Skip to main content

Mystery ancestor mated with ancient humans. And its 'nested' DNA was just found.

Homo erectus skull.
An unidentified ancestor that interbred with humans may have been Homo erectus (skull shown here).
(Image: © Shutterstock)

Today's humans carry the genes of an ancient, unknown ancestor, left there by hominin species intermingling perhaps a million years ago. 

The ancestor may have been Homo erectus, but no one knows for sure — the genome of that extinct species of human has never been sequenced, said Adam Siepel, a computational biologist at Cold Spring Harbor Laboratory and one of the authors of a new paper examining the relationships of ancient human ancestors. 

The new research, published today (Aug. 6) in the journal PLOS Genetics, also finds that ancient humans mated with Neanderthals between 200,000 and 300,000 years ago, well before the more recent, and better-known mixing of the two species occurred, after Homo sapiens migrated in large numbers out of Africa and into Europe 50,000 years ago. Thanks to this ancient mixing event, Neanderthals actually owe between 3% and 7% of their genomes to ancient Homo sapiens, the researchers reported. 

Related: See photos of our closest human ancestor

"Our best conjecture is that an early group of anatomically modern humans left Africa then encountered and interbred with Neandertals, perhaps in the Middle East," Siepel told Live Science. "This lineage [of humans] would then have been lost — either gone extinct, or absorbed by the Neandertals, or migrated back to Africa." 

Ancient mixers

The new research illustrates the complexity of humanity's deep history. Evidence has long been accumulating that humans and Neanderthals mated while their populations overlapped in Europe, before Neanderthals went extinct around 30,000 years ago. In 2010, researchers reported that between 1% and 4% of modern human genes in people in Asia, Europe and Oceania came from Neanderthal ancestors. When you add up all the snippets of Neanderthal DNA present in all modern humans today, some 20% of the Neanderthal genome may be preserved, according to 2014 research.

As scientists have been able to sequence more fragile fragments of DNA from fossils of ancient human ancestors, they've discovered a complex web of interbreeding stretching back millennia. Some Pacific Islanders, for example, carry pieces of the DNA of a mysterious ancient species of humans known as Denisovans. 

Related: Photos: Bones from a Denisovan-Neanderthal hybrid

The researchers of the new study used a computational method of comparing the genomes of two Neanderthals, a Denisovan and two modern African individuals. (Africans were chosen because modern people in Africa don't carry Neanderthal genes from the well-known human-Neanderthal interbreeding that occurred in Europe starting 50,000 years ago.) This method allowed the researchers to capture recombination events, in which segments of chromosomes — which are made up of DNA — from one individual get incorporated into the chromosomes of another. 

"We are trying to build a complete model for the evolutionary history of every segment of the genome, jointly across all of the analyzed individuals," Siepel said. "The ancestral recombination graph, as it is known, includes a tree that captures the relationships among all individuals at every position along the genome, and the recombination events that cause those trees to change from one position to the next."

One advantage of the method, Siepel said, is that it allows researchers to find recombination events inside of recombination events. For example, if a bit of ancient hominin DNA from an unknown ancestor were incorporated in the Neanderthal genome, and then a later mating event between Neanderthals and humans inserted that mystery DNA into the human genome, the method allows for the identification of this "nested" DNA. 

Complex history

The analysis turned up evidence of this sort of nested insertion of DNA. The finding that Homo sapiens seem to have mated with Neanderthals between 200,000 and 300,000 years ago meshes with previous evidence of some sort of mixing event between the two species prior to humans moving en masse to Europe, Siepel said. 

The researchers also found that 1% of the Denisovan genome hails from the genes of an unknown ancestor, from an interbreeding event that must have happened, roughly, a million years ago. This mystery ancestor could have been Homo erectus, Siepel said, because Homo erectus likely did overlap in Eurasia with the ancestors of Denisovans and Neanderthals. However, these fragments are tiny and there are no Homo erectus sequences to compare them to, so this is speculative. 

In both cases, these interbreeding events were passed along again to modern humans: 15% of the interbreeding sequences found in Denisovans are present in people living today, the researchers found. 

The new results are another piece of evidence that ancient and modern human lineages mixed relatively frequently, Siepel said. 

"A picture is emerging of a series of distinct but related populations moving around the globe and frequently interacting with one another, with occasional interbreeding events that produced hybrid offspring," Siepel said. "These hybrid offspring might in some cases have suffered from reduced fitness — this is an area of controversy — but apparently many of them were healthy enough to survive and reproduce, leaving a patchwork of archaic and modern human DNA in Neanderthals, Denisovans and modern humans."

Originally published on Live Science.

