Comparing coding regions of melanin production pathway between colour morphs
A total of 15 coding regions of genes known to be involved either in the melanin production pathway or in coloration in general were compared between colour morphs´ genomes (Table S2 and Table S3). These coding regions were selected based on literature reporting either associations or functional links to coloration across different vertebrate taxa. Coding sequences were extracted with blasr (Chaisson & Tesler, 2012) and seqtk (Li, 2012) from grey morph assembly and utilized as a reference to identify similar regions on the brown morph genome. Sequences were inspected for start and stop codons to ensure completeness as well as for synonymous and non-synonymous mutations after alignment with MUSCLE (Edgar, 2004). We then utilized NCBI’s blast to collect similar sequences (>95% similarity) to phylogenetically contextualize any observed variation between morphs. Phylogenetic analyses were performed in MEGA11 (Tamura, Stecher, & Kumar, 2021) with a Maximum Likelihood approach. We estimated nucleotide substitution model, which was then inserted as a parameter in the ML tree construction. The bootstrap consensus was inferred with 10000 replicates, and trees to initiate the algorithm were obtained aby applying Neighbor-Joining and BioNJ algorithms (for the initial tree), utilizing all sites, prior to selecting the topology with superior log likelihood value and with complete deletion. Lastly, we estimated Nei’ s evolutionary distances between and within putative copies.