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I am writing a paper regarding the hybridization of Neanderthals into AMH population and there are a few things I just cannot understand, I know you must be incredibly busy, and there is little chance you are going to answer this email, or even receive it at all, but I shall take my chances. I love Anthropology although my major is Philosophy, I am nowhere near a scientist and genetics is rather obscure within the realms of my mind, so my question might sound basic. In your research to find the lets call it statistical number or amount of sexual encounters between these two species, it is mentioned that if these encounters were in fact "occasional" or "sporadic" all non-African humans would show the same small percentage of DNA in their genome... how can--genetically speaking--you tell from the percentage of Neanderthal DNA in each person if the encounters between these species were a few or significantly larger? in other words, why if the encounters were few all humans now would show the same small amount of neanderthal DNA? and viceversa if the encounters were frequent and Neanderthals were absorbed into our population why would some regions of the world show more of their DNA present?

Small groups inevitably carry genes that are not a perfect representation of the larger population from which they came. This is called the "founder effect" in biology -- when you have a very small group, they really substantially overrepresent some rare genes, and lose many common genes entirely, giving rise to a rapid genetic differentiation.

If there had been a very small number of Neandertal-modern contacts (like a dozen or so) then everybody who carries Neandertal genes today should have the same small set of them, all inherited from the founder effect of those few Neandertal ancestors. So your Neandertal genes and my Neandertal genes should all be pretty much the same. And most of the genome should have no Neandertal genes today at all.

Now, we don't have a definitive answer yet about this, but so far the data don't look like that pattern. Your Neandertal genes and mine are mostly different, and we have a large fraction of the Neandertal genome represented today in one person or another. There haven't been a tremendous number of Neandertal genes lost entirely from humans. That suggests that the number of contacts was not very small -- more like the low thousands or high hundreds than dozens. Remember that the entire human population from that time era acted like a breeding population of fewer than 100,000 people, so 3000 Neandertal ancestors are quite a large fraction of that.

Re: "Recantation of a former genetic know-nothing":

I'm an admirer of your blog. I work in academia, but I've also had some experience writing for print media (though nothing so influential as The Guardian.)
As such, the only thing I found jaw-dropping about Mark Lynas writing anti-GMO articles without the scientific background is the idea that you found it jaw-dropping. From my experience, nothing could be more common.

From what I know of journalism it is tough enough without having to write peer-reviewed articles in science journals. Skills that papers value and pay for include the ability to write and the ability to appear competent about the subject. And meet deadlines. They're also in the business of selling news, so literally for the sake of argument editors are happy to include both sides of the story - even when there really is only one side. That's why anti-GMO people and climate change deniers are given space to air their views.

As I understand it Mark Lynas is one of a handful of journos from the environmental left in Britain who are now letting their opinions be filtered through the science. He and George Monbiot, for example, are now cautiously pro-nuclear.

The Mark Lynas thing got picked up by Slate today. As the piece notes, "To admit you were wrong for decades is terrifying. It is also the mark of intellectual rigor." He should be lauded for his change of opinion.

Thanks so much for this. I appreciate the kind words!

I agree, "jaw-dropping" is a bit of hyperbole. In my experience this particular problem is common and I find it shameful. Journalists have poor science training as a general rule. This seems forgivable if you consider that their media employers care about the news, not about getting science right. They consult experts for that.

And yet…

An op-ed piece about genetically modified crops is fairly obviously NOT news. Even as a perspective on something currently in the news, such as a court decision, it is not a news angle, it is advocacy. When it is purchased from a writer at anything less than the market rate, it is paid advocacy.

I do think Lynas' change of opinion is a good thing, whatever his motivation. I want to focus on the editors, who are typically beyond shaming.

I read with interest your post on:
http://johnhawks.net/weblog/reviews/neandertals/pigmentation/neandertal-...

in particular:
"People of Han Chinese ethnicity sampled in Beijing appear to have on
average a half percent more Neandertal ancestry than people of the
same ethnicity sampled in southern China."

Apologies if you know this already but Han Chinese civilization
started in the Yellow River area and only later expanded south. The
original people in the south of China are Viet people and have more in
common with modern Vietnamese. They all became "Han" people after
their kingdoms were conquered by the north and are really Han in name
only. Northern and Southern Chinese people look different and their
spoken dialects (languages) are mutually incomprehensible to each
other.

Chinese people from the province of Shantung have the reputation of
being the biggest in size, always attributed to their diet of wheat,
but they are probably the last purest reservoir of Neandertal genes in
the East. Shantung people generally have big noses, fair skin and big
bones.

