Coincident evolution and functional adaptation of the Caenorhabditis-restricted genes ivph-3 and gon-14
Poorly conserved or taxonomically-restricted genes represent a sizable portion of most genomes. Many of these genes participate in essential processes and can contribute to evolutionary innovation in species. However, identifying which genes are biologically important and uncovering their functions remains a significant challenge, since routine tools reliant on gene ontology or sequence orthology are of limited use. Here we evaluate two genes of the Caenorhabditis-restricted class of LIN-15B-domain-encoding genes, ivph-3 and gon-14, and compare their in vivo functions in two species, C. elegans and C. briggsae. We show that within the Elegans supergroup of Caenorhabditis, ivph-3 and gon-14 exhibit sequence constraints distinct from other family members, including maintenance of a one-to-one orthology and a higher degree of stabilizing selection. Coincidentally, mutants for either of the genes exhibit strong phenotypic defects that are similar within-species (C. elegans or C. briggsae), but with notable differences when comparing between species. These findings highlight the genetic and genomic features associated with the evolution of a taxonomically restricted gene family, and suggest mechanisms by which specific family members adapt to fulfill essential biological functions. Overall design: RNA-seq profiling of C. briggsae wild strain AF16 and mutant Cbr-ivph-3 hermaphrodites at L3 larval stage.