Denisovan Hominins Interbred With An Unknown Early Human Species, New DNA Analysis Shows

Denisova excavation_dn24603-1_300

The human family tree just got a little more crowded. A recent DNA analysis of the Denisovan (Denisova hominins) genome has revealed the presence of unusual genetic sequences not found in Neanderthal or any other known early hominin species — indicating the possible existence of a new unknown ancestor in the human family tree.

In 2008, anthropologists excavating a cave in the Altai Mountains of Siberia uncovered two teeth and a finger bone from some type of hominin (i.e., a member of the human evolutionary family) which were dated to 41,000 years ago (ya). Thanks to the cold climate, enough DNA was preserved in these fossils for scientists to sequence most of the genome with a high degree of accuracy. Comparison of the mitochondrial DNA with DNA sequences from other early hominins showed that the fossils — identified as  belonging to a juvenile female (‘X woman’) — were indeed from a distinct, and previously unknown,  hominin species.

Although there have been no reconstructions of a typical Denisovan (as so few fossils have been found),  genetic comparisons showed that they were more closely related (“cousins”) to Neanderthals than to early Homo sapiens. According to estimations of the age of certain key DNA sequences, the Denisovans split (i.e., formed a new “branch” on the human family tree) from H. sapiens some 400,000 years ago.

There was some thought initially that the Denisovans were actually Neanderthals (or a sub species). But subsequent extraction and analysis of Neanderthal DNA showed that the Denisovans were a unique species and split from the Neanderthal lineage sometime after the split from H. sapiens.

The Denisovan Genome Analysis – A More Distant Human Relative

But here’s where the human evolutionary tree gets a bit more puzzling, or more complex.  An analysis of the Denisovan genome conducted by David Reich of Harvard Medical School in Boston, Massachusetts, has found several sequences of DNA (strings of the four nucleotide letters A, T, C, and G) that do not appear to “fit” with the rest of the genome. Reich’s findings were presented a Royal Society meeting on ancient DNA in London, England, on Monday.

As already noted, the Denisovans split first from Homo sapiens and then later from Neanderthals. Theoretically, this should mean that Neanderthals and Denisovans would “look” (roughly) equally distinct from modern humans (that is, their DNA would have roughly equal percentages of distinct sequences). However, this was not what Reich found.

“Denisovans appear more distinct from modern humans than Neanderthals,” said Reich at the meeting. “Denisovans harbor ancestry from an unknown archaic population, unrelated to Neanderthals.” [quote source]

Reich’s conclusion was based upon approximately 1% of Denisovan DNA that looks much older than the remaining 99%. The most likely explanation for this slight but significant genetic age variance is that the Denisovans interbred with another early hominin species — as yet unidentified — and thus acquired some of its DNA (but see author’s comment, below).

So, this new DNA analysis could be evidence of a completely new/unknown hominin species, or, alternatively, it could be simply the first genetic evidence of one of the many other early hominin species that were known to have existed (from fossils) but from which no DNA could be extracted (due to  climate conditions that were too warm and wet for good DNA preservation in the fossils).

Who Was the Mystery Mate? The Likely Suspects

A likely candidates for this known early human is Homo heidelbergensis which lived between 600,000 ya and 250,000 ya. H. heidelbergensis spread from Africa into Europe (via the Levant region) and then to western Asia. It is believed by anthropologists that Denisovans followed a similar path out of Africa, and so, it is probable that they encountered (and interbred with) H. heidelbergensis and some point during this migration.

Denisova Cave_Turist_den-peschera

Another possibility is Homo erectus which was a contemporary species with H. heidelbergensis and was more widespread (with fossils found as far east as the island of Java; “Java man”). However, western populations of H. erectus — those living in over-lapping areas with Denisovans — may not have survived long enough for successful interbreeding, as fossil remains of this species in more western regions are scant (image, left: Denisova Cave, Siberia).

Further, anthropologists and geneticists are currently trying to extract DNA from a sizable number of recently discovered and unidentified Asian hominin fossils. If they are successful, the results could show similar genetic patterns as found in the Densovan genome, or, they may show evidence of yet more early and scientifically unknown hominin species.

There is more genetic  (“archaic admixture”) evidence from modern sub-Saharan hunter-gatherer tribes (descendents  of early Homo sapiens that did not leave Africa) pointing toward this mystery species; fairly recent studies (Lachance et al, 2012, and Hammer et al, 2011)* have revealed evidence of haplotype introgression (i.e., the introduction of  foreign gene sequences into a distinct genome);  modern hunter-gatherers in Africa did indeed interbreed with an as-yet-to-be-identified hominin species, and, that this interbreeding occurred around 35,000 ya with a hominin species that appears to have split from the H. sapiens line about 700,000 ya.

As with so much of the history of anthropology, each new discovery both elucidates our ancient hominin history and adds to its mystery.

* Lachance et al, 2012  (Cell, / Hammer et al, 2011 (PNAS,

Author’s comment: Although it is likely that this 1% of Denisovan mtDNA came from another ancient hominin, it is also possible that it — or some of it — came from some species of ancient bacteria — microbes that routinely exchange DNA with their environments (such as the human gut microbiome, which functionally impacts our immune systems) and with other bacteria and other microbes. There is some decent evidence that at least some of our DNA (perhaps mostly non-coding, “transposable”  DNA) got there via some ancient infectious pathogen (but in a hominin line long extinct). Although, whether such an infection, or series of infections, could introduce 1% of a species’ DNA (and then be positively selected and passed on) is debatable.

Some source material for this post cam from the Nov. 19 New Scientist article: ‘Mystery human species emerges from Denisovan genome‘ by Michael Marshall

Top photo: (Evidence of the Denisovan species was unearthed in a Siberian cave in 2008 (Image: Max Planck Institute for Evolutionary Anthropology via New Scientist)

Second photo: (Tourists in front of the Denisova Cave, Siberia, where “X woman” was found); credit: ЧуваевНиколай ; CC – By – SA 3.0


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