Denisovan's Dispersals into Southeast Asia and Oceania

Well writing a third installment of my Remnants of a Lost World series I came across this rather interesting perspective and thought I'd drop by and post this for those who were interested in the topic.

A few years back we learned of the Denisovians and how the Pacific's Melanesian were thought to be the only HS with any significant Denisovian DNA. This perspective somehow slipped passed me during research on older related threads.

It now appears that Denisovian contribution is much larger and wider than previously thought.

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred.

Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

Yes.. yes, yes! Fantastic as always. Ahh, those SNEAKY Denisovans!! While I don't say that I wait with baited breath for your posts, Slayer..

I do get that same giddy feeling as a kid on Christmas when I see a new one and open it for a mental treat!

S & F

So the DNA wasn't in all the groups tested yet was still widespread. I think that there is evidence for that in other groups as well. Like those pesky red haired mummies in China It's not a total shock that Denisovan's genetic are in only some stock. Cross breeding usually will occur either when two neighbors get along and trade/interact with each other or when a weaker people is conquered and enslaved by a more powerful neighbor. So the lack of Denisovan DNA in some people in regions where it is found I think is due to one of the two reasons I give.

reply to post by SLAYER69


Hey slayer,
Nice,

Denisovan admixture tells us a great deal about who we are, and where we came from.

Here's a little tidbit

There is a symmetry between the excess of “Denisovan” alleles in Papuans and the shortage of “Neandertal” alleles in Europeans (both archaic species being closely related to each other), with Northeast Asia, East Asia, Southeast Asia and the New World forming a “hub” with both paleobiological and genetic attestations of an “archaic” hominin source. There is also clear parallelism between the east-to-west decrease in the fraction of autosomal “Neandertal” ancestry and the presence of the “Amerindian” component (mislabeled as “East Eurasian” component by Dienekes) in Western Eurasia. It seems possible that Denisova Cave tells us a story of modern human origins from an East Eurasian hominin, a relative of Neandertals and Denisovans, who speciated into “us” in an isolated refugium such as America and then migrated back into the Old World (see out-of-America II). As early humans were migrating west to Europe and Africa, they lost some of that hominin ancestry and, in Africa, mixed with local archaics who contributed ancestral chimp alleles into a gene pool that had previously been largely composed of derived, or “modern,” as it were, alleles.

anthropogenesis.kinshipstudies.org...

The world of anthropology is changing at pace faster than even the experts can cope with, wh.en one looks at the whole picture of our past from a combined view across disciplines, the picture is very different from what it was even a year ago.

Here's a little more fron the discussion I referenced in my previous post.

Third, the Denisova Cave find (and, of course, ancient Neandertal DNA) opened a conversation regarding whether modern African populations are the products of a unique speciation event within Africa some 200,000 years ago or of admixture between the newly baked non-African humans and African archaics. We have statistical cues that this was likely the case, but we cannot ascertain it unless we find another phalanx or a tooth with recoverable DNA in them. We may find them in a Caucasus cave and the recovered alleles will pop up at high frequencies in South African Bushmen, but we will definitely not find this ancient DNA in Sub-Saharan Africa because DNA does not survive in hot climates. Thanks to Denisovans, it is now clear that the ideal blend between paleobiology and genetics may not be attainable for such a critical continent as Africa. One has to systematically look outside of genetics and paleobiology to reconstruct human prehistory – something that this weblog aims to do.

Dr. Dziebel is discussing this paper.

m.sciencemag.org...

And from that paper,

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

More from Dr. Dziebel discussion of that paper.

Second, the Denisova Cave find challenges our newly-established belief that, in the genetics of extant human populations, there are nice molecular clusters representing reliable proxies of the real prehistoric divergence of modern human populations as they fanned out from Africa to colonize the rest of the world. More genetically diverse populations, those that contain more of those clusters, are older than less genetically diverse populations, and the seemingly superficial process of visually progressing from counting more clusters in Africa to fewer clusters in Asia, Oceania and America actually represents the way humans colonized the world by taking with them, at every significant junction, a subset of genetic variation of the parent population. However, the Denisova Cave find shows that some modern human populations, namely Papuans, Australians and Island Melanesians, did not just lose ancient African diversity but gained archaic Eurasian diversity through interbreeding. Thanks to Denisovans, it is now clear that taken in separation (ancient) fossils and (modern) are misleading.

anthropogenesis.kinshipstudies.org...

