By the year 2008, the population of red-headed wood pigeons in Japan’s Ogasawara Islands had dwindled to fewer than 80 individuals. On Chichijima Island, invasive feral cats contributed significantly to the threats faced by this unique bird species, prompting conservationists to initiate a rigorous cat trapping program starting in 2010.
During a three-year period, conservation teams captured 131 feral cats, reducing the feral cat population on the island to under 20. Concurrently, sightings of adult pigeons soared from 111 to 966, while juvenile observations increased dramatically from 9 to 189.
This population surge presented scientists with an intriguing genetic conundrum. Research published on July 15, 2025, in Communications Biology revealed that over 80% of the pigeon’s genome was homozygous, indicating intense inbreeding. Despite this, these endangered pigeons harbored fewer severely harmful mutations than the more common Japanese wood pigeon. The researchers suggest that living as a small population for centuries may have allowed the species to purge some of its genetic defects before the recent decline.
Feral Cat Reduction and Pigeon Numbers Soar Together
The red-headed wood pigeon (Columba janthina nitens) is native exclusively to the Ogasawara Islands, which lie roughly 1,000 kilometers south of Japan’s main islands. This archipelago is recognized as a UNESCO World Heritage Site since 2011, encompassing over 30 islands and boasting exceptional levels of species found nowhere else.
The Communications Biology article links the decline of the red-headed wood pigeon to human disturbance such as forest loss and predation by introduced feral cats. Although the trapping efforts on Chichijima did not eradicate the cats entirely, their numbers dropped below 20 between 2010 and 2013, coinciding with a rise in pigeon observations.
Human habitation on the Ogasawara Islands dates back to 1830, according to the researchers. Their analysis of the pigeon’s demographic history indicates the species maintained a relatively small population before human settlement, followed by a sharp decline during periods of intensified human activity.
Using various recombination rates, genetic data suggested the effective population dropped from thousands to a minimum of 88 individuals in 1957 or 56 individuals in 1985. Estimates later rose to between 117 and 498 birds by 2007. The team cautions that estimates closer to the sampling date are less reliable and may not perfectly reflect the true population size.
High Homogeneity Across the Pigeon Genome
To investigate the species’ recovery from critically low numbers, Daichi Tsujimoto and colleagues analyzed genomic sequences, pedigree records, and fitness traits. They successfully sequenced and compared 25 pigeon genomes, including eight wild red-headed wood pigeons, eight captive birds of the same subspecies, and nine Japanese wood pigeons.
The genomes of the endangered pigeons showed extensive runs of homozygosity, where both inherited chromosome copies are nearly identical. The average inbreeding coefficient calculated from these regions was 0.84 for wild red-headed wood pigeons and 0.88 for captive individuals, compared to a much lower 0.02 for Japanese wood pigeons.
The presence of extensive homozygous regions longer than 0.1 megabases also pointed to a long-term small population size spanning approximately 895 years. Over 80% of wild red-headed wood pigeon genomes consisted of such homozygous segments.
Comparisons of harmful mutations revealed that wild and captive red-headed wood pigeons carried only 13 nonsense single-nucleotide polymorphisms, whereas the Japanese wood pigeon bore 96 such mutations. These nonsense mutations, which disrupt protein function, serve as markers for a population’s genetic load of dangerous variants.
Both wild and captive red-headed wood pigeons exhibited a significantly lower ratio of harmful nonsense to silent mutations than Japanese wood pigeons, suggesting that prolonged small populations may have allowed natural processes to weed out many dangerous variants.
Gradual Inbreeding Likely Facilitated Genetic Purging
The researchers suggest a process called genetic purging, where harmful, recessive mutations that are normally masked in heterozygous individuals become exposed as inbreeding increases homozygosity. This exposure allows natural selection to eliminate or reduce damaging alleles over generations.
Tsujimoto’s team argues that the red-headed wood pigeon’s sustained small population size enabled slow and gradual purging, contrasting with rapid inbreeding events after sudden population crashes when harmful effects may intensify before purging is effective.
Still, not all harmful mutations disappeared. Eight of the 13 nonsense mutations were nearly fixed in both wild and captive populations. The team notes that fixed deleterious mutations do not cause inbreeding depression but may still decrease overall population fitness.
Other endangered species such as the island fox, Seychelles paradise flycatcher, northern elephant seal, and Iberian lynx also show evidence of genetic purging, generally linked to long-term isolation and small population sizes.
A 2023 study on the Seychelles paradise flycatcher provides a comparative case. This species declined to just 28 individuals in the 1960s before rebounding past 250 by the 1990s. Genetic analyses revealed a tenfold decrease in diversity, partial elimination of highly deleterious mutations, and accumulation of milder harmful variants.
Inbreeding Does Not Significantly Affect Captive Pigeon Lifespan
The study also examined 119 captive-born red-headed wood pigeons with documented pedigrees and lifespans. Researchers found no significant correlation between inbreeding levels and longevity. Although data hinted at longer lifespans for more inbred birds, this trend was not statistically significant and could reflect improvements in captive care over time.
However, the study did not rule out potential fitness costs of inbreeding. Fertility effects were not investigated due to potential bias from captive management, and hatching success was not evaluated. The authors emphasize that inbreeding depression may be less apparent under controlled captive conditions versus the wild.
At Tokyo’s Ueno Zoological Gardens, a captive population of red-headed wood pigeons began in 2001 with only three founders. Breeding among founder descendants increased inbreeding until wild individuals were introduced starting in 2012 to bolster diversity. By 2022, five generations had been born, with 198 birds held in captivity during the program’s duration.
Despite the recovery, low genetic variation could still hinder the pigeons’ ability to adapt to environmental changes. Persistent small population size may lead to further genetic drift and fixation of harmful alleles. Continued expansion of captive populations and close genetic monitoring remain crucial strategies.
The UNESCO World Heritage Centre highlights invasive species as a major threat to the Ogasawara Islands’ ecological integrity. The study describes the red-headed wood pigeon as one of the few large seed dispersers left on the archipelago, following the disappearance of the endemic Bonin wood pigeon in 1889.
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