Sex with Neanderthals and Denisovans gave healthy boost to human genome: study

Aug 25, 2011

For a few years now, scientists have known that humans and their evolutionary cousins had some casual flings, but now it appears that these liaisons led to a more meaningful relationship.

Sex with Neanderthals and another close relative — the recently discovered Denisovans — has endowed some human gene pools with beneficial versions of immune system genes, report researchers at the Stanford University School of Medicine in an article to be published online by the journal Science at the Science Express website on August 25.

Although , Neanderthals and Denisovans share a common ancestor in Africa, the groups split into separate, distinct populations approximately 400,000 years ago. The Neanderthal lineage migrated northwestward into West Asia and Europe, and the Denisovan lineage moved northeastward into East Asia. The ancestors of modern man stayed in Africa until 65,000 years or so ago, when they expanded into Eurasia and then encountered the other human-like groups. In some cases, the rendezvous were amorous in nature.

Last year, a partial genome sequence of Neanderthals, who died out approximately 30,000 years ago, revealed that these trysts left as much as 4 percent Neanderthal DNA in the genetic blueprint of some present-day humans. Last December, the genome of another human cousin, the extinct Denisovans, made clear that up to 6 percent of some people's genomes are Denisovan in origin.

Now, a team of researchers led by Peter Parham, PhD, professor of structural biology and of microbiology and immunology, has found that these matings had a positive effect on modern human fitness. "The cross breeding wasn't just a random event that happened, it gave something useful to the gene pool of the modern human," said Parham, who is senior author on the study.

The useful gift was the introduction of new variants of immune system genes called the HLA class I genes, which are critical for our body's ability to recognize and destroy pathogens. HLA genes are some of the most variable and adaptable genes in our genome, in part because the rapid evolution of viruses demands flexibility on the part of our immune system.

"The HLA gene system, with its diversity of variants, is like a magnifying glass," said lead author Laurent Abi-Rached, PhD, explaining that it provides a lot more detail about the history of populations than typical gene families. Abi-Rached is a research associate in the Parham lab.

Prior to the sequencing of the Neanderthal and Denisovan genomes, Parham and his group had suspected that at least one HLA variant came from archaic humans. They determined that the variant known as HLA-B*73 is rare in present-day African populations but occurs with significant frequency in West Asian populations. The ethnic distribution of HLA-B*73 and its similarity across populations suggested that it came from a relatively recent co-mingling of modern human and archaic human DNA, which most likely would have happened outside of Africa. Parham's team wanted to discern which archaic humans were the source of the HLA-B*73 gene type. In the last year they have found the answer in the genome sequence of a recently discovered human relative, the Denisovans, whose existence first came to light in 2008 with the discovery of an unfamiliar finger bone and tooth in a cave in Siberia.

By comparing the HLA of the archaic humans with , the researchers were able to show that the HLA-B*73 allele likely came from cross breeding with Denisovans. Little is known about what the Denisovans looked like (the finger bone and the tooth are the only known fossils), but the genome sequence extracted from the finger bone gives insight into where they overlapped with modern humans. Gene flow from the Denisovans into modern humans has left the highest frequency of the HLA-B*73 allele in populations in West Asia, the most likely site for the fortuitous mating to have taken place.

Even in West Asian populations, the HLA-B*73 variant never represents more than 5 percent of all known variants of that gene. However, other human HLA types that arose from ancient matings are found in much greater frequencies. "Certain traits coming from these archaic humans have become the dominant form," said Parham. For example, another HLA gene type, called HLA-A*11, is absent from African populations, but represents up to 64 percent of variants in East Asia and Oceania, with the greatest frequency in people from Papua New Guinea. "The likely interpretation was that these HLA class variants provided an advantage to modern human and so rose to high frequencies," Parham said.

A similar scenario is seen in some HLA gene types found in the Neanderthal genome, which was also sequenced from DNA extracted from ancient bones. These gene variants are common in European and Asian populations but rare in African populations. "We are finding frequencies in Asia and Europe that are far greater than whole genome estimates of archaic DNA in modern human genomes, which is 1 to 6 percent," said Parham. Within one class of HLA gene, the researchers estimate that Europeans owe half of their variants to interbreeding with and Denisovans, Asians owe up to 80 percent and Papua New Guineans, up to 95 percent.

"This is not the pattern seen genome-wide," said Abi-Rached. "The HLA system is unique in its diversity and the strength of natural selection acting on it, but it's possible that other gene systems, particularly the ones under similar pressure for variation, could show a similar pattern."