From Dr. John Hawks' blog, his lab did the initial work on the denisovans,

My lab is in a unique position to work on this information and uncover biological details of these ancient people. The initial results of genetic sequencing have provided some starting points for our work. Mitochondrial DNA has been recovered fromtwo individuals,a distal fifth carpal phalanx (that is, a pinky bone) and a third molar. The pinky bone has produced a whole genome at roughly 1.8x coverage. The similarities with Neandertals show this individual to have come from a population roughly as divergent from living people as the Neandertals were, but almost as divergent from Neandertals as from us [1] (I explain this further in the Denisova genome FAQ). They appear to have originated froma common population with us and Neandertals around 250,000-400,000 years ago. The mtDNA sequence of these individuals presents a possible mystery -- roughly twice as different from most living people as we are from Neandertals, it may represent traces of an even more ancient population [2] (again, I describe the full scenario in the FAQ, and the initial mtDNA result in my post on the work by Krause and colleagues). It remains unclear whether these genetic results may allow us to connect the Denisovans to any known fossilpopulation. They're too close to us to represent the Homo erectus population that first inhabited Asia more than 1.8 million years ago, but we cannot yet rule out the hypothesis that the Denisovan genome has some ancestry within this ancient Asian population. We do know that the genes from these ancient people live on today, in Melanesia, New Guinea and Australia. But on the whole, the relationships of the Denisovan genome are a mystery. We just don't know if the genome comes from any known fossil population.

johnhawks.net...

From another article by Dr. Hawks

Last month, David Reich and colleagues [1] reported on estimates of Denisovan ancestry for island and mainland Asian populations. Their most memorable conclusion was that they could find no substantial sign of Denisovan ancestry anywhere on the Asian mainland, or indeed on any island that had ever been connected by land to Asia. The distribution was stark, as illustrated by the map from the paper:

I wrote about the paper when it was released ("Denisovan DNA in the islands, and an Australian genome"), noting:

Notice the apparent lack of Denisovan ancestry in anyone who lives anywhere that was once connected by land with mainland Asia. I say "apparent" deliberately: Abi-Rached and colleagues reported last month on the widespread distribution of Denisovan HLA types among today's Asian populations, and those may well be products of Denisovan genes that were later selected. I've already identified a handful of other loci that seem to reflect Denisovan ancestry in mainland Asian people. According to the comparisons by Reich and colleagues, such loci must be exceptions.

Abi-Rached and colleagues [2] had argued that HLA alleles found in the Denisovan genome are presently common in some parts of Asia, and likely reflect local adaptive introgression. Substantial introgression of a small number of genes would not be enough to create a strong genome-wide appearance of Denisovan ancestry. Still, it was a little odd that the first genes anybody looked closely at would provide strong evidence of introgression.

I was trying to find a genetic map to go with the story but nothing was found that was very accurate

so is this proving ancient people did sail far and wide?
or could all these peoples have co-existed in communities while land masses were still attached to others?

may be a stupid question

Originally posted by GezinhoKiko
so is this proving ancient people did sail far and wide?
or could all these peoples have co-existed in communities while land masses were still attached to others?

may be a stupid question

Well, I believe that the ultimate concensus will be that denisovans did not make it to the sahul, but that modern humans who carried thier DNA settled in the sahul.

There are some striking things about the distribution of denisovan dna, one is that the negrito people of the Andaman islands carry no denisovan component, while negrito tribes further east ,in Papua and melanesia in the phllipines do.
This clearly shows the cross over event was in south east Asia.

Here is a clip from a discussion on denisovan dispersal, and how modern humans out competed them.

In my post yesterday, I dismissed the possibility that the presence of Denisovan DNA in populations to the east of Wallace line and its absence to the west of the Wallace line was not easily explained by dilution of the Denisovan admixed population because East Indonesia has a substantial Paleolithic substrate and because the level of dilution required (on the order of a factor of sixty for South China relative to Papuans) would be so great. Have I dismissed this possibility too easily?

The evidence can be marshalled to give some support to a dilution narrative.

A Dilution By Paleolithic Y-DNA Haplogroup O Men Scenario

There is a stark difference in Y-DNA haplogroup frequencies on either side of the Wallace line. To the east are high frequencies of populations typical of Sahul populations (i.e. Australia and Papua New Guinea), with a modest amount of Austronesian (i.e. Neolithic seafarer) contribution that there is very strong evidence to suggest dates to the last five thousand years or so. On the other sided of the line, for example, on the island of Bali, the percentage of Y-DNA that is something other than Y-DNA haplogroup O is quite small, about 4%, with some of the Y-DNA haplogroup O attributable to Austronesian sources and some attributable to some other migration into Western Indonesia. While the ratio isn't quite sixty to one the cline is certainly steep and could explain much of the variance in Denisovan admixture.

One plausible time for the non-Austronesian lineages of Y-DNA haplogroup O to arrive in Western Indonesia would have been when Sundaland was attached to mainland Asia. The region where non-Austronesian lineages of Y-DNA haplogroup O are common correspond to the territory of Sundaland which was a continuous land mass attached by land to mainland Asia during the Last Glacial Maximum around 20,000 years ago. Even for people with some seafaring abilities more primative than that of the Austronesians, mass migration across land is easier than mass migration across water and the distribution of these lineages closely matches a terrestrial passage at that point in time.

It was the domestication of the dog that gave modern humans the edge.

