It's a new species. No it isn't. Yes it is. No it isn't. Yes it is...

When her miniature skull and tiny skeleton were revealed publicly for the first time in 2004, scientists expressed their amazement that such a small species of human could have existed on the island of Flores in Indonesia.

She became known as "the hobbit", standing just over 3ft tall with a brain the size of a grapefruit, about a third of the average brain volume of modern humans. It seemed that the last of her species, Homo floresiensis, died out not long after she lived around 18,000 years ago.

But within weeks of her discovery being announced in the pages of the journal Nature, other scientists began to voice doubts over whether she did indeed belong to a new species. The sole female "hobbit", they said, was probably a woman with an unfortunate congenital pathology known as microcephaly, when the body and brain do not grow to their full size.

After years of claims and counter-claims about the miniature person, whose remains were found buried deep in the sediment of a cave on Flores, scientists have now produced further evidence that she did indeed belong to a separate species of man, quite different to either the living Homo sapiens or any of the extinct members of the human family.

Professor William Jungers and Karen Baab, two anthropologists at the Stony Brook University Medical Centre in New York, carried out a statistical analysis of the skull and bones of the hobbit and compared her to other human species as well as to apes. They concluded that she falls well outside the normal size range for either modern humans or diseased microcephalics, which strongly suggests that the hobbit belonged to a new species.

"Attempts to dismiss the hobbits as pathological [diseased] people have failed repeatedly because the medical diagnoses of dwarfing syndromes and microcephaly bear no resemblance to the unique anatomy of Homo floresiensis," said Dr Baab, whose study is published in the Royal Statistical Society's journal, Significance.

Such a small-brained person is highly unusual and scientists agreed on one thing: she could only realistically be explained if she had indeed suffered either a congenital growth deformity or had belonged to a different human species altogether. But they were divided on whether the hobbit was truly a new species of miniature human, or just a woman born with an abnormally small skull and brain.

"Some have concluded that a head so abnormal could only have been caused by pathological disease. Despite its small absolute size, however, multivariate statistical analysis reveals absolutely no resemblance to the brain shape of modern human microcephalics," according to Jungers and Baab. "Statistical analyses of skull shapes find modern humans in one grouping, microcephalic humans in another and the hobbit, together with ancient hominins, in a third," they said.

The scientists also analysed the hobbit's limbs with the same statistical method and found that its body design and proportions were also quite unlike those of modern humans. Although the legs are far shorter in proportion to the body, the hobbit's arms are relatively long.

Professor Jungers suggested that the hobbit had evolved from a more primitive ancestral human species with a similar body plan, rather than belonging to an evolutionary branch-line of H. sapiens that had regressed to a more primitive form. "It is difficult to believe an evolutionary change would lead to less economical movement," Professor Jungers said. "It makes little sense that this species re-evolved shorter thighs and legs because long hind limbs improve bipedal walking. We suspect that these are primitive retentions instead," he said.

The remains of the hobbit were found in 2003 by a team of Indonesian and Australian scientists excavating the Liang Bua cave on Flores. The cave was known to have been occupied by early humans of some description for about 800,000 years, based on the discovery of primitive stone tools, although the hobbit herself was found in a layer of sediments dating back to just 18,000 years ago.

Mixed in with the stone tools found in Liang Bua were the bones of prehistoric animals that lived at the same time, such as a giant species of rat as big as a cat, a dwarf elephant called a stegodon and the remains of giant Komodo dragons, which are still to be found on Flores and other Indonesian islands.

The relatively sophisticated stone tools appeared to be similar to those made at other sites in different parts of the world by an earlier species of human called Homo erectus. However, the crucial difference between H. erectus tools and those at Liang Bua was that the artifacts found in the Flores cave were far smaller – suggesting that they were honed by the tiny hands of the miniature humans.

But one of the strongest objections to the idea that these tools were made by the hobbits was their exceedingly small brain case, which had a capacity of just over 400 cubic centimetres – not much bigger than a chimp's brain – compared with the 1,200cc of modern humans. The question was: how could people with such small brains make and use relatively sophisticated tools honed by chipping flakes off a "core" of rock to produce razor-sharp edges?

Professor Jungers said brain size alone should not be used to judge how intelligent these creatures were. Impressions taken from the brain case of the hobbit revealed she possessed a brain which was organised quite differently to those of apes, which are about the same size.

"This implies that brain architecture and some aspects of function are not tightly constrained by absolute size; if we go by brain size alone we may severely underestimate the cognitive capabilities of the hobbit. Their core-and-flake stone tool technology shows that they were far from unintelligent," Professor Jungers said.

"Brains are known to be expensive organs in terms of energy requirements, so it is also plausible that ecological constraints on a small island like Flores might have favoured somewhat smaller brains and bodies."

Bones of contention: Disputed ancestors

* One of the biggest disputes in human palaeontology is whether modern humans arose from a single population of ancestors who migrated out of Africa about 60,000 years ago, or whether there were several migrations, with interbreeding between new arrivals and earlier migrants already established in Asia and other parts of the world. The "out of Africa" hypothesis is now more widely preferred to the "multi-regional" model.

* A perfectly preserved fossil, nicknamed "Ida", was said to be our earliest ancestor linking the human lineage with the rest of the animal kingdom. Ida, dated to 47 million years old, was a primitive lemur-like creature said to be the "missing link" between simians (monkeys, apes and humans) and prosimians (lemur-like primates). However, subsequent studies cast doubt on this theory, and Ida is now considered to be an evolutionary branch not directly linked to humans.

* The most infamous bone of contention was "Piltdown man", a skull supposedly found in 1912 in a gravel pit in East Sussex. It took 40 years to establish it was a hoax.