Neandertal genome yields evidence of interbreeding with humans

Prof.Badass

Personally I was very sceptical of the idea we interbred with neanderthals, but it turns out we did :eek:.

Some people don’t just have a caveman mentality; they may actually carry a little relic of the Stone Age in their DNA.
A new study of the Neandertal genome shows that humans and Neandertals interbred. The discovery comes as a big surprise to researchers who have been searching for genetic evidence of human-Neandertal interbreeding for years and finding none.
About 1 percent to 4 percent of DNA in modern people from Europe and Asia was inherited from Neandertals, researchers report in the May 7 Science. “It’s a small, but very real proportion of our ancestry,” says study coauthor David Reich of the Broad Institute of MIT and Harvard in Cambridge, Mass. Comparisons of the human and Neandertal genomes are also revealing how humans evolved to become the sole living hominid species on the planet.
Neandertals lived in Europe, the Middle East and western Asia until they disappeared about 30,000 years ago. The new data indicate that humans may not have replaced Neandertals, but assimilated them into the human gene pool.
“Neandertals are not totally extinct; they live on in some of us,” says Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and leader of the Neandertal genome project.
He and other geneticists involved in the effort to compile the complete genetic instruction book of Neandertals didn’t expect to find that Neandertals had left a genetic legacy. Earlier analyses that looked at only a small part of the genome had contradicted the notion that humans and Neandertals intermixed (SN Online: 8/7/08).

taken from;

http://www.sciencenews.org/view/generic/id/58936/title/Neandertal_genome_yields_evidence_of_interbreeding_with_humans

What does boards think?

Sid_Justice

I only skimmed the Nature article this was published in and only have a vague knowledge of Human genetics and evolution. I wouldn't be skeptical at all, I don't see any reason why we wouldn't have interbred with our closest relatives. Sure isn't it a widely recognised theory that Neanderthals are subspecies of Humans rather than distinct?

I mean for me, I imagine humans (and close relatives) from 100000+ years ago to be primitive and barbaric. I wouldn't be suprised by the concepts of massive violence, rape and cannibalism. Thus, if humans became competitive with rival species I wouldn't be surprised if they interbred with the females and killed the males.

I think the other big 'discovery' from paper was the fact that Neanderthals were least closely related to humans of the most African stock, thus putting doubt into the theory that all humans originated in Africa (rather than a simultaneous development of Homo sapiens around the world).

However, it's worth noting that the paper is based on only one sequencing of the genome, if memory serves, the mtDNA Genome (from 2004 I think) was sequenced 5/6 times before the errors were ironed out.

darjeeling

The original paper is here if you want a look.

Modern humans and Neanderthals turn out to be very similar - as we expected. By ignoring all the bits of our genomes that are the same, and looking only at the differences, we can find out how much of our genome came from Neanderthals. For non-Africans, that turns out to be around 1% to 4%; for Africans, it's zero. That means that the ancestors of non-African people included Neanderthals. One to four percent of your genome is around how much you inherit from one of your 32 Great-great-great-grandparents or one of your 64 gt-gt-gt-gt-grandparents, so not a lot. Still, it's more than many scientists expected, based on early, much less complete data.

The ancestors of Neanderthals left Africa much earlier than did the later wave of modern humans - maybe half a million years ago (give or take 100k), compared to around 100K years ago for modern humans. The authors of the paper think that modern humans coming from Africa interbred fairly early on with Neanderthals, maybe in the Middle East, before going on to spread around the world. That would explain why the people they looked at from Papua New Guinea, China and France were all equally related to Neanderthals.

As for mass interbreeding with Neanderthal women - we can say that that didn't happen. We can trace a DNA molecule called mitochondrial DNA (mtDNA) that's outside the normal genome, and that is passed from mother to child. Thousands of people have had their mtDNA tested for genealogy projects, and no-one has ever shown up with the Neanderthal version.

