Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection

Chang, Chia Lin; Semyonov, Jenia; Cheng, Po Jen; Huang, Shang Yu; Park, Jae Il; Tsai, Huai-Jen; Lin, Cheng-Yung; Grützner, Frank; Soong, Yung Kuei; Cai, James J.; Hsu, Sheau Yu Teddy

CEACAM orthologs appear to expand quickly and repeatedly in multiple vertebrate lineages, which is similar to what happened with olfactory and vomeronasal receptors [26] . Due to the high divergence of CEACAM protein sequences, it is impossible to obtain a reliable alignment that includes all CEACAM homologs. We resorted to select representative genes from each lineage so that outlier sequences were not included in the multiple sequence alignment. We constructed representative sets of genes from three targeted clades: primate only, mammal only, and fish only. The amino-acid sequences were aligned using MUSLE v3.8 with default settings [33] . The pairwise genetic distances between amino-acid sequences was estimated using the JTT matrix-based method [34] . All ambiguous positions were removed for each sequence pair. The phylogenetic trees were first constructed using the Neighbor-Joining method [35] implemented in MEGA v5.05 [36] . The bootstrap consensus tree was inferred from 1,000 replicates to represent the phylogenetic relationship between sequences of the proteins analyzed [37] .