Conservation Genetics

, Volume 18, Issue 2, pp 247–260 | Cite as

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

  • Yasuyuki IshibashiEmail author
  • Toru Oi
  • Isao Arimoto
  • Takeshi Fujii
  • Kazuyori Mamiya
  • Nobusuke Nishi
  • Seigo Sawada
  • Hiroyuki Tado
  • Takaki Yamada
Research Article


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.


Balancing selection Genetic diversity Genetic drift Major histocompatibility complex Population bottleneck Threatened local populations 



We thank Dr. Yoshiki Yasukochi (University of Tokyo) for kindly providing the information about the samples used in their study. We also thank the late Atsushi Katayama and other staff members of the Wildlife Management Office, Shuji Wada (Hiroshima Environment and Health Association), Dr. Eiji Hosoi (Yamaguchi University), and members of the Kyoto Hunting Association for kindly sending bear samples. This work was supported by JSPS KAKENHI Grant Number JP23310170.

Compliance with ethical standards

Conflicts of Interest

The authors declare that they have no conflicts of interest.


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Hokkaido Research CenterForestry and Forest Products Research InstituteSapporoJapan
  2. 2.Forestry and Forest Products Research InstituteTsukubaJapan
  3. 3.Hakusan Nature Conservation CenterHakusanJapan
  4. 4.Department of Natural EnvironmentsHiroshima Prefectural GovernmentHiroshimaJapan
  5. 5.Toyama Outdoor Nature MuseumToyamaJapan
  6. 6.Department of the Environment and Consumers AffairsTottori Prefectural GovernmentTottoriJapan
  7. 7.Shimane Prefecture Mountainous Region Research CenterIinanJapan
  8. 8.Bird and Animal Damage Consultation CenterYamaguchi Prefecture Agriculture and Forestry General Engineering CenterYamaguchiJapan
  9. 9.Shikoku Institute of Natural HistorySusakiJapan
  10. 10.Department of Environmental Science, Faculty of Bioresources and Environmental SciencesIshikawa Prefectural UniversityNonoichiJapan
  11. 11.Hakusan Fumoto KaiHakusanJapan
  12. 12.Agricultural Technology DivisionHiroshima Prefectural GovernmentHiroshimaJapan
  13. 13.Tottori Prefectural Forestry Research CenterTottoriJapan

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