Thursday, December 5, 2013

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.

8 comments:

terryt said...

"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"

Intrusive to Indonesia, yes. Unlikely to have introgressed into the modern human population in Indonesia though. As your quote from John Hawks:

"Let's explore an alternative: that the Denisovans we know are in part descendants of an earlier stratum of the western Eurasian population. ... But they could share a heritage within the Middle Pleistocene of western Eurasia, deriving their mtDNA from this earlier population"

That places Denisove securely in wetern Eurasia, not in the east.

"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".

But all able to interbreed successfully.

andrew said...

The Indonesian admixture assumption is based on the location of the introgressed populations and doubt about the subsequent total replacement of that UP population. So, the origins of the Denisova and their route to Indonesia are irrelevant. A post-Wallace line introgression is still very plausible.

Able to interbreed doesn't mean that this produced fertile children with the same ease. Indeed, there is evidence of hybrid infertility in the loci where introgressed from Neanderthal alleles in modern human are located in the genome.

DDeden said...

H. floresensis is merely Hss locally adapted to unusual conditions, derived from pygmy-San ancestors...Ebu gog = (Bembu congo) IMO

terryt said...

"H. floresensis is merely Hss locally adapted to unusual conditions, derived from pygmy-San ancestors"

I agree with the 'locally adapted to unusual conditions' bit but am extremely doubtful of the 'derived from pygmy-San ancestors'.

"A post-Wallace line introgression is still very plausible".

'A post-Wallace line introgression' is basically impossible, unless the Flores population maintained a 'Denisova' element for something like half a million years. There was no-one else beyong Wallace's Line until modern hujmans crossed it. And preumably they already carried the Denisova element. It has probaly been diminished through Eurasia by the later expansion of populations lacking the element.

"there is evidence of hybrid infertility in the loci where introgressed from Neanderthal alleles in modern human are located in the genome".

Yes, there is evidence, but I'm not sure how convincing that evidence is. We have the example of Europe which seems to have undergone repeated incursions of haplogroups and genes from elsewhere which have diminished the proportion of older genes. Much of this during just the period of the Neolithic. Over amuch longer period I can easily see how ancient DNA would become greatly reduced as a proportion of current DNA.

andrew said...

A Hobbit observation that seems a good fit with the DNA link is this one:

"Tocheri et al. (2007) (including Morwood, Larson, and Jungers), compared three carpal bones believed to belong to LB1 with carpal bones of modern humans, some earlier hominids and African apes. They concluded that the carpals from the Liang Bua cave resembled ape carpal bones and were significantly different from the bones of H. sapiens, Homo neanderthalensis or even Homo antecessor, and that they were comparable to carpal bones of Australopithecus. The carpal bones of H. floresiensis were found to lack features that evolved with ancestors of modern humans at least about 800,000 years ago. These features are already formed during embryogenesis and therefore Tocheri et al. argue that it is improbable that the shape of H. floresiensis wrist bones could be a result of a developmental disease. This evidence also suggests that H. Florensiensis is not a modern human with an undiagnosed pathology or growth defect, but that it represents a species descended from a hominin ancestor that branched off before the origin of the clade that includes modern humans, Neandertals, and their last common ancestor.[9]"

The archaic hominin Flores population seems to date from about 850,000 years ago +/- about 10,000 years, which is pretty close in time to H. Heid.'s appearance.

The possibility that they thrived in Flores since they didn't have to compete with H. Erectus there because they could reach it and Erectus could not makes sense to me.

barakobama said...

I am skeptical how distinct these species were and how we are able to classify them so well. All the different skeletal remains called Neanderthals may be many very unrelated breeds. Since Densovian autosomal DNA was more related to the Neanderthal sample than Neanderthals are to modern humans but the Neanderthal mtDNA lineage is closer to modern humans. That would mean that there was mixing between different human breeds. That also means it is a possibility Heidelbergensis was ancestral to Neanderthals.

Human species must have been out of Africa for a very long time. SinceNeanderthals,Heidelbergensis, and Densovians all originated in Eurasia. It is possible modern humans descend from a back migration to Africa or didn't originate in Africa at all.

The question needs to be asked why is our species or breed the last left? Why are we so superior to the rest?

terryt said...

"The question needs to be asked why is our species or breed the last left? Why are we so superior to the rest?"

It is 'superior' because it has accumulated the 'best' genes from all the previous species. It is becoming more and more obvious that various human species have contributed to the modern human gene pool, leaving open the possibility that the various 'species' were often completely inter-fertile.

andrew said...

"The question needs to be asked why is our species or breed the last left? Why are we so superior to the rest?"

Given the timing of the point at which modern humans became dominant, dog domestication is a pretty likely candidate.