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Japanese and Ryukyu Wild Boar Formed Separate Genomic Clades

Ryukyu wild boar in Okinawa, Japan
Research · Genetics & genomics

Whole-genome analyses showed that Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus) form separate genetic clades within a shared Japanese-archipelago lineage. That broader lineage was most closely related to wild boar from eastern Russia and northern China.

The researchers resequenced genomes from five Japanese wild boar with known origins on Honshu, Shikoku and Kyushu and two Ryukyu wild boar from Okinawa and Ishigaki. They compared these with previously published genomes from other wild boar populations and domestic pigs.

Isolation within the archipelago separated the two forms

Both phylogenetic analyses and principal-component analysis (PCA), which summarises major patterns of genetic similarity and difference across many variants, separated Japanese and Ryukyu wild boar. At the same time, the two groups formed one monophyletic archipelago lineage relative to the continental populations—meaning they clustered as descendants of a shared ancestral lineage not shared with the sampled continental groups. The authors interpret this as evidence that their ancestors dispersed into the Japanese archipelago and that the two forms later diverged through geographic isolation.

Gene flow was detected for Japanese, not Ryukyu, wild boar

The genomic tests also detected a signal of introgression between Japanese wild boar and lineages from eastern Russia and northern China. No comparable signal was detected between Ryukyu wild boar and those continental populations.

The analyses do not establish when that genetic contact occurred or which direction genes moved. The study therefore supports both a shared archipelago ancestry and later differentiation between the two forms, while leaving the timing and direction of the continental gene flow unresolved.

Sources and image credit

  1. Itoi, R., Gamarra, D., Terai, Y., Gojobori, J., & Taniguchi, M. (2026). Whole-genome analyses reveal the phylogenetic history of Japanese and Ryukyu wild boars. BMC Ecology and Evolution.Primary peer-reviewed article published 11 July 2026. Five Japanese wild boar and two Ryukyu wild boar with known origins were resequenced. The two forms formed separate clades within a monophyletic Japanese-archipelago lineage. Introgression was detected between Japanese wild boar and eastern Russian/northern Chinese lineages, but not for Ryukyu wild boar; timing and direction remain unresolved.

Image: Yanbaru917 / Wikimedia Commons — live Ryukyu wild boar at Daisekirinzan, Okinawa, Japan, 19 November 2017; representative image of one of the two lineages studied · CC BY-SA 4.0 · Source

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