Denisovans harbour ancestry from an unknown archaic population, unrelated to Neanderthals

Mystery human species emerges from Denisovan genome

The best explanation is that the Denisovans interbred with an unidentified species, and picked up some of their DNA. Or as Reich puts it: "Denisovans harbour ancestry from an unknown archaic population, unrelated to Neanderthals."

The data looks convincing, says geneticist Johannes Krause of the University of Tübingen in Germany. "There's a very strong signal, difficult to question."

Krause is one of several geneticists who have studied the Denisovan genome and wondered if....

Who doesn't enjoy a good mystery?


This first article is an older one but I thought I'd start with it and then bring the reader forward a bit. First off, the Denisovan connection is still fairly new and isn't fully understood. Thankfully there are quite a few researchers in hot pursuit in unraveling this gnarled generic human family tree conundrum.

At first, in the early years of the Denisovan mystery many weren't sure yet just how they may have contributed to our modern line.

Then in 2014 we are treated to this rather interesting discovery

Extinct human cousin gave Tibetans advantage at high elevation

“We have very clear evidence that this version of the gene came from Denisovans,” a mysterious human relative that went extinct 40,000-50,000 years ago, around the same time as the more well-known Neanderthals, under pressure from modern humans, said principal author Rasmus Nielsen, UC Berkeley professor of integrative biology. “This shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species.”

The interesting thing is that up till that point many were convinced the Denisovan connection were mostly in the Pacific not Eurasia. Which is rather interesting don't you think? For a newer species with it's remains found in Siberia to have it's lineage stronger on Pacific Islands than in it's own backyard?

From Aug 30, 2012

"We find no trace of Denisovan genetic material in mainland Eurasia, including in mainland Southeast Asia, to the limits of our resolution," says study co-author David Reich of Harvard Medical School. "However, it's clear that Denisovan genetic material has contributed 3 percent to 5 percent of the genomes of people in Australia and New Guinea and aboriginal people from the Philippines and some of the island nearby."

Obviously science moves forward with better understandings coming from more in depth research as has been shown. Just keep in mind and the thrust of this and many of my thread posting is the fact that our supposed family tree has been revealing itself to be not so straight forward as it was once believed.

I'm still waiting to find out why is there a stronger ancient Siberian/Denisovan genetic presence out in the Pacific rather than in Eurasia?

The current hypothesis for human origins and evolution is based upon scant evidence which is extremely patchy and dependent on archaeological finds which are dependent on many other factors, so the chances are of their being a truly representative fossil record upon which these hypotheses are built are slim. The true ancestry of humanity IMO is probably more complex and containing as yet unrealised data.

At first I thought that Denisovans migrated out of Eurasia so long ago that it only left a small impact, settled (loosely using that word) in the Pacific. But they would have to have had some boat making skills to make it to those islands and if so was it another Polynesian type found it by mistake/being blown off course deal? Or where these ancient hominids just building boats and hoping or the best..

But perhaps they migrated out of the Pacific into Eurasia? Evolving to what we classify as Denisovans now from another hominid species that migrated into the pacific many moons back.

Too many questions with such little evidence.

Great find slayer, hats off to these researchers.


Peace

I wanted to post a video I saw on the topic on TV but so far my search online for a link is Zip.

a reply to: SLAYER69

Interesting reading! I'd be happier if they called then an ancient race, instead of species (and same for the Neanderthals), since they are clearly human (viable offspring from crossbreeding). Even so, it's fascinating stuff. Ancient races that aren't around anymore....if we had more data, we could understand more about our past.

a reply to: SLAYER69

Great topic to deal with here Slayer! I was a little surprised that there is such a heavy focus of the archaic hominid ingression into Denisovans when the original work I had read a couple of years back indicated that it was present in Neanderthal( both Neanderthal and DEnisovan remains were found in the Denisova cave and a toe bone from there was used for the Neanderthal genetic sequencing) as well and possibly HSS. But I'm going off of memory and can't find the article that made the HSS claim at the moment. Another side note to this type of research is that recent work based on findings of the Human Genome Project as well as Svante Paabo's work at the Max Planck Institute, seems to indicate that we should be able to find traces of many or all of our precursors genetics within our own. This is independent of our actually being able to have the genomes of the subject species in question decoded or even available for comparison. This would be a huge step forward in making our family tree/bush a definitive piece of data and indicate which specific lineages led to us as well as how much of a contribution they may have made, possibly even going far enough back to see if Australopithecines were in fact part of our lineage or if we did not start until H. Habilis. All in all it's a pretty fascinating time for research into Archaic Human lineages. Thanks for posting this, there are still a lot of people not terribly familiar, especially with Denisovans and this gives them another piece of the puzzle to play with.

a reply to: SLAYER69

Hey Slayer,

That illustration is on point when I read this article in the New York Times yesterday. I immediately remembered about your thread and posts about human migration across the world.

The human family is truely a gnarled bush of evolution. With more genetic information, we may elucidate the origins of the Kennewick Man mystery.
Since Gobekli Tepe has been slowly uncovered, I wonder if human "culture" goes back even further with different extinct human cousins.

