Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū
Jonas Niemann,
Shyam Gopalakrishnan,
Nobuyuki Yamaguchi,
Jazmín Ramos-Madrigal,
Nathan Wales,
M. Thomas P. Gilbert,
Mikkel-Holger S. Sinding
Affiliations
Jonas Niemann
Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; BioArch, Department of Archaeology, University of York, York, UK; Corresponding author
Shyam Gopalakrishnan
Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
Nobuyuki Yamaguchi
Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
Jazmín Ramos-Madrigal
Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
Nathan Wales
BioArch, Department of Archaeology, University of York, York, UK
M. Thomas P. Gilbert
Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
Mikkel-Holger S. Sinding
Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Greenland Institute of Natural Resources, Nuuk, Greenland; Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland; Corresponding author
Summary: The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding.
