Back from the brink of extinction

Kyoto, Japan -- For many endangered species, population decline to the brink of extinction leads to inbreeding, exposing a species to deleterious recessive mutations that severely limit its potential to recover. But the red-headed wood pigeon, endemic to the Ogasawara Islands in Japan, followed a different trajectory.

Although this pigeon population fell to below 80 individuals in the 2000s, it began to increase markedly after the removal of an introduced predator, the feral cat. Such a remarkable recovery raised questions regarding inbreeding, and why harmful mutations that could cause inbreeding depression, or a loss of genetic diversity, didn't hinder the species' revival.

In an effort to unravel this biological puzzle, a team of researchers at Kyoto University set out to investigate the factors that contributed to this unlikely comeback.

"Many endangered species struggle to recover even with intensive conservation measures," says first author Daichi Tsujimoto. "This pigeon's exceptional rebound led us to investigate the underlying genetic reasons for its resilience, hoping to uncover what makes some endangered species more capable of recovery than others."

The team sequenced and compared the whole genomes of both wild and captive red-headed wood pigeon populations, as well as a wild population of the Japanese wood pigeon. Their analysis enabled them to evaluate the level of inbreeding and genetic load in the endangered species and assess how its historical population dynamics influenced these factors.

Their results revealed that the frequency of highly deleterious mutations in the red-headed wood pigeon was lower than in the more widespread Japanese wood pigeon. This suggests that, rather than hindering it, the pigeon's success was likely rooted in its long-term persistence in a small population size prior to human impact.

Centuries of gradual inbreeding in a historically small and isolated population may have effectively allowed the species to expel deleterious mutations from its genome through a process called genetic purging. This seems to have equipped it with a robust genetic foundation, enabling its population to survive a bottleneck and rebound dramatically just three years after the removal of the predators.

"This unique evolutionary history appears to have provided these pigeons with a resilience that is not seen in other endangered populations," says team leader Yuji Isagi.

This study challenges the common assumption that inbreeding hinders recovery by expressing harmful genetic mutations.

Nonetheless, the population's long-term survival is still in question. Suffering such a severe loss of genetic diversity may have reduced the pigeon's adaptive capacity to future environmental changes, and a population below historic levels remains vulnerable to further erosion of genetic diversity and the accumulation of harmful mutations. Thus restoring the pigeon to its historic levels is essential.

Ultimately, this new insight suggests that conservation efforts should not only aim to increase genetic diversity, but also consider the unique genetic history of each species to develop more informed and effective strategies for their long-term survival.

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The paper "Genetic purging in an island-endemic pigeon recovering from the brink of extinction" appeared on 15 July 2025 in Communications Biology, with doi: 10.1038/s42003-025-08476-z

About Kyoto University

Kyoto University is one of Japan and Asia's premier research institutions, founded in 1897 and responsible for producing numerous Nobel laureates and winners of other prestigious international prizes. A broad curriculum across the arts and sciences at undergraduate and graduate levels complements several research centers, facilities, and offices around Japan and the world. For more information, please see: http://www.kyoto-u.ac.jp/en