The most plausible explanation I can muster is a simple one. The Paleolithic Y-DNA haplogroup O people had domesticated dogs; the people who were vastly diluted by them did not.

The Sahul people did not have dogs until an archaeologically well documented moment when a handful of dingos migrated to Australia around 8,000 years ago from a stock found in Southeast Asian wild dogs. The arrival of the dingo in Australia caused a continent wide secondary mass extinction that eliminated many species that had survived the megafauna extinction that accompanied the appearance of modern humans in Australia. This mass extinction is a testiment to the impact that domesticated dogs could have on hunting and gathering economics.

dispatchesfromturtleisland.blogspot.com...

Hey Slayer good topic

This may be of interest

I didn't have time to read the entire thread so I hope the above has not been posted earlier

Originally posted by Hanslune
Hey Slayer good topic

This may be of interest

I didn't have time to read the entire thread so I hope the above has not been posted earlier

Hi Hans,
You've been scarce lately,

Yes I believe that is the paper referenced by Dr. Hawks in one of my above posts, his lab did the initial genetics work
When you get a chance I highly recommend reading the discussions on newer denisovan DNA work, it is quite illuminating.

Both Dr's Hawks and Dziebel blogs have quite a bit of material on denisovan studies,
with Dr Hawks taking a traditional view, and Dr. Dziebel a more less than traditional viewpoint.

I don't know if this is relevant to this tread but it is interesting.Ancient DNA reveals humans living 40,000 years ago in Beijing area related to present-day Asians, Native Americans Read more at: phys.org...

An international team of researchers including Svante Pääbo and Qiaomei Fu of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced nuclear and mitochondrial DNA that had been extracted from the leg of an early modern human from Tianyuan Cave near Beijing, China. Analyses of this individual's DNA showed that the Tianyuan human shared a common origin with the ancestors of many present-day Asians and Native Americans. In addition, the researchers found that the proportion of Neanderthal and Denisovan-DNA in this early modern human is not higher than in people living in this region nowadays. Read more at: phys.org...

reply to post by punkinworks10


Thanks Punkinworks I'll see if I can get to it next weekend. I'll be more active on the board after this semester ends

Originally posted by d8track
I don't know if this is relevant to this tread but it is interesting.Ancient DNA reveals humans living 40,000 years ago in Beijing area related to present-day Asians, Native Americans Read more at: phys.org...

An international team of researchers including Svante Pääbo and Qiaomei Fu of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced nuclear and mitochondrial DNA that had been extracted from the leg of an early modern human from Tianyuan Cave near Beijing, China. Analyses of this individual's DNA showed that the Tianyuan human shared a common origin with the ancestors of many present-day Asians and Native Americans. In addition, the researchers found that the proportion of Neanderthal and Denisovan-DNA in this early modern human is not higher than in people living in this region nowadays. Read more at: phys.org...

Nice contribution,

It is absolutely relevant, because it shows that physically modern humans in Asia at that place and time have no particular relationship to the denisovans who's territory they supposed passed through. How did this come to be? when clearly the ancestors to papuans and melanesians aquired denisovan genes as they passed through their territory.
In my.view it is another piece of the "Out of the Americas" puzzle, and it backs up this statement from one of my previous posts.

There is also clear parallelism between the east-to-west decrease in the fraction of autosomal “Neandertal” ancestry and the presence of the “Amerindian” component (mislabeled as “East Eurasian” component by Dienekes) in Western Eurasia. It seems possible that Denisova Cave tells us a story of modern human origins from an East Eurasian hominin, a relative of Neandertals and Denisovans, who speciated into “us” in an isolated refugium such as America and then migrated back into the Old World (see out-of-America II).

What Dr. Dziebel is saying is, that an archaic homonin, that was a close relative to denisovans and neanderthal, was the first to make it to the new world and that they evolved into modern humans in isolation and then.back migrated into Asia and east eurasia to form the basis for modern eurasians.

reply to post by Hanslune


Good to hear from you Hans,
It's been quiet in here lately.

They found a bone in Denisova cave and concluded that entire Denisova population originated there?
That is quite an assumption, considering the fact that there are no other evidence.
They could have easily originated further south and made some rare expedition to the Siberia.

Originally posted by DangerDeath
They found a bone in Denisova cave and concluded that entire Denisova population originated there?
That is quite an assumption, considering the fact that there are no other evidence.
They could have easily originated further south and made some rare expedition to the Siberia.

No body said they originated there, it is thought that since their DNA trace can be found all the way into melanesia, that they ranged throughout south east Asia.
It is my thought that Denisova cave represents the northern boundries of their range.

The plot thickens.

Neanderthals were around a lot longer than human beings have been around.

Would it be that hard to believe that Neanderthals made it to the new world. I think it is more surprising that they didn't make it to the western hemisphere, or much further east, as homoerectus did.

But we should see examples in the fossil record.

But by this information, it sounds like Neanderthals, or some of their descendents, made it around the planet.