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User comments : 25

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Guy_Underbridge
3.7 / 5 (3) Aug 25, 2011
Sex with Neanderthals and another close relative, the recently discovered Denisovans, has endowed some human gene pools with beneficial versions of immune system genes
It also gave them something to do until Reality TV was invented.
jscroft
4.6 / 5 (11) Aug 25, 2011
Wow. I'm actually feeling a lot better about my first marriage now.
emsquared
3.7 / 5 (3) Aug 25, 2011
Wow. I'm actually feeling a lot better about my first marriage now.

I dunno, were you the Neanderthal or Denisovan in this scenario...? ;)
Hev
4.3 / 5 (6) Aug 25, 2011
Not surprized - any "out-of-Africa modern human" when encountering a hunky blond Neanderthal, or hunky oriental Denisovian - with their much more advanced tools, warm fur coats, and cosy yurts, would have waved her weedy "gracile out-of-Africa modern human" partner goodbye.
Skepticus
1 / 5 (2) Aug 25, 2011
...was it consensual sex, or rape and pillage happy hours? And who did it to whom?
EdMoore
1 / 5 (12) Aug 25, 2011
Human genetic bootleneck: Noah and his three sons; and their three wives. Although the authors might not be aware of this piece of history, it's gratifying that their work validates the written historical acocunts.
LuckyBrandon
4.3 / 5 (6) Aug 25, 2011
@edmoore-I hope that was a joke...if not, re-examine the DNA fingerprint and you will find that bottleneck to be 3000-3500 or so humans left on the planet. That's hardly a few dudes, their wives, and some old dude who just looove incest apparently...
but even that data set is based on a very small percentage of the population of earth as a whole, what can be said for sure, is it was at LEAST that many people, and in all liklihood, significantly more...
draa
5 / 5 (8) Aug 25, 2011
@edmoore-I hope that was a joke...if not, re-examine the DNA fingerprint and you will find that bottleneck to be 3000-3500 or so humans left on the planet. That's hardly a few dudes, their wives, and some old dude who just looove incest apparently...
but even that data set is based on a very small percentage of the population of earth as a whole, what can be said for sure, is it was at LEAST that many people, and in all liklihood, significantly more...


People like EdMoore don't need your stinking facts. That's what's destroying their world veiw now. Facts. You and your uppity facts.

Thankfully there are many people that do not buy into the superstitions anymore. There numbers are growing thanks to science such as this. Just imagine, 400,000 years ago there were 3 different groups of near-humans living together. Incredible.
Shootist
2.3 / 5 (3) Aug 25, 2011
@edmoore-I hope that was a joke...if not, re-examine the DNA fingerprint and you will find that bottleneck to be 3000-3500 or so humans left on the planet. That's hardly a few dudes, their wives, and some old dude who just looove incest apparently...
but even that data set is based on a very small percentage of the population of earth as a whole, what can be said for sure, is it was at LEAST that many people, and in all liklihood, significantly more...


People like EdMoore don't need your stinking facts. That's what's destroying their world veiw now. Facts. You and your uppity facts.

Thankfully there are many people that do not buy into the superstitions anymore. There numbers are growing thanks to science such as this. Just imagine, 400,000 years ago there were 3 different groups of near-humans living together. Incredible.


No, or yes! We got us some new superstitions; AGW, UFOs, GM food, irradiated food, vaccines, mercury in fillings, fluoride, the list is endless.
jscroft
5 / 5 (3) Aug 25, 2011
Wow. I'm actually feeling a lot better about my first marriage now.

I dunno, were you the Neanderthal or Denisovan in this scenario...? ;)


I was whichever one grew the biggest antlers. :)
mezmama
1 / 5 (1) Aug 26, 2011
spam
Ramael
1 / 5 (2) Aug 26, 2011
...was it consensual sex, or rape and pillage happy hours? And who did it to whom?


I was wondering that too. For all we know that >6% could simply account for the offspring of rape victims that were "sapien" enough to pass in early human society, while the rest were conquored and slaughtered over thousands of years?

I could be completely wrong, but in retrospect it seems almost typical of human behaviours when considering our more recent and documented millenia.

Another interesting idea, how does thirty thousand years, till the last of the neanderthals, compare to the tradition oral story telling? I wonder if some of our most ancient and mythical stories bear any accuracy to a conflict or interaction with 'near human entities.'
dub1
1 / 5 (1) Aug 26, 2011
Garbage.
DocM
not rated yet Aug 26, 2011
Not necessarily rape or pillaging at all.

