However, Alan Templeton, a population geneticist at Washington University in St Louis, questioned the authors’ assumption that changes in the human genome are randomly distributed, rather than clustered around certain hotspots within the genome.
I’m curious how changing this assumption would affect their results, if anyone knows.
“We can tell those regions of the genome are highly enriched for genes that have to do with neural development and brain function,” said University of California, Santa Cruz computational biologist Richard Green, a co-author of the paper.
Earlier tonight I had found a thread on Noah as I was searching for TMR10A duscussions. A poster mentioned autism increasing, which I had argued may be evidence of humans degrading (when discussing Genetic Entropy). So something just clicked in my brain - how do we know the parts of our genome that modern humans share that affect our brains aren’t actually deleterious instead of beneficial?
Perhaps a very unintelligent question…but I’m confused. This does seem to be referring to the whole genome, but if we share 95%, 99% with chimps (I can’t remember the percentage anymore) then why is 7% really low? How can we be less alike to other humans than to chimps? What am I missing, or am I really dense? 
7% of the 1% doesn’t seem to quite makes sense in context of what they’re saying either…so I’m really not trying to poke holes, I actually don’t get it. Please help me out.
Yes, the 1.5% (or 1.23%) figure seems in blatant conflict with 7%. That is because they aren’t measuring the same thing. I just read the paper (quickly) and the 7% seems to be an inference of what fraction of our genome is not shared with other archaic humans such as Neanderthals and Denisovans. Not how many mutations have since occurred in those regions. So the two numbers cannot be compared, The methods used to make these inferences, to reconstruct an Ancestral Recombination Graph, are novel but may be controversial. (I am a bit informed about this because Mary Kuhner and Jon Yamato in my lab did pioneering work on inferring ARGs by other, more statistically-correct methods). Alan Templeton has raised the issue of taking recombination hotspots into account, and that is worthy of serious consideration. I’m sure we are going to hear a lot more from others evaluating the methods of this paper.
But that doesn’t make much sense either.
Perhaps they mean fraction of recombination blocks shared with them? Certainly, if measured at the basepair level, the amount share will be upwards of 99%. If that’s the case, it seems they chose a idiosyncratic measure of similarity that artificially inflates the perceived amount of difference.
Here is the section:
Our ARG strategy allows us to bin the human genome into regions containing archaic admixture in at least some humans, regions of ILS, and regions free of both archaic admixture and ILS in all humans (hereafter archaic “deserts”). We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where one or more humans has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome (Fig. 4A). Despite comprising very little of the genome, however, human-specific regions are significantly enriched for genes, exons, and regulatory element binding sites, while deserts are enriched for both genes and regulatory element binding sites (table S4). In line with previous studies ( 21 , 31 ), we find admixed regions to be depleted of genes. Regions of ILS are enriched for overlap with genes but significantly depleted of exons (table S4).
I don’t know @Joe_Felsenstein it reads to me as the mutations that have happened since a split, but what do I know? 
Certainly not much.
Whatever they mean by “archaic deserts” is the 7% and then narrowed down to “high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”)” is the 1.5%
…so maybe it is 1.5% are mutations that have fixed in the human population after the split?
I’m probably still very confused.
@Patrick not so sure this paints a story that is more negative for creationism than any other mainstream science. They still make a 13 million years ago for the TMRCA with chimp assumption in their timeline.
Yup it is exactly what I thought. They mean long recombination blocks, but each of these blocks are nearly identical to start with. So this is a very very strange way to measure similarity.
I don’t understand what you’re talking about 
, but this seems to be the difference.
“We have, you know, around 20,000 genes, and somewhere around 40 of them have these actual coding differences that all humans have one version, and the Neanderthals have the other version,” he says.
With only 3 ancient genomes, who knows how reliable their results are… And maybe they should be using .2% instead?
The two numbers (1.7% and 7%) are not computing comparable quantities. We can take a local region in our genome and estimate from small differences among sequences, within that region, what the genealogy of that local part of the genome is. Many regions will show occasional Neanderthal and/or Denisovan contribution. The overall contribution of Neanderthals to (say) present-day Europeans is about 1.5%, but which 1.5% differs in different parts of our genome. The paper under discussion tries to find local blocks of our genome that do not have any Neanderthal or Denisovan contribution, and which all seem to come from one genome after the split from chimpanzees. They found that only 7% of our genome satisfies those requirements. In that 7% of the genome, there are variations of nucleotides, but the 7% tells us little or nothing about how different the sequences are there, Nor does it tell is what the difference is with chimps. So the 7% is not a “how much does the DNA differ from chimps” figure.
My son is 5 years old and very tall. A full 120 tall, in fact. But I am just 6 tall.
So that 7% is the the approximate size of so-called Neanderthal Deserts? That sounds about right.
How much of this is due to drift and how much of this might be under purifying selection?
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