Exome analysis reveals species divergence in TYR and identifies species genetic markers in five endemic Macaca species on Sulawesi Island.

Background: One of the greatest challenges for evolutionary biologists is explaining the vast diversity observed in nature. On Sulawesi Island, macaque species (genus Macaca) have rapidly diverged from their common ancestor, displaying remarkable variability in body morphology and coat color. Despite low overall genetic variation among these macaques, limited hybridization occurs between neighboring species, possibly due to genomic divergence or local adaptations that act as barriers to interbreeding. This study aims to investigate highly divergent regions that might contribute to the distinct genetic and phenotypic characteristics differentiating the five Sulawesi macaque species. Additionally, it explores how these genetic differences influence biological functions, and identifies species-specific genetic markers for species identification and conservation.

Results: Using whole exome sequencing of 46 individuals, approximately 550 highly divergent genes were identified across four pairwise species comparisons. Gene Ontology (GO) analysis revealed that these genes were enriched in critical biological processes, including cell adhesion, pigmentation, signal transduction, and stress responses. Among these, pigmentation-associated genes, such as TYR and LRIT3, exhibited highly divergent single nucleotide polymorphisms (SNPs). Missense mutations in TYR (D132N) and LRIT3 (S394P, Y363D) were likely linked to the dark coat colors of Macaca nigra and Macaca nigrescens, highlighting their contribution to species-specific traits. Furthermore, hundreds of fixed SNPs were identified as potential species-specific markers for species discrimination, providing valuable resource for distinguishing Sulawesi macaque species.

Conclusions: This study provides critical insights into the genetic mechanisms underlying species divergence and coat color variation in Sulawesi macaques. Highly divergent genomic regions between neighboring species likely contribute to species divergence and reinforce reproductive isolation. Enriched GO terms and pathways suggest that genetic divergence impacts key biological processes, including pigmentation, signal transduction, cell adhesion, and stress responses. Specifically, divergence in pigmentation-related genes such as TYR may play a role in interspecies differences in coat color, facilitating local adaptation, mate selection, and species identification. Additionally, the identification of species-specific genetic markers holds significant potential for conservation efforts, such as monitoring populations at risk of hybridization or genetic introgression. These findings advance our understanding of the genetic diversity in this unique primate group.