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Japanese Rock Ptarmigan Has a Distinct Mitochondrial Lineage That Diverged About 80,000–120,000 Years Ago

Japanese rock ptarmigan in summer plumage on Mount Tsubakuro, Japan
Research · Genetics & genomics

Japanese rock ptarmigan (Lagopus muta japonica) form a genetically distinct mitochondrial lineage that appears to have separated from other rock ptarmigan populations roughly 80,000–120,000 years ago. The result comes from a PLOS ONE study published in February 2026 using museum specimens, including birds collected more than a century ago. Because mitochondrial DNA is inherited through the maternal line, this divergence estimate primarily describes the population’s maternal evolutionary history rather than its complete nuclear-genome history.

The researchers analysed 18 preserved specimens: 16 from Japan, including three associated with extinct Japanese populations, plus one bird from the northern Kuril Islands and one from Scandinavia. Despite highly fragmented DNA in many of the older specimens, they reconstructed the complete mitochondrial genome of every individual. Across the Japanese mitochondrial genomes they identified ten haplotypes. Several mitochondrial regions varied among individuals, but the analyses found no clear geographic genetic subdivision between the sampled Japanese regions.

The Japanese lineage remained distinct in the global comparison

To place the Japanese birds in a wider context, the team also compared control-region sequences from 209 rock ptarmigan across the species’ global range. The Japanese birds formed three unique control-region haplotypes in a monophyletic group and differed by at least three nucleotide substitutions from the closest haplotypes found elsewhere. The closest control-region haplotypes were found in Greenland and Scandinavia, while another closely related haplotype occurred across the northern Kuril Islands, Aleutians, Siberia and Alaska. The Japanese lineage nevertheless remained clearly distinct. Despite that isolation, control-region haplotype and nucleotide diversity in Japan were not markedly lower than in several other regions across the species’ range. In biological terms, the long-isolated Japanese maternal lineage still retained a level of mitochondrial sequence variation comparable to several other sampled regions.

A long-isolated relict lineage

The authors argue that the results strengthen the view of the Japanese population as a long-isolated relict lineage with its own evolutionary history. They also show that old museum specimens kept under challenging storage conditions can still yield complete mitochondrial genomes, providing material for reconstructing population history that would otherwise be inaccessible.

Sources and image credit

  1. Nagata, N., Sugita, N., Kawakami, K., & Nishiumi, I. (2026). Genetic diversity and phylogenetic relationships of the rock ptarmigan (Lagopus muta) in Japan based on mitochondrial genome analysis of museum specimens. PLOS ONE, 21(2), e0339266. https://doi.org/10.1371/journal.pone.0339266Primary open-access study published 6 February 2026. Complete mitochondrial genomes were reconstructed from 18 preserved specimens: 16 from Japan, including three associated with extinct Japanese populations, plus comparative specimens from the northern Kuril Islands and Scandinavia. A control-region network based on 209 birds worldwide placed the Japanese population in a distinct monophyletic group; divergence-time estimates placed separation of the Japanese maternal lineage at roughly 80,000–120,000 years ago.

Image: Daisuke Tashiro / Wikimedia Commons — Japanese rock ptarmigan (Lagopus muta japonica) in summer plumage on Mount Tsubakuro, Japan, photographed 1 June 2014; representative image of the subspecies. · CC BY-SA 2.0 — https://creativecommons.org/licenses/by-sa/2.0/ · Source

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