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Wednesday, August 25, 2010

A couple of new genetic papers I'd love to read


But by the moment just mentioning them briefly.


Both are published by the European Journal of Human Genetics (Nature) and both are mentioned by Diekenes today (link 1, link 2).


African genetic structure shows novel elements

There has been some negligence in mapping the genetic structure of African populations, with most papers taken a West African proxy (typically Nigerians), sometimes enriched with some of the last hunter-gatherers of the continent, to represent the whole complexity of the ancestral continent.

This paper seems to address this lack.

Martin Sikora et al., A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. EJHG 2010. Pay per view.

Abstract

Studies of large sets of single nucleotide polymorphism (SNP) data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2841 SNPs in 12 sub-Saharan African populations, including a previously unsampled region of southeastern Africa (Mozambique). We show that robust results in a world-wide perspective can be obtained when analyzing only 1000 SNPs. Our main results both confirm the results of previous studies, and show new and interesting features in sub-Saharan African genetic complexity. There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography. Hunter-gatherer populations (Khoisan and Pygmies) show a clear distinctiveness with very intrinsic Pygmy (and not only Khoisan) genetic features. Populations of the West Africa present an unexpected similarity among them, possibly the result of a population expansion. Finally, we find a strong differentiation of the southeastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region.

This Mozambican specificity was already spotted accidentally in Patin's paper on Pygmy Genetics last year but himself downplayed its importance because of his focus on Pygmy structure specifically.


West European R1b is distinct

Nothing really new for those who have kept a keen eye on the research of this Y-DNA haplogroup, the most characteristic of West Europe. But I'd still like to know more about the details. I doubt I could concur with the suggested timeline in any case.

Natalie M. Myres et al., A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. EJHG 2010. Pay per view.

Abstract

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

M412 seems to be a novel SNP not yet reported at ISOGG. S116 (defined as its major subclade) used to describe R1b1b2a2, most diverse around the Pyrenees (unless this paper says the opposite). So I doubt the LBK hypothesis can hold, regardless of frequency.

7 comments:

aargiedude said...

They used some obscure SNP labels for L21 and other SNPs. I translated those names to their better known counterparts and overall made their supplementary data easier to read in this xls file:

http://www.sendspace.com/file/hzyt2f

The file also adjusts their reported DYS461 results, because they reported the values with 1 repeat less than is standard in studies and commercial databases.

This has to be one of, if not THE, best y-dna study in years. We've been waiting a long time for geneticists to fast-forward half a decade and start testing for stuff like U152, U106, etc. Excellent. And they did it with flying colors. What an infernal study.

For me personally, it was interesting to see that Italy, with 282 samples, 105 of them R1b1b2, had only 1 L21, my own haplogroup. He was from North Italy, as in my case, too. And 57 of the 105 R1b1b2 were U152. Incredible. This study is going to give much to talk about. Beautiful.

If anyone spots any errors or corrections needed in the xls file, let me know.

Maju said...

Hi, Argie. Got your spreadsheet.

So, according to you the M412 marker is the same as L51 and hence describes nothing but R1b1b2a1? That's interesting.

The other strange marker is M529 that, according to you is the same as L21, meaning R1b1b2a1a2f.

I was making a map with the supp. data but now I will have to alter the legend.

Makes sense but I'm going to hate these researchers for doing that, really.

"This has to be one of, if not THE, best y-dna study in years".

Maybe. At least it has a good, extensive sample and have tested for some key markers. I still think a more detailed research of SW European clades downstream of R1b1b2a1a is much needed. Iberians show up with 80-95% apportions of R1b1b2a1a*, and that also happens at lower apportions in South France, through the Alpine area and some other spots like Central England. Some of this low level haplogroups are known but they have not tested for them. Others still await discovery.

"For me personally, it was interesting to see that Italy, with 282 samples, 105 of them R1b1b2, had only 1 L21, my own haplogroup".

It does not surprise me the least, after all L21 is in principle a NW European clade, right?

"And 57 of the 105 R1b1b2 were U152. Incredible".

It looks like a Mediterranean clade to me: not only common in Italy and Switzerland but also Slovenia, Croatia... and Crete! However it is also important in Central Europe and France up to South England, but not really in Iberia.

Maju said...

I just got a copy of the paper, btw. Right now reading it.

aargiedude said...
This comment has been removed by the author.
aargiedude said...

[Delete and post again due to mistake in my link]

So, according to you the M412 marker is the same as L51 and hence describes nothing but R1b1b2a1? That's interesting.

No, it's from the study itself. They list the rs identifier of the SNPs, and you can see in the ISOGG page that they're the same SNP.

ISOGG SNP/rs list

Makes sense but I'm going to hate these researchers for doing that, really.

Yeah, I don't get it. The ISOGG "official" names are L21, L51, etc. There shouldn't have been any reason for them to use these obscure out-of-the-blue labels.

Iberians show up with 80-95% apportions of R1b1b2a1a*

What? Really? You mean L11+ U106- P312-? That's 80% to 95% in Iberia? I'm stunned. By the way, though I've made the xls file and all that, I actually still have only barely glanced over it, and haven't even looked at the Cruciani study yet. I had no idea about this Iberia thing until you pointed it out. And wait a minute... This study didn't look at SRY2627 and M153, which are downstream of P312, and they're pretty signficant. They must be taking up almost all of the remaining 5% to 20%. So there's virtually no U106, U152, and L21 in Iberia? This would put a hell of a ceiling on potential Roman historic ancestry in Iberians, wouldn't it?

Maju said...

It's R1b1b21a1a2*, sorry. Going nuts with the nomenclature.

I posted a review here, btw. You seem to have missed it.

"... it's from the study itself. They list the rs identifier of the SNPs, and you can see in the ISOGG page that they're the same SNP".

Alright. Good job, thanks.

Maju said...

"So there's virtually no U106, U152, and L21 in Iberia?"

Just for repeated clarification: it's all U152*. My bad. See the other post for details.