Loss of allelic diversity in the MHC class II DQB gene in western populations of the Japanese black bear Ursus thibetanus japonicus

In Japan, the black bear, Ursus thibetanus, is distributed on Honshu and Shikoku Islands. Most populations in western Japan declined considerably during the twentieth century, but a few populations are now rebounding due to conservation efforts. Here, we examined the sequence variation in the second exon of the major histocompatibility complex class II DQB gene (270 bp), which is critical for pathogen recognition. We measured variation within six populations in western Japan, including two threatened populations in the Chugoku region on Honshu and one on Shikoku. Eight sequence variants were observed among the examined bears (n = 417), and two to eight variants were retained within populations. Our samples, collected in 2001–2013, retained a smaller number of sequence variants in each population compared with the allelic diversity in an earlier study that examined the same gene and used samples collected mainly during the last century. Many rare variants that were observed previously and may have been maintained by balancing selection have disappeared from recent populations. Although the earlier study suggested a loss of genetic diversity in western Japan, the present study shows that further loss of rare variants has occurred, probably due to genetic drift during the end of the last century.