Genetic characterization of Macaca arctoides: A highlight of key genes and pathways

• Published in: Primates Vol. 64; no. 4; pp. 451 - 462
• Main Authors: Novak, Taylor E., Bailey, Nick P., Stevison, Laurie S.
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 01.07.2023; Springer Nature B.V
• Subjects: Animal Ecology; Animals; Behavioral Sciences; Biological Evolution; Biomedical and Life Sciences; Coloration; Data analysis; Evolutionary Biology; Genes; Genomes; Hedgehog protein; Hedgehog Proteins - genetics; Immune response; Life Sciences; Macaca - genetics; Macaca arctoides; MicroRNAs; Non-coding RNA; Original Article; Outliers (statistics); Permutations; Phenotypes; Pleiotropy; Signal transduction; Wnt protein; Zoology; Evolution; Genetics; Bear macaque; Bioinformatics; Coloration
• ISSN: 0032-8332; 1610-7365
• DOI: 10.1007/s10329-023-01064-x

When compared to the approximately 22 other macaque species, Macaca arctoides has many unique phenotypes. These traits fall into various phenotypic categories, including genitalia, coloration, mating, and olfactory traits. Here we used a previously identified whole genome set of 690 outlier genes to look for possible genetic explanations of these unique traits. Of these, 279 genes were annotated miRNAs, which are non-coding. Patterns within the remaining outliers in coding genes were investigated using GO ( n  = 370) and String ( n  = 383) analysis, which showed many interconnected immune-related genes. Further, we compared the outliers to candidate pathways associated with M. arcotides’ unique phenotypes, revealing 10/690 outlier genes that overlapped these four pathways: hedgehog signaling, WNT signaling, olfactory, and melanogenesis. Of these, genes in all pathways except olfactory had higher F ST values than the rest of the genes in the genome based on permutation tests. Overall, our results point to many genes each having a small impact on phenotype, working in tandem to cause large systemic changes. Additionally, these results may indicate pleiotropy. This seems to be especially true with the development and coloration of M. arctoides. Our results highlight that development, melanogenesis, immune function, and miRNAs may be heavily involved in M. arctoides’ evolutionary history.