Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques

Ito, T.; Hayakawa, T.; Kurihara, Y.; Hanya, G.; Kaneko, A.; Natsume, T.; Aisu, S.; Honda, T.; Wakamori, H.; Yachimori, S.; Anezaki, T.; Omi, T.; Hayama, S.-i.; Kawamoto, Y.

doi:10.64898/2026.10.02.752851

bioRxiv · 10.64898/2026.10.02.752851

Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques

Ito, T.·Hayakawa, T.·Kurihara, Y.·Hanya, G.·Kaneko, A.·Natsume, T.·Aisu, S.·Honda, T.·Wakamori, H.·Yachimori, S.·Anezaki, T.·Omi, T.·Hayama, S.-i.·Kawamoto, Y.

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Abstract

The relative roles of genetic drift, inbreeding, and natural selection in island evolution have been fundamental themes in evolutionary biology for nearly a century. However, empirical studies have yet to reach a consensus, and research integrating both genotypes and phenotypes in primates remains limited. The present study aims to estimate the demographic history of an island primate population, the Yakushima macaque (Macaca fuscata yakui), and evaluate the genomic and morphological consequences of its isolation. To this end, we conducted population genetic analyses based on whole-genome sequencing and geometric morphometric analyses of cranial shape. Our results indicate that M. f. yakui has been isolated with an effective population size of several thousand individuals for over 100,000 years. Although we detected signatures of purifying selection, deleterious alleles have not been sufficiently purged. The degree of fluctuating asymmetry in males was slightly, yet significantly, higher in M. f. yakui than in mainland populations, whereas this trend was not observed in females. Marginal evidence of directional selection was found for cranial size, but not for shape. Overall, our findings suggest that due to long-term isolation, genetic drift and inbreeding have exerted a substantial influence on shaping genotypic and phenotypic variation in this island population.

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Ito, T., Hayakawa, T., Kurihara, Y., Hanya, G., Kaneko, A., Natsume, T., Aisu, S., Honda, T., Wakamori, H., Yachimori, S., Anezaki, T., Omi, T., Hayama, S.-i., Kawamoto, Y.. 2026-10-04. Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques. https://doi.org/10.64898/2026.10.02.752851

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