As first first science officer Spock would have said "Fascinating".

Cheers,

Kratos

a reply to: theabsolutetruth

Just as a reminder, the whole genome of Neanderthal has been mapped. About 4% of Europeans still carry Neanderthal DNA. This is why statistical methods in genetics can fill in the gaps where we can't find that elusive fossil containing that precious DNA. Using mathematics we can predict for genetic drift and certain changes in the epigenome.
Genetic tools are greatly improving. But I will concede that obtaining a true specimen of DNA is the best way to get information.

Cheers,

Kratos

a reply to: Kratos40

Just wanted to add a minor correction here. It's not 4% of Europeans who carry the genes, its all people of European descent who carry up to 4% of the genes. This is present in a large swath of Asians as well and affects literally, billions of individuals. Because of different genes expressing themselves in different populations, there is actually about 20% of the full genome present in modern populations based on comparisons with the full Neanderthal genome. Additionally, up to 6% of Denisovan DNA is present in select populations such as Micronesians and natives of New Guinea.

a reply to: peter vlar

Yes, you are correct. I wish I would have kept the news article, but wasn't it also that Autralian Aborigines also carry Denisovian genes?

a reply to: Kratos40

Yes, they carry both Neanderthal and Denisovan genetics. They have only recently had their own DNA sequenced and it's been found that they are descended from some of the first humans to migrate out of Africa 60 KA.

www.nature.com...

originally posted by: Kratos40
a reply to: SLAYER69

Hey Slayer,

That illustration is on point when I read this article in the New York Times yesterday. I immediately remembered about your thread and posts about human migration across the world.

The human family is truely a gnarled bush of evolution. With more genetic information, we may elucidate the origins of the Kennewick Man mystery.
Since Gobekli Tepe has been slowly uncovered, I wonder if human "culture" goes back even further with different extinct human cousins.

As first first science officer Spock would have said "Fascinating".

"Aboriginals in the New world"


Sci/Tech 'First Americans were Australian'

However, the new evidence shows that these people did not arrive in an empty wilderness. Stone tools and charcoal from the site in Brazil show evidence of human habitation as long ago as 50,000 years.

The site is at Serra Da Capivara in remote northeast Brazil. This area is now inhabited by the descendants of European settlers and African slaves who arrived just 500 years ago.

But cave paintings found here provided the first clue to the existence of a much older people...

Also...

Aboriginal people had Siberian ancestors

To make the link between the Denisovans and indigenous Australians, the study looked at two Aboriginal populations, one of which was from the Northern Territory. The researchers concluded that Denisovans interbred with modern humans in South-East Asia 44,000 years ago, before Australia separated from Papua New Guinea.

"This paper helped fill in some empty pieces in the evolutionary puzzle that began after early humans left Africa, and reinforces the view that humans have intermixed throughout history," say the scientists behind the research in a summary of the findings.

"The study also confirms controversial claims that the ancestors of all living Eurasians interbred with the Neandertals, while past Asians/Oceanians also mated with the mysterious ancient humans from Denisova cave[s] in Siberia," comments Darren from UNSW. "This is clear and independent validation of DNA work on both these extinct humans [the Neanderthals and the Denisovans], confirming today's other big announcement about their deep connections to Australians and other indigenous people in our region."

a reply to: SLAYER69

You posted while i was composing this at work

Hi Slayer,

This reply got delayed because, it seems that the ATS uploader will not recognize certain image files from my mobile, after the latest android update, but the exact same image will upload from the desktop, odd.
Anyhow,

Here is some of the latest on denisovan ancestry

Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.

This map shows us some interesting things on the distribution of Deniosovan and HSN DNA.

www.biorxiv.org...
The authors of this study also mention the fact that tibetans inherited their altitude tolerence from denisovans, that fact is a clue as to how modern humans and the archaics intermingled.
Since the altitude adaptation can be found among tibetans and han chinese, and not among Native Americans, implies that Native Americans split off before the ancestors of East Asians admixed with denisovans.

a reply to: Sparta

If it was the Hobbits who migrated out of the pacific then that might make a lot of things make more sense in both the historical record and the accounts of myth and folklore surrounding "little people"

If we consider the likelihood that these hobbits would establish their own cultures then it might account for why they are so often found in remote areas, living in caves, etc....and considering their size, the remains could have just been regarded as childrens bones and treated accordingly.

a reply to: SLAYER69

However, the new evidence shows that these people did not arrive in an empty wilderness. Stone tools and charcoal from the site in Brazil show evidence of human habitation as long ago as 50,000 years.

There is no doubt that the current notions of how the americas were populated are woefully lacking, as so many sites so very early entrances into the new world.
Some so early that it might have to haver been HSN, HSD, or maybe even HE or HH.

Notice how on the map of HSN and HSD distribution, you see a hot bed , so to speak, of neanderthal ancestry in NE south america.

