Some of the oldest Neanderthal bones have been DNA tested, showing more than 70 differences from the species that died out 80,000 years later.
The research suggests that the cavemen migrated eastward from Europe to Siberia and indicated that their ancestors might be an as-yet-undiscovered group.
Scientists mapped the complete genomes of the 120,000-year-old bones from Western Europe, shedding fresh light on the history of our closest extinct ancestors.
Remarkably, the individuals were more genetically similar to the last of their species that died out 40,000 years ago in Siberia than other 120,000-year-old bones found in the region.
The findings reveal a stable ancestry and also suggest this group may have migrated east and replaced some populations in Eastern Europe.
It begins to unravel the early history of Neanderthals, which has otherwise been inaccessible since DNA before 100,000 years ago was lacking.
Study supervisor Dr. Kay Prufer, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, said: "The result is truly extraordinary and a stark contrast to the turbulent history of replacements, large-scale mingling and extinctions that is seen in modern human history."
Her team analyzed ground up samples of the thigh and jaw bones belonging to a male and a girl, respectively.
They were each discovered in caves — the former in 1937 at Hohlenstein-Stadel in Germany and the latter in 1993 at Scladina in Belgium.
Both lived around the same time so pre-date most of the Neanderthals whose genomes have been sequenced to date.
Interestingly, the mitochondrial DNA of the male – which is inherited from the mother – is quite different from that of later Neanderthals, with more than 70 mutations that distinguish it.
The study published in Science Advances suggests early Neanderthals in Europe may have inherited DNA from a yet undescribed population.
Lab member Stephane Peyregne, who led the analysis, said: "This unknown population could represent an isolated Neanderthal population yet to be discovered, or maybe from a potentially larger population in Africa related to modern humans."
Bone samples and genetic evidence indicate Neanderthals lived in Europe and Central Asia until about 40,000 years ago.
Recent studies have shown those last Neanderthals all belonged to a single group — they descended from a common ancestor who lived 97,000 years ago.
But a 90,000-year-old Neanderthal found in Denisova Cave, in modern-day Siberia, appears to be more closely related to them than the 'Altai Neanderthal' that was found in the same cave, but dated to 120,000 years ago.
This suggests there had been an early Neanderthal migration into Siberia, followed by a later migration from Europe that replaced the earlier population.
So Mr. Peyregne, a Ph.D. student in evolutionary genetics, and colleagues used state-of-the-art techniques to account for microbial and present-day human DNA contamination in their specimens.
This showed the male and female were members of a population in Western Europe that gave rise to all currently identified Neanderthals — except the Altai Neanderthal.
It indicates the tribes to which they belonged lived in Western Europe contemporaneously with the Altai population in Siberia and later migrated east to replace them.
Surprisingly, the researchers also found highly divergent mitochondrial DNA in the male, revealing an even more complex history that warrants further investigation.
Neanderthals interbred with ancestors of today's Europeans when modern humans began spreading out of Africa.
Around 2 percent of the DNA of anyone living outside Africa today is Neanderthal in origin.
Mr. Peyregne said: "Little is known about the population history of Neanderthals over the hundreds of thousands of years of their existence.
"We retrieved nuclear genomic sequences from two Neanderthals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago.
"Despite the deeply divergent mitochondrial lineage present in the former individual, both are genetically closer to later Neanderthals from Europe than to a roughly contemporaneous individual from Siberia.
"That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neanderthals suggests all later Neanderthals trace at least part of their ancestry back to these early European Neanderthals."
Although human like us, Neanderthals were a distinct species called Homo neanderthalensis.
The Neanderthals have a long evolutionary history. The earliest known examples of Neanderthal-like fossils are around 430,000 years old.
The best-known Neanderthals lived between about 130,000 and 40,000 years ago, after which all physical evidence of them vanishes.