Ancient mtDNA from Homo heidelbergensis rocks paradigms

A Siberian cave at Denisova yielded autosomal and mitochondrial DNA samples from several individuals who lived sometime in the Upper Paleolithic. This ancient DNA from an archaic hominin species was more similar to Neanderthals than to modern humans, but was clearly its own distinct archaic hominin species. Significant archaic admixture of Denisovan DNA was found in Papuans and aboriginal Australians, but no where else that could be sourced to these east of the Wallace line modern human populations. However, since the finger bones from which the DNA samples were extracted were not accompanied by sufficient skeletal remains, no identification of this rare ancient DNA could be made with any known archaic hominin species.

Now, the first sample of ancient mtDNA from Homo heidelbergensis bones in Northern Spain reveal that this archaic hominin species was more closely related to the Denisovans than to the Neanderthals and modern humans who share a common mtDNA ancestor more recent than the H. heidelbergensis departure from the the clade that they share with Denisovans.

This is notable for two reasons.

Implications For Hominin Evolution

First, the widely shared conventional wisdom, which I shared, was that Homo heidelbergensis was ancestral to the Neanderthals in Europe, a hypothesis that the ancient mtDNA sample disclosed yesterday disfavors. This is particularly surprising given the Homo heidelbergensis skeletal remains appear to have some Neanderthal derived features, although not all of them.

 It also strongly supports those who had argued that Homo heidelbergensis was a separate species that should not just be lumped into the range of variation within Neanderthal, for example. But, it is a seemingly clear defeat to those who had suspected that Homo heidelbergensis might have been a common ancestors of both modern humans and Neanderthals (although Maju, rightly retains some skepticism). He comments at his blog that:

So we could well ask, if H. heidelbergensis is not ancestral to Neanderthals, then where do Neanderthals come from?

It must be answered that we do not know yet if H. heidelbergensis is or not ancestral to Neanderthals or in what degree it is. The mitochodrial (maternal) lineage may well be misleading in this sense. Denisovans themselves were much more related to Neanderthals via autosomal (nuclear) DNA than the mtDNA, so it may also be the case with European Heidelbergensis.

In fact it is still possible that these individuals represent some sort of admixture between older and newer layers of human expansion. But there is no clear answer yet. What is clear is that no Neanderthals have these mitochondrial sequences but others closer to those of H. sapiens - and this is the most puzzling part in fact.

Who indeed?

In response to this new data point, John Hawks notes that the case for Neanderthals evolving in Western Europe, as H. heidelbergensis fossil evidence had strongly supported is now undermined. Considering this fact together with the presence of more genetic diversity in ancient DNA from Central European Neanderthals than in Western European ones he notes that:

From this perspective, the evolution of Neandertals looks less and less like a European phenomenon. Instead, Europe may have been invaded repeatedly by Neandertal populations that were much more numerous elsewhere, such as western or central Asia.

More generally, this evidence seems to support the notion that the hominin evolutionary tree was much bushier than previously suspected with many more unattested species that were not closely genetically related co-existing than we had previously believed.

Implications For Denisovan Species Identification

Second, this ancient mtDNA data positions the mysterious Denisovans much more clearly on the archaic hominin tree. They were closer to Homo heidelbergensis than to Neanderthals or modern humans. The Denisovan as Homo heidelbergensis hypothesis was one possibility discussed at this blog in late May and June of this year before anyone involved had this new ancient DNA data point.

On the other hand, the mtDNA split between Denisovans and Homo heidebergensis is actually older than the Neanderthal-modern human split by almost 50%.  Thus, while they share a common mtDNA clade relative to other hominins for whom we have ancient DNA, their common ancestry is actually very ancient.

This can be added to the observations of John Hawks from earlier this year that the mtDNA lineage of the Denisovans is probably too close to modern humans (as estimated by mtDNA mutation rates) for the Denisovans to be a direct ancestor of Homo Erectus, the first hominin species to leave Africa. Now, better informed, John Hawks, in his post on the new ancient DNA on the subject of Denisovan ancestry, emphasizes how little we really do know about the key issues:

[W]e know essentially nothing about the morphology of West or Central Asian hominins of 300,000 years ago. South Asia and Southeast Asia were likewise inhabited throughout this period but we have only the barest hints about the morphology of their inhabitants. These peoples existed just inside the range of archaeological visibility but we lack any but the most rudimentary fossil evidence of them.

To be sure, many people have been assuming that the Denisovans were some kind of East Asian population, for example in China or Southeast Asia. In the process, they have projected the characteristics of the Asian fossil record upon them. That idea has been supported by the existence of Neandertals to the west, and also the sharing of some Denisovan similarity in the genomes of living Australians and Melanesians.

But that's a big assumption. Let's explore an alternative: that the Denisovans we know are in part descendants of an earlier stratum of the western Eurasian population. Although they are on the same mtDNA clade, the difference between Sima and Denisova sequences is about as large as the difference between Neandertal and living human sequences. It would not be fair to say that Denisova and Sima represent a single population, any more than that Neandertals and living people do. But they could share a heritage within the Middle Pleistocene of western Eurasia, deriving their mtDNA from this earlier population.

Thus, we do now that this "sub-genus" identification for the Denisovan implies that the source of Denisovan mtDNA in modern humans must have been intrusive to Indonesia where it probably introgressed into modern human DNA rather than being a population that sprang out of Asian Erectus populations to a Siberian refugium. They replaced or coexisted with Homo Erectus.

This also leaves open the question of where in the genetic phylogeny Homo Florensis belongs. Their proximity to ground zero in modern human introgression of Denisovan DNA still makes H. Florensis a prime candidate for the source of that DNA in modern humans, until ancient DNA can rule them out. But, if Homo Florensis (aka hobbits) were the source of this archaic DNA introgression, then it follows that they must have been not pygmy Homo Erectus as many people have previously supposed, but pygmy Homo heidelbergensis clade member.