There are tantalizing clues that tell us HSN might have made it to the new world or at least a very very recently admixed population of modern humans.

Some interesting things about HSN and NAtive Americans

he Neanderthal had a feature which was unique to them (they ALL had it) and is found in some modern humans: the retromolar gap or retromolar space.


A paper published in March 2015, "The Retromolar Space: A Morphological Curiosity Observed Amongst the Protohistoric Arikara and Mandan" by C. de la Cova DOI: 10.1002/oa.2451 International Journal of Osteoarchaeology, noted that it is quite frequent among two American Native groups, the Arikara and the Mandan peoples:



Abstract
The retromolar space (RMS), defined in paleoanthropology as a space posterior to the third molar, between the distal edge of the tooth and the anterior margin of the ascending ramus when the mandible is held in lateral view, has been described as an autapomorphic trait unique to Neandertals despite its presence in anatomically modern humans (AMHs). This study examined RMS prevalence in a sample of Protohistoric Arikara and Mandan Amerindians to determine what craniofacial morphology is correlated with the RMS. It was hypothesized that the feature would be present in the Amerindians studied and associated with a long cranial length, a large nasal height, midfacial prognathism, a broad mandible, and dental wear. The results indicated that RMSs were present in the Arikara and Mandan and significantly correlated with cranial length, cranial breadth, nasal height, bizygomatic breadth, basion-nasion length, basion-nasiospinale, mandible length, gonial angle, bigonial breadth, and dental wear. Thus, RMSs are associated with a dolichocephalic skull, wide cranial and facial breadth, a prognathic face, large nose, and a corresponding wide and long mandible with a reduced gonial angle. This suggests that the RMS is the result of these features merging together in the craniofacial complex and should not be considered a Neandertal autapomorph.



Of course, the conclusion that Ms. Cova reaches is that it is not an exclusive Neandertal feature but that it is related to a certain skull morphology that these natives have...


How about testing another hypothesis: the natives have it because they have a high admixture with Neandertals and got the genes that produce the retromolar gap from the Neandertals themselves... maybe even admixing in America and not in Asia before migrating to the New World.
[/ex]

retromolar gap

Patagonian Monsters

And more musings from Austin

Neanderthals, Psoriasis and Native Americans... a Link



A very interesting paper by Yen-Lung Lin, Pavlos Pavlidis, Emre Karakoc, Jerry Ajay, and Omer Gokcumen, " Variants Shared with Archaic Hominin Genomes" takes a look at "polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human–Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed)...", some of these deletions are the cause of well known diseases.


I decided to see if there were any hints at a link between Native Americans and diseases prevalent among Neanderthals and this is what I found:

The previous paper by the same team (The Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes by Yen-Lung Lin, Pavlos Pavlidis, Emre Karakoc, Jerry Ajay, and Omer Gokcum. Mol. Biol. Evol. doi:10.1093/molbev/msu405 Advance Access publication January 2, 2015) states that one of the deleted sequences shared by humans and Neanderthals is the LCE3C gene deletion: "...which has been strongly associated with psoriasis (de Cid et al. 2009). The allele frequency of LCE3C gene deletion is extremely high among Eurasians, reaching to over 70% allele frequency in some European and Asian populations..." it is the authors' "understanding that this deletion has been maintained in high allele frequencies since before Human– Neandertal divergence."

patagoniamonsters.blogspot.com...




And about Native americans inheriting the diabetes risk gene from Neanderthal

Mexicans and other Latin Americans have a higher risk of diabetes because of a Neanderthal gene mutation, researchers say.

and

Although this gene variant is common among people with recent Native American ancestry and is also found in about 20 percent of East Asians, only 2 percent of Europeans have it, and no known Africans carry SLC16A11. This pattern is somewhat unusual; modern humans arose in Africa, so nearly all common human genetic variants are found in African populations. [Top 10 Mysteries of the First Humans]

To uncover the roots of this odd pattern, the researchers investigated ancient human DNA and found the high-risk mutation of this gene was apparently inherited from Neanderthals, the closest extinct relatives of modern humans. Recent analysis of Neanderthal DNA revealed the ancestors of modern humans interbred with Neanderthals; the first high-quality genome sequence from a Neanderthal suggests about 1.5 percent to 2.1 percent of the DNA of modern humans living outside Africa is Neanderthal in origin. In contrast, Neanderthal DNA is much less common among modern Africans, matching these latest findings.

Diabetes in Native Americans

What's most interesting about that work is that another recent paper, im trying to track it down, shows that meso americans, specifically a group of yucatan maya have the highest levels of neanderthal ancestry of all modern humans.

This just in, via Dienekes blog,

Neandertal in the (immediate) family tree
Early European may have had Neanderthal great-great-grandparent

One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.

The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone's genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

Dienekes blog

Hmm
so it seems that neanderthal admixture happened on numerous occasions, and over a wide area, from western europe to east asia. This admixture event was later than the eurasian event but before the east asian and siberian events.

It also confirms that there is cultural continuity between AMH and HSN in some places.