Multiple drivers of genomic novelty across ruminants.

Ruminants are among the most ecologically and economically important groups of mammals and have accumulated some of the most remarkable traits and genomes across metazoans. Using genomic-scale data representing all ruminant families, we examined the traits that explain evolutionary rates across ruminant lineages and genes. Bayesian phylogenetic regression revealed that ruminant genome-wide rates are associated with chromosome number, longevity, sexual dimorphism, and domestication. Orthogonal dimensions of genomic rates showed that genes with the greatest rate change are associated with domestication, suggesting these events have a strong impact on ruminant genome evolution. Decomposition of d N/d S rates captured a signal of body size impacting a narrow and yet important portion of the genome in which larger ruminants show consistently weakened purifying selection. Protein-coding loci were associated with the greatest change in evolutionary rates across metabolic, gene signaling, and neurologically functional pathways, suggesting these are core to ruminant evolutionary diversity. This study reveals the primary forces driving biological novelty across the ruminants.