Since then alternative analyses have cast doubt on the discovery.
For example, a study led by Robert Martin at the Field Museum of Chicago published this May in the journal Science also concluded that the hobbits were diseased modern humans, not a new species.
The new study was led by Teuku Jacob, a paleoanthropologist at Gadjah Mada University in Indonesia.
Jacob's team compared the hobbits' skull, face, teeth, and other limb bones to the Rampasasa pygmies who currently live on Flores. According to the analysis, the hobbits and pygmies share many features.
Earlier papers, Eckhardt says, relied mostly on comparisons with Europeans.
"If you're looking at skeletal remains from a particular geographic area and wish to make the case that they are showing characteristics that are not otherwise found, it seems to be that an obvious thing to do is to look at other populations in the area," Eckhardt said.
According to the new study, one telling piece of evidence is that both the Liang Bua fossils and the local pygmy population lack chins.
"It turns out the absence of chins is common," Eckhardt said, adding that local museums are filled with skeletons of recently deceased pygmies who lack chins.
The researchers also say that a host of asymmetries between the left and right half of the LB1 hobbit skull are consistent with abnormalities associated with microcephaly.
Similar abnormalities, they say, are found in the limb bones.
David Frayer, an anthropologist at the University of Kansas in Lawrence and co-author of the PNAS study, says he expects the work to be controversial and doesn't think it alone will remove the new species designation.
"But I think in the long run [the hobbits' small size] will be shown to be pathology," he said.
But several scientists discredit the PNAS study as a superficial analysis that doesn't present enough firm evidence that H. floresiensis was a modern human.
Peter Brown is a paleoanthropologist at the University of New England in New South Wales, Australia. He led the team that originally described the fossils in 2004.
He wrote in an email that "the authors provide absolutely no evidence that the combination of unique features found in H. floresiensis can be found in a modern human skeleton of any sort."
Colin Groves, a biological anthropologist at Australia National University in Canberra, commented via email that the study deals with the skeletal evidence in a "rather superficial" manner.
From the outset, he says, the authors were determined to use whatever evidence they could find to make the case that LB1 was diseased.
"They are unsuccessful," Groves said.
Groves believes that the Flores pygmies display prognathisma prominent mouth that de-emphasizes the chin.
"You can easily detect prognathism on a human skullAfricans, aboriginal Australians, and indeed Indonesians are very frequently prognathic," he said. "But in no case do these skulls lack the human chin structure."
Groves adds that the H. floresiensis jaws found to date have structures called transverse tori, which have never been found on modern humans. The PNAS paper, he says, never addresses the transverse tori.
In addition to their skeletal analysis, Jacob's team argues that hobbits could not have been isolated long enough to evolve into a distinct species.
In the original paper Brown and colleagues suggested that H. floresiensis evolved from an isolated group of individuals that traveled to Flores about 840,000 years ago.
The hobbits' diminutive size, they argued, was a result of island dwarfing, a process that causes larger species to become smaller due to a lack of food and other resources.
More recently Brown and colleagues have suggested that whichever species gave rise to the hobbits was already small when individuals arrived on the island.
According to Eckhardt, the theory that Flores was isolated from the rest of the world for more than 800,000 years is "so unlikely as to be preposterous. It's not something supported by the evidence."
He and his colleagues cite a study showing that stegodons, a type of extinct elephant, migrated to Flores at least twice during that time.
In addition, analysis of sediment cores by team member K. Hsu of the National Institute of Earth Sciences in Beijing, China, suggests that Flores was separated from other Indonesian islands by only a few kilometers during periods of low sea level.
"So the idea the island was isolated and allowed dwarfing of humans to occurirrespective of anything else the bones sayis demonstrably false," Frayer of the University of Kansas said.
Australia National University's Groves says that the isolation argument is irrelevant for the identification of a new species.
But he believes the island was isolated for most of the Pleistocene epoch (about 10,000 to 1.6 million years ago).
Groves added that the dwarf elephant found alongside LB1 "was directly descended from the large species whose remains occur there at 800,000 years ago."
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