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Wednesday, February 4, 2009

Breaking news: Neanderthal genome fully sequenced

at A Very Remote Period Indeed (and thanks to Tim for mentioning it at supper) : the full Neanderthal genome from Vindija Cave (Croatia) has been sequenced and will be published later this year. The same team of the Max Plank Institut is already working on other five different Neanderthal genomes.

Once this is published and analyzed the claims of Neanderthal introgression in modern humans will be finally proven or disproven.

More at Nature News.


Manjunat said...

How about Horizontal Gene Transfer from Neanderthals to Sapiens? Even that would be proven or disproven from this research? Or is it possible detect genes because of HGT?

Maju said...

I am not sure what you may mean by "horizontal gene transfer" but once we get the fully sequenced Neanderthal genome published (and soon to come more individuals' full genome, just in case) we can compare it nucleotide by nucleotide with the also fully sequenced H. sapiens one.

That should clarify everything. Whatever Neanderthal input should be limited to some and not all modern humans (most likely West Eurasians), so it should be easy to detect. If there is nothing shared by West Eurasians and Neanderthals, beyond the common H. erectus fundamentals (i.e. shared by all modern humans), then we can safely discard any Neanderthal introgression. If there is something that only Neanders and some modern humans share, then we can safely describe it as of Neanderthal origin and it will be very interesting to know about its extension and (maybe in a second moment) its possible effects in phenotype.

Even if there are zero matches, the knowledge of the Neanderthal genome will also allow us to know more about the process of divergence between the two species.

Manjunat said...

Horizontal Gene Transfer

Maju said...

Doesn't seem it'd make any difference. We could get confused about how the gene was transfered but, if it's there, we should see it anyhow.

Manjunat said...

Will that explain why no Neanderthal Y-chromosome or mtDNA are found in Sapiens?

Maju said...

Well if the ammount of Neanderthal admixture is small, it should be easy that Neanderthal haploid lineages would have been drifted out after that, while some autosomal genes may have persisted.

But I sincerely do not expect many Neanderthal genes to have survived in us. Maybe no one at all. We'll find out soon.

Tod said...

A Week With Gregory Cochran: Day Four

2Blowhards: Your contention is that 1) modern humans and Neanderthals may well have interbred. 2) Any beneficial alleles we picked up from these interbreedings would have spread throughout the population even if the instances of interbreeding were few. 3) These developments may help explain the cultural explosion of 40,000ish years ago. Is that a fair summary?

Gregory Cochran: Yes.

2B: How should readers take this contention? As a hypothesis? A provocation?

GC: A hypothesis that we think probable. But there are unlikely circumstances that might have blocked such gene flow, so we could be wrong.

2B: What kinds of evidence is there so far for interbreeding with Neanderthals?

GC: There are a lot of paleontologists who think that the skeletal record suggests some interbreeding. In addition, there are a few genes with strange patterns that might have parachuted in from another hominid species such as Neanderthals.

2B: How and why did you come to this hunch?

GC: Before I learned some of the relevant theory in population genetics, playing with simulations left me aware of the fact that even a few copies of a better version of a gene had a good chance of becoming common. Turns out that there was an exact result that shows just how likely this is: for a single copy, the chance of ultimate success is twice the gene's advantage. For example, one copy of a gene with a 1% advantage has a 2% chance of becoming universal in the population

Maju said...

Genes are seldom so extremely advantageous or disadvantageous. So a Neanderthal introgression would not have time nor strength to spread through all humans, much less if we include the most isolated groups, like Bushmen or the aborigins of Sahul.

If there was some genetic input from Neanderthals, we should see a cline.

Anyhow, so far all the evidence is negative. The rest is mere speculation.

The only maybe prossitive evidence would be the Lagar Velho kid, who obviously did not have any descendants himself (died too young) and who may well belong to the last Neanderthal populations, among whom is possible that AMH genes progressed (rather than the opposite) before they went extinct.

NW Iberia, where the Lagar Velho kid lived and died c. 24,000 BP was maybe the last stand of Nenderthals (the region was not really colonized by AMHs until the late Neolithic) but we have no direct evidence of that maybe because the acidity of Atlantic Iberian soils is not good for bone preservation (there are few remains from later times too for that reason).

But that's all: a very late admixed Neanderthal kid in the last stand of that species. Not too promising.

Tod said...

Adaptive introgression of coat color in wolves

Black coats are better for woodland wolves. Introgression from dogs might have become adaptive when wolves were forced into forests to avoid humans trying to wipe them out. Camouflage inside forests which may have been a darker environment than their own genes were adapted to was available and must have been very advantageous. (I have read that male dogs are usually too scared of being eaten to try and mate with female wolves).

Maju said...

Well, it's not clear if it's the color or some kind of immune advantage associated with it.

I have read that male dogs are usually too scared of being eaten to try and mate with female wolves

Depends what kind of dog, I guess. Probably not Pyrenean Mastiffs (large anti-bear dogs) and other large dogs of the kind.

Whatever the case, the introgression must have gone from dogs to wolves, what means mating with female wolves (as cubs born of female dogs would be raised as dogs or terminated).