The REL algorithm in HyPhy showed that piscidin codons 25 and 29 are under adaptive selection (p = 0.99 and p = 1.00, respectively).
In this study, the Bayesian approach in model M3 revealed three positively selected sites at positions 25 (p = 0.97, where p denotes posterior probability of assigning a site to the positively-selected class), 29 (p = 1.00) and 43 (p = 0.99), whereas only position 29 was found to be under adaptive selection according to model M8 (p = 0.95).
In our previous study, we demonstrated that tlr22 genes from several teleost taxa (Cyprinidae, Gasterosteidae, Salmonidae, Adrianichthyidae, Tetraodontidae) are under adaptive selection pressure [ 11].
The various tlr22 paralogues are evolving at different molecular rates and several codons in the region coding for their ligand binding domain are under adaptive selection, which may contribute to their functional diversification through neofunctionalisation.
Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection.
In this study, although most paralogs and orthologs of these young duplicate gene families had Ka/Ks ratios lower than 1, some Ka/Ks ratios greater than 1 were also found both in species-specific and lineage-specific expansions, demonstrating that they were under adaptive selection.
The excess of genes under adaptive selection is still more striking when balancing selection is considered.
These data indicate that both proteins are under strong purifying selection and, therefore, they must maintain some function, perhaps related to their original enzymatic activity, and that they are not on the process of becoming pseudogenes or are under strong adaptive selection.
A comparison between the PAML, DataMonkey, and Selecton results gave no consensus of any sites adjudged to be under strong adaptive selection with high probabilities.
Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection.
