Scientists extract ancient DNA from 32,000-year-old bear skull

Photo of a brown bear skull - not the same skull used in the study

A brown bear skull (Not the same skull used in the new study) (Image credit: Shutterstock )
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DNA extracted from a 32,500-year-old bear skull hints that ice age brown bears migrated to Honshu, Japan's largest island and lived near present-day Tokyo before eventually dying out.

Today, Japan's only brown bears (Ursus arctos) live in Hokkaido, the northernmost island in the Japanese archipelago. Evidence suggests that the ancestors of these bears migrated to the island from Sakhalin, an island just north of Hokkaido that is now part of present-day Russia. The bears likely lumbered over a land bridge that connected Sakhalin and Hokkaido at various points in the Pleistocene, a time period that lasted from 2.6 million to about 11,700 years ago.

Although brown bears no longer traipse around Tokyo, their fossils — dated between 340,000 and 20,000 years old —have been discovered in several locations on Honshu Island, researchers noted in a new report, published Tuesday (Aug. 3) in the journal Royal Society Open Science. That raises the questions of when and how the Honshu bears first got to the island, but unfortunately, there's little fossil evidence of the beasts' migration.

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"The number of brown bear fossils excavated from the Pleistocene in Japan is scarce, with less than ten incomplete specimens," lead author Takahiro Segawa, a senior assistant professor at the University of Yamanashi's Center for Life Science Research in Japan, told Live Science in an email. 

But one unique specimen, excavated from a cave in the Gunma Prefecture, northwest of the Greater Tokyo area, includes the skull of a bear, complete with right and left petrosals — dense portions of the temporal bones that surround the inner ear. 

The dense structure of petrosals helps shield ancient DNA from degradation, so these bone fragments retain more DNA than other fossilized bones, according to a 2015 report in the journal PLOS One. Knowing this, the research team collected a tiny amount of powdered petrosal from the brown bear skull and brought it to their lab for DNA analysis.

The samples were roughly 32,700 to 32,200 years old, the team determined. The team then compared recovered genetic sequences from the petrosals with 95 near-complete genomes from other brown bears, including all those available from the nearby Hokkaido lineages. 

Based on this analysis, they concluded that the Honshu bear belonged to a "previously unknown lineage" that split off from its sister lineage, the so-called Southern Hokkaido brown bear clade, about 160,000 years ago. The authors theorize that the bears crossed the Tsugaru strait, which separates Hokkaido and Honshu, sometime around that split. 

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And in fact, fossil evidence suggests that other large mammals, including Naumann's elephants (Palaeoloxodon naumanni) and the giant deer (Sinomegaceros yabei), crossed from Hokkaido and Honshu a few thousand years later, around 140,000 years ago, during a glacial period when sea levels were low, according to a 2005 report in the journal Paleoceanography and Paleoclimatology. Brown bears may have taken advantage of the same shallow waters to reach Honshu, the authors suggested. 

The oldest brown bear fossil ever found in Honshu is estimated to be 340,000 years old, the authors noted. That fossil was uncovered in a limestone quarry at the northernmost point of Honshu, and the specimen predates both the Honshu bear skull and the Southern Hokkaido clade. This suggests that different lineages of brown bear ventured to Honshu at different times — once more than 340,000 years ago, and then again during the late Pleistocene. 

Whenever they reached the island, "for reasons unknown, the bears were extirpated by the end of the late Pleistocene in Honshu," along with the Naumann's elephants, giant deer and other large mammals, like bison (Bison priscus), the authors wrote in the study. The exact timing and reason for these animals' disappearance remains shrouded in mystery. 

Originally published on Live Science. 

Nicoletta Lanese
News Editor, Health

Nicoletta Lanese is a news editor on Live Science's health desk. She first joined the publication in 2019 as a staff writer. She holds degrees in neuroscience and dance from the University of Florida and a graduate certificate in science communication from the University of California, Santa Cruz. Her work has appeared in The Scientist Magazine, Science News, The San Jose Mercury News and Mongabay, among other outlets.