In Japan, Crested Ibis Nipponia nippon is a special natural treasure and a specified national endangered species of Wild Fauna and Flora. This species became extinct in the wild in Japan in 1981. The current captive population, which was established in Japan in 1999, stems from a total of seven founders provided by China to facilitate captive breeding for release back into the wild. Since the reintroduction program was initiated in 2008, the captive population has played a critical role as the source of the released birds and hence the gene pool of the reintroduced population. In this study, several population genetic parameters and the genetic diversity of the captive population were estimated using pedigree data of individuals including all of the founders. The effective population size was estimated to be 11.2 in 2004 and 25.8 in 2021 with a gradual increase in recent years. The average degree of inbreeding was 2.2% in 2004 and 8.9% in 2018, after which it began to decline. The effective number of founders was 2.67 in 2004, rising to 4.96 in 2021, while that of non-founders was 22.8 in 2021. The value of founder genome equivalents was 4.08 in 2021, showing a consistent increase from 2.38 in 2004. The total loss of genetic diversity in 2021 was 0.123, and had decreased steadily from 0.210 in 2004. This was found to be attributed to the losses of 0.071 (58%), 0.029 (24%) and 0.020 (18%) due to the limited number of founders, the unequal genetic contributions of founders, and the population bottleneck and Mendelian sampling, respectively. In conclusion, while this study has revealed generally desirable trends of genetic diversity and population genetic parameters over about 20 years, it is suggested that further efforts should be made to increase genetic diversity beyond the current level.
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