Development of a framework for the study of selecting pressures on differentially expressed genes and its application to the study of genes involved in immunity response in mantellin frogs (Anura: Mantellidae: Mantellinae)

Positive selection stands at the base of adaptive evolution by fixing over time a beneficial genetic mutation into a population. A measure to assess the selective pressure occurring on sites, proteins or genes is a parameter known as dN/dS ratio, calculated as the ratio between the non-synonymous and synonymous substitution rate. According to its estimated value, it shows evidences of negative (<1), neutral (=1) or positive (>1) selection, which allow to understand whether selection acting on that part of the genome is the likely source of new adaptive traits or whether it encodes traits that will likely be conserved In this work, I first developed a tentative framework for the study of selecting pressures acting on differentially expressed genes. Later, I used this dataset to explore the nature and strength of selective pressures acting on differentially expressed genes involved in the immune system functions in Malagasy frogs of the subgenus Brygoomantis (Anura: Mantellidae: Mantellinae: Mantidactylus). The dataset is composed by genes which were found to be differentially expressed in the liver and in the skin and that Gene Ontology analyses suggested are related to immune system functions. The identification of these genes in Malagasy frogs is here documented for the first time. These genes can have an important role in the immunological responses to pathogens, one of the main threats to amphibians worldwide. We found evidences of positive selection acting in the immunological genes from skin and liver here analyzed, suggesting a possible role of immune system in driving the speciation process of Brygoomantis subgenus.