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

Linking genetic variation with traits of interest has been a longstanding challenge for evolutionary biologists. Here, we explore elements of genome evolution in the hero shrew (Soricidae: Scutisorex somereni): a small, elusive mammal with the most distinctive vertebral column in the entire tree of life. We first assembled and annotated a draft genome from short-read, long-read, and chromosome-conformation-capture sequencing for S. somereni. We combined this genome with publicly available genomes from 30 other mammal species spanning millions of years of evolutionary history to search for genes potentially 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 the hero shrew's extreme phenotype. Overall, our study is a critical first step that has highlighted candidate genes and gene families for further genomic exploration, underscoring the continuing challenge of understanding the genomic underpinnings of unusual phenotypes.