Hundreds of thousands of years ago, the ancestors of modern humans diverged from a lineage that gave rise to Neanderthals and Denisovans.

Yet the exact relationship between these ancient groups has remained unclear.

Now, a new method of studying DNA is beginning to unravel the mystery - and the findings appear to contradict conventional theories about human evolution.

The study claims that the number of Neanderthals that walked the Earth could have been tens of thousands more than scientists first thought.

It also suggests Neanderthals and Denisovans diverged from each other around 744,000 years ago - around 300,000 earlier than previously believed.

This implies that Homo heidelbergensis - which lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago - was an early Neanderthal.

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The number of Neanderthals that walked the earth could have been tens of thousands more than many scientists thought, according to new research. Pictured is the revised history of early human history across Africa and Europe based on the new findings (dates are estimates)

THE DNA STUDY The human genome has about 3.5 billion nucleotide sites and, over time, genes at certain sites mutate. If a parent passes down that mutation to their children, who pass it to further generations, that mutation acts as a 'family seal' stamped onto the DNA. Scientists use these mutations to piece together evolutionary history hundreds of thousands of years in the past. By searching for shared gene mutations along the nucleotide sites of various human populations, scientists can estimate when groups diverged and the sizes of populations contributing to the gene pool. The team compared the genomes of four human populations: Modern Eurasians, modern Africans, Neanderthals and Denisovans. They estimated the percentage of Neanderthal genes flowing into modern Eurasian populations, the date at which archaic populations diverged, and their population sizes. Advertisement

The discovery was made after researchers came up with a new way to analyse our ancestors' DNA.

Many researchers have estimated there were only about 1,000 Neanderthals, which shared 99.7 per cent of their DNA with modern humans.

But scientists from the University of Utah have now estimated the figure was likely in the 'tens of thousands'.

A team led by Professor Alan Rogers created used an analysis technique that recreates the early history of ancient human populations including Neanderthals and Denisovans.

They found the Neanderthal-Denisovan lineage nearly went extinct after separating from modern humans.

Then, just 300 generations later, Neanderthals and Denisovans diverged from each other - around 744,000 years ago.

The global Neanderthal population then grew to tens of thousands of individuals living in fragmented, isolated populations scattered across Eurasia.

Professor Rogers said: 'This hypothesis is against conventional wisdom, but it makes more sense than the conventional wisdom.'

With only limited samples of fossil fragments, anthropologists must assemble the history of human evolution using genetics and statistics.

An earlier study in 2015 showed estimates of a 1,000-strong Neanderthal population was underrepresented if they were subdivided into isolated, regional groups.

The Utah team suggest this explains the discrepancy between previous estimates and their own much larger estimate of Neanderthal population size.

Professor Rogers told MailOnline: 'Previous estimates document the small sizes of local Neanderthal populations.

'Our estimates document the large size of the Neanderthal metapopulation that contributed genes to modern humans.'

These gene trees show how mutations can generate nucleotide site patterns. The four branch tips of each gene tree represent genetic samples from four populations: Modern Africans, modern Eurasians, Neanderthals, and Denisovans. In the left tree, the mutation (shown in blue) is shared by the Eurasian, Neanderthal and Denisovan genomes. In the right tree, the mutation (shown in red) is shared by the Eurasian and Neanderthal genomes

WHAT KILLED OFF THE NEANDERTHALS? The first Homo sapiens reached Europe around 43,000 years ago, replacing the Neanderthals there approximately 3,000 years later. There are many theories as to what drove the downfall of the Neanderthals. Experts have suggested that early humans may have carried tropical diseases with them from Africa that wiped out their ape-like cousins. Others claim that plummeting temperatures due to climate change wiped out the Neanderthals. The predominant theory is that early humans killed off the Neanderthal through competition for food and habitat. Homo sapiens' superior brain power and hunting techniques meant the Neanderthals couldn't compete. Advertisement

Dr Ryan Bohlener, co-author of the study, said: 'Looking at the data that shows how related everything was, the model was not predicting the gene patterns that we were seeing.

'We needed a different model and therefore a different evolutionary story.'

The team's findings also suggest that Homo heidelbergensis - an ancient human ancestor that lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago - was an early Neanderthal.

The human-like species went extinct long before modern humans migrated to Eurasia from Africa, but its evolutionary tree has largely baffled scientists due to scarce fossil records.

The similarity between Neanderthal, Homo heidelbergensis and Homo sapien fossils means researchers previously thought heidelbergensis fossils are mere variants of Homo sapiens.

A new way to analyse our ancestors' DNA reveals there were likely many more Neanderthals (artist's model) than expected. Many researchers estimate there were only about 1,000 Neanderthals, which shared 99.7 per cent of their DNA with modern humans

The team developed an improved statistical method, called legofit, which accounts for multiple populations in the gene pool.

They estimated the percentage of Neanderthal genes flowing into modern Eurasian populations, the date at which archaic populations diverged from each other, and their population sizes.

The human genome has about 3.5 billion nucleotide sites and, over time, genes at certain sites mutate.

