The study by The Australian National University (ANU) found Homo floresiensis, dubbed "the hobbits" due to their small stature, were most likely a sister species of Homo habilis - one of the earliest known species of human found in Africa 1.75 million years ago.
Data from the study concluded there was no evidence for the popular theory that Homo floresiensis evolved from the much larger Homo erectus, the only other early hominid known to have lived in the region with fossils discovered on the Indonesian mainland of Java.
"The analyses show that on the family tree, Homo floresiensis was likely a sister species of Homo habilis. It means these two shared a common ancestor," Argue said.
"It is possible that Homo floresiensis evolved in Africa and migrated, or the common ancestor moved from Africa then evolved into Homo floresiensis somewhere," she said.
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Homo floresiensis is known to have lived on Indonesian island of Flores until as recently as 54,000 years ago.
Argue said none of the data supported the theory that Homo floresiensis evolved from Homo erectus.
"We looked at whether Homo floresiensis could be descended from Homo erectus," she said.
"We found that if you try and link them on the family tree, you get a very unsupported result. All the tests say it doesn't fit - it is just not a viable theory," said Argue.
Argue said this was supported by the fact that in many features, such as the structure of the jaw, Homo floresiensis was more primitive than Homo erectus.
"If this was the case Homo floresiensis would have evolved before the earliest Homo habilis, which would make it very archaic indeed," she said.
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