Positive Selection in NADH Dehydrogenase 2 (ND2) Gene in Two Billfishes Xiphias gladius, L. 1758 and Istiophorus platypterus

The assumption of neutrality for mitochondrial DNA has been widely questioned due to the functional importance of the encoded proteins. Mitochondrial genes involved in the oxidative phosphorylation (OXPHOS) pathway can be subjected to selection due to changes in some environmental conditions or in the living habits of specimens in order to adapt to their environment. In this study, We search for evidence of positive selection in COI, Cytb, and ND2 mitochondrial OXPHOS genes in 100 specimens of Xiphias gladius belonging to Atlantic, Indian, and Mediterranean stocks through codon models for inference of site-specific positive selection. For comparison, the same analysis was conducted on sequences of the same genes belonging to the closely related species Istiophorus platypterus, which are present in GenBank. The ND2 sequence analysis identified a non-synonymous transversion (T to A) at the nucleotide position 293, resulting in a codon change in the Greek population of X. gladius. Selection tests showed diversifying positive selection for only the ND2 dataset in both species, at 324 codon positions by MEME and FUBAR in X. gladius and only by the FUBAR test at 19 codon positions in I. platypterus.