Genetic diversity and phylogeny of the endangered Okinawa Rail, Gallirallus okinawae

Genetic diversity of the wild population of the endangered Okinawa Rail, Gallirallus okinawae, was revealed by analyzing haplotypes in the mitochondrial control region for 177 individuals. We found 6 haplotypes with nucleotide differences at 6 sites. The four major haplotypes, Type 1 to Type 4, were present in 121 (68.4%), 21 (11.9%), 8 (4.5%) and 25 individuals (14.1%), respectively. Type 5 and Type 6 were each found in one individual. The gene diversity (h) and nucleotide diversity (pi) of Okinawa Rail were calculated to be 0.499 +/- 0.040 and 0.00146 +/- 0.00098, respectively. Gene diversity in Okinawa Rail is higher than that found in other endangered avian species, but the relative nucleotide diversity is lower due to few nucleotide differences among the haplotypes. Our sample of 177 individuals represents 20-25% of the total population, and thus allows a rigorous estimate of the population structure of Okinawa Rail, and makes it unlikely that more haplotypes would be found with additional sampling. The low nucleotide diversity in the control region may indicate that Okinawa Rail has gone through a recent bottleneck. The minimal span network of haplotypes, and the distribution pattern of sampled individuals, indicate that the number of birds with rare haplotypes, Type 5 and 6, decreased during the recent population decline caused by habitat loss and introduced predators. Our results are relevant to the current conservation program for the endangered Okinawa Rail, and perhaps for other species of flightless rails.