The Red-crowned Crane (Grus japonensis) is an endangered species that inhabits Hokkaido and Far-eastern Eurasia, and has been classified as VU in IUCN and Ministry of Environment in Japan. In Hokkaido, it was nearly extinct in the 1800s because of hunting pressure and degradation of habitats. However, the current Hokkaido population has been recovered from the brink of extinction due to conservation efforts such as artificial feeding in agricultural fields. Serious bottleneck in the past could have led severe inbreeding and loss of genetic diversity, which potentially have negative impacts on their fitness: immunity, reproductive success and ability of adaptation to the environmental changes. Hence, it is essential to reveal the potential risk of extinction by clarifying the genetic diversity and the degree of inbreeding for establishing effective conservation management of the Red-crowned Crane.
We conducted whole genome analysis for two populations of Red-crowned Cranes, “Hokkaido (n = 7)” and “Continent (n = 3)”. Genetic population structure was evaluated by PCA and Admixture, and the past demography of these populations were simulated using PSMC and Stairwayplot 2. Genome-wide heterozygosity was also calculated as the indicator of current genetic diversity. Finally, runs of homozygosity (ROH) were detected from the genome of these cranes to evaluate the extent of inbreeding.
The results of population structure analyses supported the explicit differentiation between two populations of the Red-crowned Crane, Hokkaido and Continent. Demographic history analyses revealed the constant decline of effective population size of the Hokkaido population from 300,000 years ago. The result of genome-wide heterozygosity indicated the lower genetic diversity in the Hokkaido than Continet. ROH analysis indicated the strong and recent inbreeding in the Hokkaido population.
Those results indicated that the Hokkaido population of Red-crowned Crane still has quite high risk of extinction considering strong inbreeding and low heterozygosity. Since the loss of genetic diversity could lead deleterious effects on the immune function, it is urgently required to investigate genetic diversity of immune genes and to disperse the feeding sites for preventing the mass mortality by outbreak of avian influenza. In addition, it is also needed to establish captive breeding program in Hokkaido while maintaining the genetic diversity of this species to address the potential further loss of diversity that could occur in the future.