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Figure S1. Phylogenetic analysis of UOX. Bayesian inference of UOX amino acid sequences. Numbers on branches indicate posterior probability values (>95). Amino acid model: mixed (Jones posterior probability: 0.892; WAG posterior probability: 0.108). The Branchiostoma floridae sequence was the out-group.

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Figure S2. Phylogenetic analysis of PRHOXNB. Bayesian inference of PRHOXNB amino acid sequences. Midpoint rooting. Numbers on branches indicate posterior probability values (>95). Amino acid model: Jones.

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Figure S3. Phylogenetic analysis of ALN. Bayesian inference of ALN amino acid sequences. Numbers on branches indicate posterior probability values (>95). Amino acid model: WAG. The Strongylocentrotus purpuratus sequence was the out-group.

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Figure S4. Phylogenetic analysis of ALC. Bayesian inference of ALC amino acid sequences. Numbers on branches indicate posterior probability values (>95). Amino acid model: mixed (WAG posterior probability: 0.999; Jones posterior probability: 0.001). The Branchiostoma belcheri tsingtauense sequence was the out-group.

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Figure S5. Microsyntenies of UOX. Arrows indicate the transcriptional orientation, brackets indicate the arrangement of distant loci on the same chromosome.

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Figure S6. Microsyntenies of PRHOXNB. Arrows indicate the transcriptional orientation.

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Figure S7. Microsyntenies of ALN. Arrows indicate the transcriptional orientation, brackets indicate the arrangement of distant loci on the same chromosome. ALN of Anolis carolinensis (not annotated in Ensembl) was identified by homology and is delineated by the coordinates reported in the figure.

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Figure S8. Microsyntenies of ALC. Arrows indicate the gene orientation, brackets indicate the arrangement of distant loci on the same chromosome.

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Table S1. Accession number list of the sequences used in the phylogenetic analyses and for UOX multiple sequence alignment.

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