search this blog

Sunday, May 1, 2016

ESHG 2016 abstracts

See the Programme Planner here. Below is an abstract on the population history of the Caucasus. The emphasis is mine. Who actually believes the 20,000 year estimate? It sounds far fetched to me; probably blown out by minor East and/or South Asian admixture not accounted for by the authors.

Abstract: Archaeological findings suggest that modern humans have inhabited the Caucasus since Paleolithic times but little is known about their origin and how they have interacted with neighboring populations. Previous genetic studies of present-day populations from the Steppe suggested the Caucasus acted as a barrier, leading to genetic discontinuity between the Caucasus and the East European Plain. Furthermore, geography, ethnicity, and language are also expected to influence the mating patterns of the populations inhabiting the Caucasus and thus create genetic structure within this region.

Here we use whole-genome genotyping and sequencing data to fully understand the genetic diversity of the Caucasus and its role in the demographic process that shaped modern Eurasian genomes.

Combining data from 12 high-coverage whole-genome sequences, four each from Georgia, Armenia, and Azerbaijan with SNP-genotype data from more than 250 individuals from the same populations, we present one of the most comprehensive datasets for this region. Principal component analyses, followed by model-based clustering, reveal previously unreported structure among the Caucasus populations. In particular, we discovered three different clusters among Georgians and two in Azerbaijan, in addition to different ancestral proportions in these clusters. MSMC analysis of the whole genomes shows Caucasus populations have diverged in the last 20,000 years from other Eurasians and have experienced different demographic changes in recent times.

We thus provide a detailed analysis of the past and present demography of the Caucasus which will be useful for understanding the genetic diversity of this region and the relationship with European populations.

Mezzavilla et al., Genetic structure and demographic history of the Caucasus: insights from whole-genome sequences, ESHG EMPAG 2016 Presentation Abstract, P18.020D

See also...

Ancient Polish admixture in Denmark


Shaikorth said...

MSMC analysis in Wong et al. got 20k years for French and Kalmyks so 20k for French and Georgians would make no sense. Maybe they used less haplotypes to get less accurate estimates, or they mean earliest divergence from some other Eurasians since they don't specifically mention West Eurasians.

George Okromchedlishvili said...

Lol about three previously unseen clusters among Georgians - that such a heterogeneity would be obvious to anyone who knows at least a little about the history of the region.

Olympus Mons said...

Not to poke the bear, but….
We need to stop looking at this things according to our own pet theories.
Having said that… I think this is going to play right with my pet theory.

What they are finding is the result of a simple story- Southern Caucasus was consistent of a single (sort of) and specific stock (structure) up until the 8th millennia BC (seen in J2 and J1) then a new stock raised (arrived) and settled in the area near the Caucasus mountains( R1b) and dominated what is today a part of Georgia, Armenia and Azerbaijan (so, the Shulaveri-shomu and related) from the end of the 7th millennia BC and the 6th millennia BC and by 5000BC/4900BC they were gone from the region, expelled by the Ubaid going to Uruk, going to Sumeria that brought the J2/J1 up until even north Caucasus.
That roaming R1b stock, where in Tel tsaf Israel by 4900 BC, in Merinda and El-omari (Egypt) by 4500 Bc ( stood a bit longe there as part of Maadi) then part of the desertification nightmare in the acacus mountains in sahara by 3800BC and by 3500BC full flooding of Iberia as going fast to become the Bell beaker and conquer Europe.
That is why in one of your posts of 2015 there is a table linked with Yammna, CW and BB (k 15 ancestry proportions + other data) and its obvious only in Bell beakers not only the Caucasus Mtdna (H13) the H1 picked up in north Africa and most telling of all is the Sub-Saharan genetics only the Bell beaker have. Do you think is a coincidence. That Genetics was given to the bell beaker by the L3f Mtdna they brought with them while in Merimde and El-omari being the reason why you only find L3 in there and also really L3f with R1b –V88 in sub-Sahara and in Iberia. Not in between! Portugal has a good percentage of Mtdna L (5%) and most is L3 not slave related.

I think that is what you will find in Caucasus. First structure (driven by J2) , second (Driven by R1b) and late driven by mix with lots of G2a.

Not wanting to be pushy, but for all to read my Shulaveri to Bell beaker thesis :

Gökhan said...


I dont think that r1b in southern caucaus is neolethic clade. They must arrived the trans-caucaus during early bronze age which aproximately 3500 BC. There is no reason to think that R1b is exiled clade from Caucaus unless you dont have any agenda to prove something. On the other hand R1b in Georgian is in low frequency. G2a must settled southern caucaus earlier then R1b. R1b is excatly late arrival.

Olympus Mons said...

I think everyone who comes/comments here has an agenda, preference, so forth. It doesn’t matter. Time will tell.