If a parent passes down that mutation to their children, who pass it to further generations, that mutation acts as a 'family seal' stamped onto the DNA.

Scientists use these mutations to piece together evolutionary history hundreds of thousands of years in the past.

By searching for shared gene mutations along the nucleotide sites of various human populations, scientists can estimate when groups diverged and the sizes of populations contributing to the gene pool.

Homo heidelbergensis (artist's model) lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago. It was an early human ancestor that went extinct long before modern humans migrated to Eurasia from Africa

HOMO HEIDELBERGENSIS Homo heidelbergensis lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago. It was an early human ancestor that went extinct long before modern humans migrated to Eurasia from Africa. Researchers have previously suggested that, between 400,000 and 300,000 years ago, a group of heidelbergensis migrated into Europe and West Asia via yet unknown routes and eventually evolved into Neanderthals. The new research suggests Neanderthals and Denisovans diverged from each other around 744,000 years ago - much earlier than previously believed. This could prove that heidelbergensis was an early Neanderthal. The similarity between Neanderthal, Homo heidelbergensis and Homo sapien fossils means researchers previously thought heidelbergensis fossils are mere variants of Homo sapiens. Advertisement

Professor Rogers said: 'You're trying to find a fingerprint of these ancient humans in other populations.

'It's a small percentage of the genome, but it's there.'

They compared the genomes of four human populations: Modern Eurasians, modern Africans, Neanderthals and Denisovans.

The two ancient samples - both the Neanderthal and the Denisovan - came from Denisova Cave, in the Altai Mountains of Siberia.

The Utah team used two modern data sets, both from the '1000 Genomes Project'.

One of these is designated 'CEU' and consists of Utah residents with ancestry from northern and western Europe.

The scientists found the Neanderthal-Denisovan lineage nearly went extinct after separating from modern humans (skeleton pictured right). Then, just 300 generations later, Neanderthals (skeleton pictured left) and Denisovans diverged from each other - around 744,000 years ago

The other is 'CHB', which represents Han Chinese from Beijing.

The researchers analysed a few million nucleotide sites that shared a gene mutation in two or three human groups, and established 10 distinct nucleotide site patterns.

The new method confirmed previous estimates that modern Eurasians share about two per cent of Neanderthal DNA.

But other findings questioned established theories.

Their analysis revealed that 20 per cent of nucleotide sites showed a mutation only shared by Neanderthals and Denisovans, a genetic timestamp marking the time before the archaic groups diverged.

The team calculated that Neanderthals and Denisovans separated about 744,000 years ago, much earlier than any other estimation of the split.

If a parent passes down a DNA (artist's impression) mutation to their children, who pass it to further generations, that mutation acts as a 'family seal'. Scientists use these mutations to piece together evolutionary history hundreds of thousands of years in the past

ANCIENT DNA CARRIES ADVANTAGES Modern humans carry traces of DNA from mixing with other hominids, including Neanderthals and Denisovans. In February researchers at the University of Washington School of Medicine analysed the DNA of 1,500 people, including those from Europe, Asia and the Pacific islands, to see where these ancient genes remain. They identified 126 areas of the modern human genome where ancient DNA persists. They found genes relating to the immune system and skin function. Neanderthal gene expression likely contributes to traits such as height and even our susceptibility to lupus and schizophrenia. Scientists believe these genes from our extinct cousins helped modern humans to thrive as they moved outwards from the African continent. Advertisement

Professor Rogers added: 'If Neanderthals and Denisovans had separated later, then there ought to be more sites at which the mutation is present in the two archaic samples, but is absent from modern samples.'

Neanderthal DNA contains mutations that usually occur in small populations with little genetic diversity, leading scientists to believe for decades that only 1,000 of the ancient human ancestors ever lived in Eurasia.

But the scientists said Neanderthal remains found in various locations are genetically different from each other.

This supports the study's finding that regional Neanderthals were likely small bands of individuals, which explains the harmful mutations, while the global population was quite large, they said.

Dr Bohlender said: 'The idea is that there are these small, geographically isolated populations, like islands, that sometimes interact, but it's a pain to move from island to island.

'So, they tend to stay with their own populations.'

Professor Rogers added: 'There's a rich Neanderthal fossil record - there are lots of Neanderthal sites.

The two ancient samples used in the study - both the Neanderthal and the Denisovan - came from Denisova Cave, in the Altai Mountains of Siberia

'It's hard to imagine that there would be so many of them if there were only 1,000 individuals in the whole world.'

Asked if he found his team's results surprising, Professor Rogers told the MailOnline: 'Extremely - when we first got results like this nearly a year ago, we didn't believe them.

'The Neanderthal population was way too large, the separation time of Neanderthals and Denisovans was too old, and the confidence interval around this separation time was implausibly narrow.

'So we began trying to figure out what was wrong; a long process involving a hunt for bugs in the computer code and various experiments to figure out what could be causing these weird results.

'Eventually, we excluded everything we could think of, and at that point, we began to think the results might actually be right.'