Several studies have shown that ovulating women who smell mens t-shirts find the ones most most different immunologically different have the most plesant smell (to them).

This tends to confirm that human sexual attraction has a large smell component - meaning we seek a partner with differences in the HLA complex via "smelling" their pheromones. A new guy in town like a migrating modern human may well have been very attractive to Neanderthal or Denisovan females.
sherriffwoody
not rated yet Aug 26, 2011
Is it still rape if they're a slave??
iiibogdan
4 / 5 (1) Aug 26, 2011
I have this gut feeling that the Neanderthals were smart dudes but were overwhelmed by the hordes of "modern" humans...
lauranathalasa
not rated yet Aug 27, 2011
Is it still rape if they're a slave??


I don't think it was so dramatical. They were all cavemen. They could share the same cave if it was cold, sometimes food... and sometimes they coluld find someone was interesting because of the wolf-teeth necklace or similar, or because she had blond hair or he caught the biggest boar.
There was problably no marriage, and a different society.
Why could't they simply find someone was interesting and have some fun?
Moebius
not rated yet Aug 27, 2011
For a few years now, scientists have known that humans and their evolutionary cousins had some casual flings, but now it appears that these liaisons led to a more meaningful relationship.


Not to mention boosting self-esteem and paper bag sales.
scienceminusegotrip
1 / 5 (2) Aug 27, 2011
Fact: Africans are the solitary progenitors of all "humans". Neanderthals and ... "us Modern Humans" aka Modern Africans have the same progenitor from Africa. Modern Africans left the continent met with some Archaic Africans and had sex with them, producing African/African hybrids. The end... Any Questions? You Euro/Asian ... Africans should forgo your authoritarian-supremacist societies bullshit and blood lust. Embrace the fact that your ancient African ancestor never gave up and for millions of hard years carried your Genes. Shit ... for one minute some recessive skin/hair gene found footholds in foreign lands for this alone your going crazy and dising your exploited brothers and sisters.
sherriffwoody
not rated yet Aug 28, 2011
Fact: Africans are the solitary progenitors of all "humans". Neanderthals and ... "us Modern Humans" aka Modern Africans have the same progenitor from Africa. Modern Africans left the continent met with some Archaic Africans and had sex with them, producing African/African hybrids. The end... Any Questions? You Euro/Asian ... Africans should forgo your authoritarian-supremacist societies bullshit and blood lust. Embrace the fact that your ancient African ancestor never gave up and for millions of hard years carried your Genes. Shit ... for one minute some recessive skin/hair gene found footholds in foreign lands for this alone your going crazy and dising your exploited brothers and sisters.

Touchy Touchy
ubavontuba
1 / 5 (1) Aug 28, 2011
Sex with Neanderthals and another close relative the recently discovered Denisovans has endowed some human gene pools with beneficial versions of immune system genes,


This article smacks of genetic elitism. It's essentially suggesting Africans are less immunologically evolved than other races, yet provides no clear evidence other than to state a genetic variation exists.

scienceminusegotrip
1 / 5 (1) Aug 28, 2011
ubavontuba "
This article smacks of genetic elitism. It's essentially suggesting Africans are less immunologically evolved than other races, yet provides no clear evidence other than to state a genetic variation exists."

Clearly you see through the pseudo science that this profit oriented magazine "physorg.com" publishes to please the will of the ignorant advertisers.
scienceminusegotrip
2.3 / 5 (3) Aug 28, 2011
This magazine pretends be scientific yet lets it's essayist babble with zero data. Science without substance is authoritarians propaganda, to weaken the critical thinker and eventually society at large.
Djincss
not rated yet Aug 29, 2011
Indeed it is stupid explanation, what scientists say, that eurasians must have better immune system, they just passed some resistance, something like what europeans passed in the americas, and the people there better survived the new diseases they brought nothing more.
The fact that what left in us is 4-6 % means neandertal indeed had nothing so good to give to us but resistance to its diseases after all we went to play on their ground, and we busted them a lot, and something more we even gave up their cold resistance to remain more humans, if we were to take their cold adaptation and everything we will have much more than only 4% in us, thats what I think.
LuckyBrandon
not rated yet Sep 24, 2011
This article smacks of genetic elitism. It's essentially suggesting Africans are less immunologically evolved than other races, yet provides no clear evidence other than to state a genetic variation exists.


I would have to disagree here...I see it as it means the only TRUE BLOODED humans still live in africa, and they are the source of our inevitably diverse species at this time (and also the original source of our intelligence).