Neanderthal Genome Study Reveals Homo sapiens Lineage Diverged 744,000 Years Ago, Huge Gap in Fossil Record Indicated

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New DNA data has overturned the understanding that modern humans and Neanderthals diverged a little over 550,000 years ago. It is now apparent that Neanderthals and Denisovans diverged from their shared ancestor close to 744,000 years ago, only 300 generations after splitting from the line ancestral to modern humans. The size of the global Neanderthal population has also been recalculated, shifting from perhaps 1000 to tens of thousands.

[This article explores the conclusions reached in a new study, and offers the opinion of this writer as to the possible interpretations of some of the associated scientific findings].

A team of scientists from the University of Utah have astonished the scientific community thanks to finds made using a new DNA analysis method that helps to reconstruct the mysterious history of archaic hominins (extinct human relatives). The new findings offer a revised story of human origins that contradicts the current scientific consensus on the evolutionary history of modern humans, Neanderthals and Denisovans.

“This hypothesis is against conventional wisdom, but it makes more sense than the conventional wisdom.” said Alan Rogers, professor in the Department of Anthropology and lead author of the study, published in the Proceedings of the National Academy of Sciences.

The University of Utah team were very cautious in releasing their findings; they were potentially so controversial and revolutionary that it took considerable time for them to be satisfied that the results were indeed accurate. The conclusions included the finding that the Neanderthal-Denisovan lineage diverged away from the ancestor shared with modern humans around 750,000 years ago, then just 300 generations later, Neanderthals and Denisovans diverged from each other.

Another radical change is the understanding of the size of the global population of Neanderthals. Where it was previously speculated that Neanderthals might have numbered only a thousand or so individuals at their height, the new study supports a model in which Neanderthals numbered in the tens of thousands. The Neanderthals likely lived in fragmented groups with high intergroup genetic diversity arising from extended periods of isolation. The fact that a significant number of Neanderthal fossils have already been uncovered had already caused some suspicion that there must have been many of these archaic humans at some stage in prehistoric times.

Looking at the data that shows how related everything was, the model was not predicting the gene patterns that we were seeing,” said Ryan Bohlender, post-doctoral fellow at the M. D. Anderson Cancer Center at the University of Texas, and co-author of the study. “We needed a different model and, therefore, a different evolutionary story.

These population trees with embedded 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. Credit: Alan Rogers, University of Utah

The team developed an improved statistical method, called legofit, that accounts for multiple populations in the gene pool. Through estimation of the percentage of Neanderthal genes flowing into modern Eurasian populations, it became possible to calculate the date at which archaic populations diverged from each other, and predict their population sizes.

The researchers compared the genomes of modern Eurasians, modern Africans, Neanderthals and Denisovans. The modern samples were sourced from Phase I of the 1000-Genomes Project while the Neanderthal and Denisovan samples were sourced from the Max Planck Institute for Evolutionary Anthropology – specifically being samples gathered from the Denisova cave site in Siberia. The Utah team analysed a few million nucleotide sites that shared a gene mutation in two or three human groups and established ten distinct nucleotide site patterns.

The analysis process revealed that 20 percent of nucleotide sites bore a mutation shared by Neanderthals and Denisovans, but not seen in modern humans, a kind of 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 previous calculations for this divergence event.

The analysis also clarified that although Neanderthals DNA often contains mutations that tend to occur in small populations, Neanderthal remains found in various locations are genetically distinct. The mutations detected support the view that regional Neanderthals were likely small bands of individuals, which explains the problematic mutations (from inbreeding), but that the global population was quite large.

It is easy to get caught up in the immediate excitement of this discovery and forget that the findings also have ramifications for the greater story of human origins and the consensus model known as ‘Out of Africa’ theory. The oldest Homo sapiens fossils in Africa, at Jebal Irhoud in Morroco, are dated to around 300,000 years ago. The surprise redating for the divergence of our human ancestors leaves a huge gap in the fossil record, we now need to identify fossils from our ancestral lineage that take us from 300,000 to 744,000 years ago – these are notably absent from known African archaeological sites.

There are also no finds of Neanderthal or Denisovan fossils anywhere in Africa. The oldest fossils of Neanderthal ancestors are found in Spain, at three archaeological sites in Atapuerca. The earliest discoveries ‘potentially’ related to the evolution of Spanish Neanderthal populations are those at Sima del Elefante dated at 1.2 million years ago, Gran Dolina, dated to 800,000 years ago, and the Sima de Los Huesos site dated to 430,000 years ago. Very early forms of Neanderthals and similar extinct humans have been found across Eurasia.

If it transpires that Neanderthals evolved in Eurasia between 1.2 million years ago and 430,000 years ago, rather than in Africa, where fossils are not found to support their evolution, the date of modern humans divergence from Neanderthal and Denisovan lineages at around 744,000 years ago would then strongly suggest modern humans also emerged somewhere on the Eurasian continent. In this scenario, there might be a temptation to place human evolution in Europe (something Euro-centric scientists are keen to establish), but detailed analysis of the European fossil record has already discounted this as a possibility. In a comparative fossil study lead by  Indiana University back in 2013, it was found that no direct ancestor of modern humans could be identified among known fossils.

Homo erectus is understood to be ancestral to archaic Homo sapiens, we now know that this hominin form had not made its way into Europe over one million years ago, but groups of these hominins were already in Southeast Asia by 1.8 million years ago. The existence of Asian Homo erectus at such an early point in time has long been factored into arguments suggesting a multi-regional evolution of modern humans, the basic argument being that if modern humans emerged from Homo erectus, why would we see this happening among only African populations and not among Asian H. erectus?

Neanderthals and Denisovans are subspecies of the Homo sapiens lineage; they were so closely related to modern humans that we interbred with them successfully and still carry elements of their DNA with us to this day. With this new data in mind, we should be thinking of the Homo sapiens family as being no less than 744,000 years old, with high diversity and a significantly large global population at some stages in prehistoric times.

There is no longer solid evidence that any of these three human lineages can be pinned down to exclusively African emergence events, two forms are found only in Eurasia and the third is found both there and in Africa. Denisovans are known only from fossil remains in Central Asia and DNA detected in the genome of modern humans in Australasia. Modern humans appeared in Africa 300,000 years ago, where were their ancestors during the preceding 440,000 years? If the three forms diverged in Africa 744,000 years ago it is certainly puzzling that we find little evidence of any of the intermediate forms at archaeological sites across that continent during the next several hundreds of thousands of years. We have a lot of fossils to find, the question is are they to be found in Africa or in Eurasia?

 

Sources

New Look at Archaic DNA Rewrites Human Evolution Story – University of Utah

Early history of Neanderthals and Denisovans – PNAS

New gene study rewrites Neanderthal history – News.com.au

Neanderthals and Denisovans find their place in human family tree – Cosmosmagazine.com

New look at archaic DNA rewrites human evolution story – Phys.org

The genes that rewrite the history of human evolution: DNA mutations reveal ‘tens of thousands’ more Neanderthals walked the Earth than first thought – DailyMail.co.uk

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Independent investigative journalist and science-minded researcher busy inquiring into human origins and the development of formative human cultures. Writer, speaker and author of 'The Into Africa Theory of Human Evolution'.

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