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.