For studies on CNEs related to candidate genes, we manually aligned the genomic loci with more reference fish including nonmodel species to refine the CNEs and determine candidate regulatory aspects that can be lineage or species specific, using the above criteria. Six wild four from Thailand and two from Cambodia, respectively and 28 randomly particular domesticated fish were sequenced with 500 bp insert libraries supplementary table S8, Supplementary Material online. Nine “elephant ear” mutants, that is, with phenotype of overgrowth of pectoral fin, were further sequenced to identify the genetic locus supplementary table S8, Supplementary Material online. Raw sequencing reads were filtered using the above method. Sequence mapping and variant calling were performed using BWA mem Bessa et al. 2009 and Picard/GATK v4.