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Table S1. Locality information for rhodopsin samples included in the study and associated GenBank accession numbers.

Table S2. MutPred scores and significant structural or functional hypotheses representing the probability that a mutation is deleterious for each unique rhodopsin mutation in cave and surface percopsiform lineages.

Table S3. Eye structures in amblyopsid cavefishes. The eyes of Speoplatyrhinus poulsoni and newly recognized Typhlichthys lineages have not been histologically examined.

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