Genome evolution and the enigmatic axial skeleton of the hero shrew (Soricidae: Scutisorex somereni)

Linking genetic variation with traits of interest has been a longstanding challenge for evolutionary biologists. Aided by the "genomics revolution", comparative genomics studies now routinely connect genes with traits in non-model organisms. Here, we explore elements of genome evolution in the hero shrew (Soricidae: Scutisorex somereni) a small, rare mammal with the most distinctive vertebral column in the entire tree of life. We first assembled and annotated a draft genome for S. somereni and then used publicly available genomes from 30 other mammal species spanning millions of years of evolutionary history to search for genes that could be related to the evolution of the S. somereni axial skeleton. We first performed an orthology clustering analysis to identify gene duplications and single copy orthologs. With orthogroups, we tested for gene family expansion and contraction. The single copy orthologs that we identified were used to test for positive selection or changes in selective constraint in S. somereni compared to the other species considered. We found significant gene family size change in immune, sensory, and metabolic gene families, and identified multiple HOX genes under positive selection that might help explain the evolution of this extremely modified phenotype. Our study underscores the importance of using non-model organisms in comparative genomics studies to learn about the origin of biodiversity.