Differential gene expression in Passer sparrows and the effect of hybridization and adaptation

Abstract

RNA-sequencing is a tool which provides an opportunity to study the differential gene expression of organisms both with and without prior knowledge of their genomic sequence, expanding genomic studies also to non-model organisms. RNA-sequencing was used in this study to detect differentially expressed genes between Passer sparrows in an evolutionary context to study the effects of hybridization and adaptation. This study is based on tissue samples from three Passer species: house sparrow P.domesticus, the Italian sparrow P.italiae, Spanish sparrow P.hispaniolensis and a group of first generation house and Spanish hybrids. The house sparrow and Italian sparrow are human-commensal and are associated with human cities and agriculture, while the Spanish sparrow is not human commensal. Through performing genome mapping with Hisat2 and differential gene expression analysis with EdgeR, I identified the most differentially expressed genes and the expression patterns between these sparrow species. The differential expression analysis found higher expression of genes related to pathogen-defence, metabolism and skull morphology in the commensal sparrows relative to the non-commensal sparrows, and differential expression between hybrid and parent species for genes related to learning and cognition. These differences may aid our understanding of the adaptations to human and urban environments, and the consequences of hybridization.