Comparing coding regions of melanin production pathway between colour morphs
A total of 15 coding regions of genes known to be involved in the melanin production pathway were compared between genomes (Table S2). 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-Join and BioNJ algorithms, 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.