Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshu

The Japanese or Honshu wolf was one the most distinct grey wolf subspecies due to its small stature and endemicity to the islands of Honshu, Shikoku, and Kyushu. 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. Its uncertain relationship with present-day and ancient wolf populations has puzzled researchers for years, although research based on mitochondrial genomes suggests a basal placement of the Honshu wolf to all extant grey wolves. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshu wolf specimen to an average depth of coverage of 3.7x. We find Honshu 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 Honshu wolf, corroborating previous reports on Honshu wolf dog interbreeding.