and ambulacrarians, are grouped together, and their LCA (the LCA of deuterostomes) is denoted with a blue dot. The LCA of bilaterians is indicated with a red dot. In the other 2 scenarios, one of the deuterostome branches is grouped with protostomes, resulting in polyphyletic deuterostomes. In these latter 2 scenarios, the LCA of deuterostomes and bilaterians is the same. (b) Distinct chromosomal rearrangement events of each species, including fusion, split, and spread events, are recorded into the category data based on changes deviated from the 1N = 24 BALGs. For example, there are 3 categories for the bilaterian ALG K, including (1) no rearrangement event (BFL, SPU, POC, SCA, PFL), (2) O2⊗K (RPH, SCO, PYE, PEC), and (3) J1⊗(O2⊗K) (SBE). (c) Conversion of the category data into a binary data matrix. Dark vertical lines distinguish different chromosomes. Red box denotes the chromosomal status of each species as compared to the BALGs. For the 10 species that we examined, the number of the chromosomal rearrangement categories ranges from 2 (BALGs F, G, N, and I) to 8 (BALG B2). A detailed binary code table is provided in S1 Data. (d, e) Bayesian phylogenetic analysis (d) and clustering analysis (e) based on the binary data shows that the 5 deuterostome species (shaded in blue) are grouped together. The data underlying this figure can be found in S1 Data. BALG, bilaterian ancestral linkage group; LCA, last common ancestor.

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