Yes indeed, these are very deep differences, at least as great as between northern and southern Europe genetically, and maybe more. That's why we find the contrast so useful in comparison with the archaic human genomes. The current samples are not ideal because the "South Chinese" were sampled in Beijing based on ancestry, and so are a diverse set. We are hoping soon to have data from many more Southeast and Northeast Asian populations, which will give us some resolution on when things changed.

Good morning

The BBC TV Prehistoric Autopsy programme was fascinating.

I couldn't help noticing that Neanderthal's range was roughly the same as that of early white-skinned Homo sapiens. No mention was made of the possibility that we inherited white-skin genes from breeding with Neanderthals, they after all had had a longer time to evolve this trait than us.

Is there any evidence for or against such a hypothesis?

We have good representation in the Neandertal genomes of the DNA sites that affect light skin in Europeans. So far it appears that the Neandertals did not carry any of the alleles that are associated with lighter skin in Europe today.

They did have some changes to the genes that affect pigmentation that are not present in any living people. We speculate that these changes may have lightened skin or hair in the Neandertals, but we will not know this until we have experimental evidence about them. If this is correct, then the Neandertals will represent another case of convergence toward light pigmentation in the high latitude geographic range.

I happened upon your weblog a couple of months ago and find it fascinating, thanks for your effort. If the timeline/data of http://www.sciencedaily.com/releases/2012/10/121016084936.htm is accurate do you think it could be a contributing factor in the demise of the Neandertals?

Thanks so much for your kind words!

I wrote about the Campanian Ignimbrite a couple of years ago, when a group of Russian researchers suggested the resulting climate change as a factor in Neandertal disappearance:

http://johnhawks.net/weblog/reviews/climate/paleo/neandertal-volcanoes-2...

I'm skeptical of any particular event, considering how the Neandertals survived many climate fluctuations long before this time, with more rudimentary technology. I would say that several archaeologists I respect think that the climate change was a factor acting together with increased stress from competition with modern human populations. Personally, I want to know how much mixture was going on within Europe before I am willing to believe a lot of competition was happening on the ground. Anyway, this field is definitely developing fast. I'll have something new up about coexistence and possible competition in Italy sometime soon.

Re: Denisova at high coverage"

Dear John

I can hardly keep up with all the archaic human stuff coming out - partly as my main occupation is health genetics - but I wanted to run something past you. Given that there is reasonable agreement that Papuans and to a lesser degree Han Chinese (and peoples in between) have Denisovan ancestry, is there still any evidence that they have Neandertal ancestry? Or is the signal of presumed Neandertal ancestry just a signal of archaic ancestry which is in fact from Denisovans?

Of course, if there is no strong evidence of Neandertal ancestry in Papuans and Chinese then it removes the need for the interbreeding to have occurred immediately out of Africa. It already seems that modern humans interbred with Neandertals and Denisovans (and perhaps with some other archaic hominin in Africa), but it seems to me that the place and time of Neandertal interbreeding could be significantly different from where first proposed?

Then the timing of the Denisovan admixture would be of interest - I haven't read today's paper yet. Did you or anyone look in Japan and Tibet (and indeed the Andamanese) where we see relict Y chromosome lineages (and to a lesser extent relict mtDNA lineages eg M12). Perhaps they could have higher proportions of Denisovan as they have been less affected by the expansions accounting for the majority of Han ancestry? Perhaps not, but there is GWAS data available for all, so methods using this could be applied.

Finally - getting out on a limb - I wonder if the Flores hominins were Denisovans? Can only be speculation, but has anyone commented on this.

Thanks for your thoughts, I hope you'll spare a second to reply.

Many thanks for your kind words. It is indeed hard to keep up, even for us!

We are very confident that these populations do have Neandertal ancestry and that it does not all come via Denisovans. The Neandertal and Denisovan genomes each have a large number of unique alleles that allow us to differentiate these signatures. In Australians and PNG, the fraction of around 6% Denisovan is in addition to around 3% Neandertal.

I agree, Tibet is a promising area. The paper by David Reich et al. last year did include a broad range of Chinese regional and ethnic minority populations, including Tibet, and did not find any evidence of Denisovan admixture there. This is very strange to me, and it remains to be satisfactorily explained.

I doubt that Flores was Denisovan although it is possible. The initial habitation of Flores more than 1 million years ago was too early to have been accomplished by the same people that gave rise to Denisovans. The Denisovans diverged from Africans and Neandertals less than 600,000 and maybe as recently as 300,000 years ago. However, the initial habitation of Flores is known only from archaeology, and the hobbit itself is much more recent, only 18,000 years old. So possibly these are not a single population, in which case it is conceivable that the hobbit is Denisovan-derived.