The findings further confirm that the skeleton is of a fossil human species, Homo floresiensis, researchers said.
From the start, fossils of a tiny population of human-like creatures from Flores, dubbed the "Hobbits" of Southeast Asia, have been controversial.
Experts have debated whether the remains were evidence of a new species of fossil human, Homo floresiensis or belonged to a population of small-bodied humans (Homo sapiens), like ourselves, but suffering from a developmental disorder.
New analysis of features from across the skeleton led by Karen Baab, Assistant Professor at Midwestern University in the US shows that LB1 did not have Down syndrome.
In addition to measuring individual bones, scientists used CT scans to reconstruct the brain and view internal structures of the skull, as well as assessing the 3D shape of the skull.
Down syndrome is a chromosomal disorder characterised by cognitive delays and often certain physical features, including reduced stature and brain size.
The study provides new information about the size and shape of the brain and skull in the Down syndrome population.
While people with Down syndrome are not identical to one another, it was clear that LB1 was very distinct from all humans, including those with Down syndrome.
The study found that LB1's brain was much smaller than that seen in Down syndrome individuals. Likewise, the shape of the skull vault, which surrounds the brain, and chin anatomy were both outside the range seen in humans, with or without Down syndrome.
The diminutive LB1 individual, estimated to be just over a meter in height, was well below the height range of comparable individuals with Down syndrome.
The femur is disproportionately short in LB1 relative to the feet and arms compared to all humans, regardless of whether they have Down syndrome, researchers said.
The study indicates that LB1 not only differed from individuals with Down syndrome, but was more clearly aligned with more archaic human species.
Its small brain, low cranial vault shape, absence of a chin, smaller body size and limb proportions all point to a pre-Homo sapiens ancestry.
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