There's a thread on this in Palaeontology (link).

adamski8

My OH is friends and grew up with one of the guys that wrote that paper, pretty cool stuff alright. They set up a graduate programme with 10PhD's to get this work done

norrie rugger

Sid_Justice wrote: »

I mean for me, I imagine humans (and close relatives) from 100000+ years ago to be primitive and barbaric. I wouldn't be suprised by the concepts of massive violence, rape and cannibalism. Thus, if humans became competitive with rival species I wouldn't be surprised if they interbred with the females and killed the males.

Not much has changed so?

Prof.Badass

darjeeling wrote: »

As for mass interbreeding with Neanderthal women - we can say that that didn't happen. We can trace a DNA molecule called mitochondrial DNA (mtDNA) that's outside the normal genome, and that is passed from mother to child. Thousands of people have had their mtDNA tested for genealogy projects, and no-one has ever shown up with the Neanderthal version.

Let's assume 50% of our neanderthal ancestors were male and 50% were female. Then surely we could expect 0.5-2% of non-africans to possess neanderthal mtDNA, so why haven't we detected this yet?

The fact that we haven't would suggest to me one of two things,

Either (a) We're doing something wrong

or

(b) Most/almost all of our neanderthal DNA comes from matings between neanderthal males and human females.

This huge deviation from the expected gender ratio would suggest to me that male neanderthals raping human females is the most likely cause of most of our neanderthal DNA.
Although that's not to say human males didn't rape neanderthal females.

The crucial difference is that hybrids born to human mothers would have been raised among humans and thus had a vastly greater chance of entering our genetic stock than those raised by neanderthal mothers (among neanderthals), who probably would have gone on to mate with other neanderthals, thus excluding themselves from our genetic heritage (unless one of their descendants raped a human female, but of course you still wouldn't see any neanderthal mtDNA in humans).

darjeeling

vinylmesh wrote: »

Let's assume 50% of our neanderthal ancestors were male and 50% were female. Then surely we could expect 0.5-2% of non-africans to possess neanderthal mtDNA, so why haven't we detected this yet?

The fact that we haven't would suggest to me one of two things,

Either (a) We're doing something wrong

or

(b) Most/almost all of our neanderthal DNA comes from matings between neanderthal males and human females.

This huge deviation from the expected gender ratio would suggest to me that male neanderthals raping human females is the most likely cause of most of our neanderthal DNA.
Although that's not to say human males didn't rape neanderthal females.

The crucial difference is that hybrids born to human mothers would have been raised among humans and thus had a vastly greater chance of entering our genetic stock than those raised by neanderthal mothers (among neanderthals), who probably would have gone on to mate with other neanderthals, thus excluding themselves from our genetic heritage (unless one of their descendants raped a human female, but of course you still wouldn't see any neanderthal mtDNA in humans).

Don't forget that we've not found anyone with a Neanderthal Y chromosome either. In your scenario, we'd expect humans to have none to very little Neanderthal mtDNA, yet a fairly high proportion of Neanderthal Y chromosomes, coming from those rogue Neanderthal males.

I expect the reason has more to do with a quirk of population genetics. There's a phenomenon called genetic drift, whereby versions of a gene can get lost from a population over generations by chance, depending on who does and doesn't breed, and - if they do - which copy of a gene they pass on.

We expect to get more random loss of alleles over generations for mtDNA because (i) it's only inherited from the female side and (ii) each female has only one version (no-one's to come back & start on about heteroplasmy!). In population genetic terms we say that the mtDNA genome has 1/4 the 'effective population size' of the nuclear genome. This also applies to the Y chromosome (one version in males and inherited only from males).

If we have a small genetic input from Neanderthals tens of thousands of years ago, it's therefore more likely that this will be detectable today in the autosomal nuclear genome than in mtDNA or the Y chromosome, where Neanderthal versions are more likely to drop out through drift.

I've not mentioned selection yet. It's not impossible that parts of the Neanderthal genome were selectively advantageous (though we've no evidence for this yet). That *could* give you an elevated level of Neanderthal DNA in the nuclear genome too.