Friday, March 18, 2016

Dirty Online Blog Tactic #392: Slag the paper of your competitor anonymously, using a not so transparent pseudonym

A commenter, Matt, who is very likely an author of a paper that opposes this newly published R.M. Key paper, comments on the Eurogenes blog thread New insights into human adaptation and population structure thanks to ancient genomes.  My comments are under my own name.  This is very out in the open rotten behavior, childish, and tolerated by the paleo genomics community.

It will be a good example to bring up at the ethics committee meeting of the upcoming AAPA conference, in Atlanta.

Eurogenes blog thread comments:
Blogger Matt said...
I kind of had the following thoughts on this:

IIUC, the things this paper does is estimate that:

- At the most differentiated (from African) alleles Eurasians are enriched in genic SNPs .

(Makes sense; it's relatively difficult for an allele to drift its way to very high degrees of differentiation)

- Of these, modern day Europeans are relatively more enriched at genic SNPs compared to non-genic SNPs, compared to East Asians, particularly due to weaker effects of drift in modern day Europeans

(Makes sense; but note doesn't necessarily mean Europeans have more absolute numbers of highly differentiated genic SNPs from Africans, and in fact they probably have fewer based on previous work.

See also the figure S24 which shows that on a PCA based on genic SNPs, EAs as far away from Africans than Europeans are, so about as differentiated.)

- (I think) They claim Europeans being particularly more enriched at genic SNPs compared to non-genic SNPs compared to East Asians is also likely to be due to more differing selection forces in Europe (I'm not so sure about this).

- "In the genic European tail, Stuttgart has 10.4% fewer of the alleles that are highly differentiated from Africans in present day Europeans, compared to Loschbour"

- "Hunter gatherers contributed disproportionally to the highly differentiated alleles within genes in Europe but, intriguingly, not outside of genes"

What they don't do, really (although the probably can't), is estimate whether:

- WHG has an enrichment of genic SNPs relative to non-genic SNPs, compared to EEF

That's pretty important. It's particularly important due to the fact that WHG seems to have had really low population sizes compared to EEF, and to have had a much higher effect of drift (see - http://www.nature.com/ncomms/2015/151116/ncomms9912/images_article/ncomms9912-f3.jpg for instance), then lower contribution to Europeans.
Possible WHG had more highly differentiated SNPs both among genic and non-genic SNPs, and the genic SNPs "introgressed" out of proportion to the WHG population contribution.

I think they probably couldn't test this though. They did try to simulate out whether differences in NE (effective population size) could have contributed to the differences in contribution to Europeans highly derived SNPs, but I'm not too convinced by this indirect evidence.
March 18, 2016 at 4:25 PM
Blogger
 
 Matt said...
One thing I do question about the finding is:

"No ancestral genome carries rs16891982’s derived allele, but Loschbour carries the haplotype that, in present-day populations, is linked to the derived allele"

So does this contradict previous findings by Mathieson and Gamba that WHG did not have the rs16891982 variant on SLC45A2 (e.g. http://www.nature.com/ncomms/2014/141021/ncomms6257/images/ncomms6257-f3.jpg) or is more like WHG likely did not have the variant, but some related HG did?

And one thing particularly they do seem to be quite wrong about was "No ancestral genome carries rs16891982’s derived allele" yet Mathieson already showed that a good 40% of the Anatolian_Neolithic already did http://biorxiv.org/content/biorxiv/early/2015/10/10/016477.full.pdf (and lower frequencies in the Iberia EN with higher WHG ancestry), by directly sampling the SNP. The AN also had some degree of the derived OCA2 variant.

If Reich lab have sampled AN, who may or may not have actually been admixed with WHG, and they actually have the SNPs, it seems a bit pointless to go "Oh, well EEF (based on Stuttgart) didn't have these haplotype", when the AN have the SNP.