  • Moisai
    I am not a scientist, but evidence suggests that humans may have overtaken our ancestors by deliberately mating with them. Sending small numbers of the group to migrate into lands occupied by other groups, mating with them, then sending in the larger group to dilute it further, after time the results would be zero or close to zero people of the other lineage left. It seems horrible, but humans, it seems, have always had an aptitude for divide and conquer. And maybe this is the way they did it in the ancient past. This also suggests that it may be part of human DNA
    Reply
  • paperpushermj
    Moisai said:
    I am not a scientist, but evidence suggests that humans may have overtaken our ancestors by deliberately mating with them. Sending small numbers of the group to migrate into lands occupied by other groups, mating with them, then sending in the larger group to dilute it further, after time the results would be zero or close to zero people of the other lineage left. It seems horrible, but humans, it seems, have always had an aptitude for divide and conquer. And maybe this is the way they did it in the ancient past. This also suggests that it may be part of human DNA
    Did they plan all that on their Laptops
    Reply
  • Valentine Michael Smith
    @Moisai : the selfish gene alone accounts for this kind of behavior.
    Reply
  • kristi276
    What you're proposing is a very long stretch of the imagination, and the justification of the attitude of divide and conquer. I would highly doubt that early homo sapiens sent out a coordinated attack on Neanderthals and other species around the world, but primarily in Europe. "Ok, we will send in a first batch of invaders, where they will mix with the locals. Then we will send in a larger force one hundred years later, and that would deplete the natives in the area making us the dominate species." "Yes sir." The span of time goes back one million years to 30.000 years ago; that is prior to the last Ice Age. The authors of the article makes no mention of Native peoples here in the hemisphere, and it is acknowledged fact that Native people have been here for at least the past 30,000 years. Do Native Aboriginals have this genome sequence? Like talking about the value of Human Labor, without mentioning Chattel and Indentured labor. You are in fact stating that colonization is a natural part of your human DNA. Are rape, incest, the need to carry firearms, racial superiority, and the need to bully others part of your DNA? Do not lay and crimes of today on the feet of your ancestors.
    Reply
  • hellopunyhumans
    Valentine Michael Smith said:
    @Moisai : the selfish gene alone accounts for this kind of behavior.
    HA! Just read that book last week.
    Reply
  • Psuedobrain
    admin said:
    Today's humans carry the genes of an ancient, unknown ancestor, left there by hominin species intermingling perhaps a million years ago.

    Mystery ancestor mated with ancient humans. And its 'nested' DNA was just found. : Read more
    Oh come on, we all know it was.....................Aliens!
    Reply
  • Sally
    admin said:
    Today's humans carry the genes of an ancient, unknown ancestor, left there by hominin species intermingling perhaps a million years ago.

    Mystery ancestor mated with ancient humans. And its 'nested' DNA was just found. : Read more
    Contentious I know, but the Earth appears to have suffered a number of significant to enormous catastrophes in it's past. Some to the point of extinction/near extinction for hominoids/humans and many other species. If after such events there were intermingling of any survivors that grouped together (that includes food gathering, building shelter, problem solving, tech even) is it not likely that over many tens/hundreds of thousands of years that surviving genetics would be altered (ie surviving Neanderthal genes)...?
    We cannot assume the level of technologies developed by those ancestors either as there seem to be some extraordinary artifacts which don't appear to fit with expected timelines....
    Reply
  • Valentine Michael Smith
    hellopunyhumans said:
    HA! Just read that book last week.

    And you posted at 727 (1927). FNOOORRDH.


    @Sally : hominids congregate and fraternize, and sometimes conspire - the more so as Societies developed.

    Esoteric/extraordinary artifacts mean very little if they provide no insight.
    Reply
  • TorbjornLarsson
    This seems good, albeit the algorithm is new and the new discoveries needs to be repeated.
    Among new finds is a high frequency of Erectus introgression:

    - "Thus, our analysis suggests that at least about 4 Mb of modern human genomes derives from an unknown but highly diverged archaic hominin, possibly Homo erectus, through at least two separate introgression events. Considering our lack of power, the true contribution could be as much as six times larger."

    - "While these fractions are too small to draw strong conclusions, it is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans. Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."


    And among older finds is the 200-300 kyrs introgression of humans into Neanderthals, which likely signify an earlier human migration out of Africa.
    Reply
  • TorbjornLarsson
    Sally said:
    Contentious I know, but the Earth appears to have suffered a number of significant to enormous catastrophes in it's past. Some to the point of extinction/near extinction for hominoids/humans and many other species ....
    We cannot assume the level of technologies developed by those ancestors either as there seem to be some extraordinary artifacts which don't appear to fit with expected timelines....

    There is no evidence for any of that, and you don't even try that route.

    As far as we can see geology and biology is mostly a tale of continuity, which is why superstition inspired* "catastrophism" was rejected long ago. And those observations are *precisely* based on that we never find sediments, fossils or artifacts out of sequence (but mind that earth quakes, say, can locally turn a sequence upside down). If we did, all of geology, geophysics and biology would instantly go out the window.

    Meanwhile, in the real world, it is a fact that Homo has been fairly unsuccessful as ape lineages go until recently. Chimp populations bottlenecks were always 10 times larger, they still have 5 times the allele diversity, and both our bodies (can live with fat) and our culture (increased sociality and 1-4 year delayed weaning - as seen in teeth minerals - to sustain food gathering among the new drier and grassy landscape) evolved under food stress.



    Reply