More Neanderthal Data

One of the better sources for up-to-date information regarding Neanderthal admixture has been John Hawks' weblog. Hawks is a paleoanthropologist at the University of Wisconsin, and in addition to providing links to and commentary upon some of the latest research, Hawks and his students have been working at replicating and extending some of the more interesting findings regarding the Neanderthal genome and its presence in modern humans.

An excellent overview of the process is contained in this post from last week, and in it you will find a thorough but easily accessible explanation for how scientists arrive at the 1-4% admixture estimate of Neanderthal genetic material into non-African humans. In the original paper describing Neanderthal admixture (Green 2010), only five modern human genomes—two African and three non-African—were compared to the Neanderthal draft sequence. Hawks and his students have been making much the same comparison against a much larger database of modern genomes, with some clarifying results. Their work is of course still preliminary and not reviewed (and thus should be taken with a grain of salt), but if it proves to be accurate, it leads to some interesting conclusions:

• The admixture finding from (Green 2010) is being convincingly replicated and confirmed as the genomes from more and more present-day humans are being compared to the draft sequence of the Neanderthal genome. Either the draft sequence has some very bad data, or the assumptions behind the genome comparison techniques are totally without merit, or Neanderthal admixture into non-African humans is a confirmed reality—there doesn't seem to be any other way around it.
• The mean amount of Neanderthal admixture into non-African populations (over and above any admixture into African populations) looks to be around 3%.
• Although 3% is the mean, the variability remains significantly wide: any given non-African individual might easily fall within the range of 2-4% admixture, and there are indications some individuals will fall well outside that range. Even within families, there might be significant variability.
• All indications are that the Neanderthal admixture is shuffled throughout much of the modern human genome. That is, person A might have 3% admixture and person B might have 3% admixture, but the two may share relatively little admixture in common. It's not specific parts of the modern genome that are Neanderthal derived; instead, it appears that much of the modern non-African genome has been impacted in a shuffled-up sort of way.
• The mean Neanderthal admixture difference between Europeans and Asians is extremely small. This result goes against the idea that an out-of-Africa migrating population interbred primarily with Western European Neanderthals around 35 to 40 thousand years ago. Instead, this result points more plausibly to the idea that admixture happened earlier in time and/or at another locale (such as the Middle East).
• All these findings are based solely upon SNP analysis. The other sources of genetic differentiation—such as duplication, deletion, insertion, inversion—still await less costly and more accurate analysis. But in these areas too, Neanderthal admixture might be expected to have significant impact.

None of these findings provide any direct evidence for my idea that autism is a species-differentiation event (in particular, a species dis-recognition event), but neither do any of these findings contradict the idea. As I've said elsewhere, what we can look for now are studies comparing the Neanderthal draft sequence to modern humans diagnosed with such things as autism, schizophrenia and bipolar. If my idea is going to have any legs, then what we might expect to find are Neanderthal-distinguishing genetic signatures among these diagnosed populations, either admixture amounts outside the norm (most likely higher than the typical range) or a specific pattern of relationship against the Neanderthal genome unique to the diagnosed population. Given the rapid rate of technology advancement in this area, we might not have to wait all that much longer.

One other thing: as I read through these Neanderthal admixture findings, I can't help but be reminded of the genetic research conducted so far in the areas of autism, schizophrenia and bipolar. In each instance, researchers have been uncovering extremely lengthy lists of candidate genetic markers for the condition, markers that show up in only a tiny percentage of the affected population and markers that are scattered almost at random throughout the genome. This of course also does not provide any direct evidence that Neanderthal admixture is playing a role in such conditions, but the genetic similarities are difficult not to notice. And contrast this with the dubious conclusion being drawn by the autism research community, a community that insists on casting all these genetic variations as genetic defects, each leading (by miraculous coincidence, it would seem) to the same neurological and phenotypic outcome. There is a difference between the words “speculative” and “implausible,” and I see that difference on display here.

(Green 2010): Green, Richard E. and others. 2010. “A Draft Sequence of the Neandertal Genome.” Science 328:710–22