At the same time, "But the European tail includes a large number of alleles in the lactase enhancer region and the LP haplotype (chr2:135859371-136740900) that are exclusively present in Stuttgart (65% of Stuttgart specific targets; Fig. 6c). Thus the haplotype that is today associated with LP in Europe originated most likely in this genetic background, which we detect only in the Stuttgart farmer, although this individual itself did not carry the LP allele. "

Yet it seems like the European LP variant is not necessarily likely to have come from an EEF like population (rather a Yamnaya / CHG like one).

This paper was kind of written on 16 June 2015, but then the first version of the Mathieson paper was published online 14 Mar 2015, and they actually reference it, already showing SLC45A2 in the EN, so kind of don't quite get that...

March 18, 2016 at 4:25 PM
 
Blogger
 
 Marnie said...
"Matt", I'll be sure to bring up, in the AAPA ethics discussion, that some authors actually slag their colleague's competitive papers using false identities online.

Are you really that much of a coward and a creep?

Why not at least blog under your real name?

March 18, 2016 at 5:02 PM


Blogger Romulus said...
"No ancestral genome carries rs16891982’s derived allele"

What about Stora Forvar? Reich lab created this myth of dark skinned hunter gatherers which has turned out to be totally false. Looks like 19th century anthropologists are proven to be SPOT ON once again thanks to ancient DNA.

The Stora Förvar 11 remains were found on Stora Karlsö, a small island off the west coast of the larger Swedish island of Gotland, in the Baltic Sea. The remains were dated to 7,500 to 7,250 years ago, and they were found in a late Mesolithic context.

Stora Förvar 11 belonged to mitochondrial haplogroup U5a1. He had two copies of the depigmentation allele in the gene SLC45A2, and since Motala 12 had at least one copy of the depigmentation allele in the gene SLC24A5, we now know that both of the two major Caucasoid depigmentation mutations were present in the hunter-gatherers of Mesolithic Europe.

March 18, 2016 at 6:49 PM
 

 
 
Blogger Marnie said...
@Romulus

"What about Stora Forvar? Reich lab created this myth of dark skinned hunter gatherers which has turned out to be totally false. Looks like 19th century anthropologists are proven to be SPOT ON once again thanks to ancient DNA. "

Without getting into the skin color of European Mesolithic gatherers, I will say that thinking that you can determine the skin color of people 10,000 years ago based on a few alleles that determine, to some degree, the skin color or hair color of people today, is a complete joke.

A very well known paleoanthropologist at UC Davis told me personally that this is methodologically very ill conceived, and not just for traits like skin color.

Certain traits come under selection. Traits determining appearance based on various papers, do seem to be under selection. But the alleles that lead to these traits can vary over time. So again, we don't know the skin color of Europeans 10,000 years ago. But chances are, they didn't look all that different from people today.

Methodologically, it would be far better to look at multiple alleles known to relate to appearance. Then maybe, you could start to get an understanding of how human appearance might have varied over time.

Anyway, I think far, far to much money has been thrown at this question.

But, hey, someone has to generate advertising revenue for Science/Nature/PNAS in order to pay those $300,000+ per year salaries of their executives.

So its all "Sex with Neanderthals" and hunter-gatherer skin color studies inferred from one or two alleles.

March 18, 2016 at 7:06 PM
Delete

 
Blogger Krefter said... 
@Matt,

The frequencies of SLC24A5 and SLC45A2 in pre-3000 BC times doesn't matter. They tell nothing about natural selection. They had been popular for 1,000s and 1,000s of years before the Neolithic(except in WHG). Their high frequency today have nothing to do with farming or Ice age climate or whatever.

The key is the Late Neolithic/Bronze age Europe. SLC45A2 more than tripled in frequency between 3000 and 2500 BC. That's pretty significant.

March 18, 2016 at 7:28 PM
 
Blogger Marnie said...
@Krefter

"The key is the Late Neolithic/Bronze age Europe. SLC45A2 more than tripled in frequency between 3000 and 2500 BC. That's pretty significant."

So? People went from being tanned to more fair skinned. Not exactly the earth shattering result that would warrant sucking up half the genomics budget of Europe for the last three years.

Only nuts spend this much time thinking about skin color.

March 18, 2016 at 8:14 PM

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