When scientists first discovered Homo floresiensis in 2003, the diminutive early humans — nicknamed “hobbits” — a lot of questions were raised. The remains of the species found in Liang Bua cave on the Indonesian island of Flores were dated at 12,000 to 95,000 years old. The youngest remains suggested a huge overlap between Homo floresiensis and Homo sapiens in the region, which was puzzling.

But according to a study published Wednesday in Nature, scientists simply needed more pieces of that puzzle to clear things up. Further investigations of Liang Bua cave suggest that the sediments used to date those suspiciously young fossils were misleading, and that the individuals actually died about 60,000 years ago.

Tool evidence suggests that the species may have used the cave as much as 10,000 years later — which is just when our own species was starting to spread into that part of the globe. So it’s still possible that our ancestors met Homo floresiensis. But far from co-existing with the smaller humans for tens of thousands of years, H. sapiens would have had a brief — and perhaps deadly — encounter with these cousins.

“It’s a great example of the scientific process in action,” study co-author Matt Tocheri of Lakehead University, also a research associate at the Smithsonian, told The Post. Tocheri wasn’t involved in the first exploration of the cave in 2003, but he’s not some feuding scientist who set out to prove those researchers wrong: He actually joined the original team not long after that first discovery, and most of the authors on the latest paper put their names on the first, now-debunked fossil dates as well.

“It’s not that those dates were wrong,” he explained. “But they were incorrectly applied.”

When dating ancient remains, scientists often rely on the age of the sediment in which the fossils are buried. Initially, the remains found near the wall of the cave seemed to be much younger than the remains in the middle – because of the age of the sediments they were found in. But recent excavations revealed that the rocks used to date the “younger” fossils were misleading.

“As more of the cave was exposed, we saw that there had been a period of erosion that had swept away a lot of the original deposits from that eastern wall,” Tocheri said. “In the past 20,000 years, new sediments accumulated up this slope and smothered them. It’s not that the dates are incorrect, but they just don’t apply to the remains.”

The earliest excavations simply hadn’t covered the cave in enough detail for researchers to know that.

“The new chronology looks superb,” Richard Potts, who directs the Smithsonian’s Human Origins program and wasn’t involved in the study, told The Post in an email. “The new research cross-checked 5 different dating methods, and so the Flores research team has done a great job.”

The new dates take away one previous puzzle — how our ancestors could have successfully shared stomping grounds with three-foot-tall hominins for some 40,000 years — but raises other questions. Although it’s possible that modern humans and hobbits never crossed paths, the time that they might have done so now seems to coincide rather perfectly with the latter’s demise, and with the disappearance of vultures, giant marabou storks, Komodo dragons and several other taxa from the island.

“The overlap does point to the possibility that our species may well have had a hand in their disappearance,” Tocheri said.

Potts agreed, although both scientists cautioned that this accusation against our ancestors is purely speculative. “Island populations are certainly vulnerable during fluctuations in food supply. A drought possibly related to a lowering of sea level during global ice age conditions might have contributed to the loss of population size and ultimately extinction, and this same lowering of sea level could have brought Homo sapiens more easily to the small eastern Indonesian islands in boats,” Potts explained. “Could it be that the coup de grace — for both floresiensis and other species — occurred as weakened populations met up with the first H. sapiens to make their way to Flores? It’s hard to know.”

There are a lot of things about floresiensis that are hard to know. For starters, how did they get to Flores? The hobbits are similar in appearance to early humans that lived in Africa and Asia between 1 and 3 million years ago, and there’s evidence of tool use on the island dating around that far back. It seems likely that the species lived in isolation on Flores for a long time — but there’s no skeletal evidence of their earliest ancestors yet.

“To really nail down their relationships with us and Neanderthals and other archaic humans, we really need to know what they looked like when they first arrived on the island,” Tocheri said. Finding those first settlers is a top priority.

Tocheri and his colleagues also need to pinpoint when, exactly, Homo sapiens made it to Flores. They were in the general vicinity as early as 50,000 years ago, but for now the oldest direct evidence of human occupation on Flores is just 11,000 years old. If our ancestors really did push the hobbits out of their home, there should be older evidence of their arrival somewhere on the island. And if there isn’t — well, that’s one more mystery.

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