Mine is very simple. Neolithic (all (6th millennia BC) Southern Caucasus (Kura river) was R1b. they came and they were gone in little over a millennia. Pushed by Ubaid (actually I think Hussana-Samarra) out of the Caucasus because they really were different. And I say so, because to me (and I may be wrong, sure!) can’t help but see the staggering similarities between Shulaveri-Shomu and pre bell beaker Iberia (or bell beaker if you want). If for nothing else (and there is plenty of else’s) you can track the Shulaveri round architecture, cattle binge, up to Merimde, then chalcolithic Iberia (as bell beaker Castros) then even, as the round dwellings of Celts. To me one has to be intentionally blind not to see that.

Like I said in above comment. See the table davidski as post less than one year ago… and where does anybody thinks bell beaker from Germany middle 3rd millennia got that mix of Mtdna and ancestral substratum?

Olympus Mons said...

And Gokhan, to your point.
What trans Caucasian by 3500 BC coming south? What you saw by then was Ubaid/Uruk , sophisticated , snake people, pushing into as far north as the northern part of Caucasus. They (J2/J1) from bellow (present Iraq) even crossed the perpetual frozen mountains to the other side (north). They then those J2 had already overrun the Shulaveri for centuries like a tsunami.

If I was mad (which I am not… much) I would even dare to say something like: Natufian is going to turnout R1b as so I think (this I think so) the Shulaveri-Shomu were.
I have no, repete no, indication of these. Carefull. Is just that I am not even 100% sure that the Shulaveri_shomu were R1b coming from the Volga during the 9th millennia BC. They could even be R1b coming from the Volga by 15 millennia BC to the Jordan valley, via North Iran and later kicked out up north by the climatic 8.2 kiloyear event… Just to say how little we know.

This mad fixation of R1b from the steppes during bronze age is starting to smell. Just a little bit :-)

George Okromchedlishvili said...


This guy is clearly mentally ill. Don't bother arguing with him.
The Bronze Age Trialeti and Kura Araxes cultures were extremely different from previous neolithic package of Shulaveri-Shomu. The later has most likely been brought there by G2a folks.

Olympus Mons said...

@George Okromchedlishvili

Hey, You don’t know me, never debated me, never even exchange a single argument with you... and the first thing you say is that I am mentally ill?
Don’t do that. Is unwarranted. And actually there is no need.

Especially when the first thing you say is to concur with me (part of). Yes the Sioni, Kura-Araxes culture and of course Trialeti were a different package. No shit, Sherlock, that is what I started by saying! :-)

Arch Hades said...

Well, there is certainly a very large genetic barrier that seperates the Caucasus with Slavic Eastern Europe...but to say there's been no geneflow between the two regions the last 20,000 years just flat out wrong. As we've seen here on David's blog Georgians are significantly closer to modern Slavs than CHGs were to EHGs from the same regions, and that can only be because of geneflow. So yeah this is bad science to say the least. Just because there's a barrier doesnt mean there's no exchanged just means it was regulated.

Olympus Mons said...

@Arch Hades
Could it be a typo? because Marc Haber1 and Massimo Mezzavilla wrote a previous paper (oct 2015) on the matter and it looks that they say there that "no gene flow" in the latest 2,000 year, not 20,000 years we are talking here.

"Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations"

Matt said...

Mezzavilla was also involved in the - The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection paper which David was critical of which provided a very ancient divergence time for the Kalash. This used the MSMC method they mention here as well (although it's curious that in that Kalash paper, the MSMC method does not give such an ancient date for divergence or Armenian / Adygei to other West Eurasian populations).

Shaikorth said...

Matt, the Armenians and Adygei should be more similar to at least European populations than Kalash are, so the lower date is expected.

Actually the MSMC date for Kalash they got is only 8000 years which is probably still exaggarated (by ASI?) but in line with more general MSMC results.

They don't say whether they used multiple haplotypes and how many which is a problem. MSMC dates can apparently be affected (though not always) by lower haplotype numbers in the test. Andreapol Russians are West Russians and similar to Belarusians, but look at their divergence time from Kalmyks using 4 haplotypes and 8 haplotypes.

Matt said...

@ Shaikorth, yes, I'm talking about what seems to be an inconsistency between using the MSMC method for the Caucasian populations they had in that paper, vs what seems to be reported here.


Other ESHG of of potential interest to various posters - - P18.091C - Nationwide genomic study in Denmark reveals remarkable population homogeneity - "This homogeneity was reflected in PCA and AMOVA, but also in more sophisticated LD-based methods for estimating admixture. Notwithstanding Denmark’s homogeneity, we observed a clear signal of Polish admixture in the East of the country, coinciding with historical Polish settlements in the region before the Middle Ages. In addition, Denmark has a substantially smaller effective population size compared to Sweden and Norway, possibly reflecting further lack of strong population structure. " - P18.052D - Genetic determinants of pigmentation in admixed Latin Americans - "Our analyses revealed eleven independent genome-wide significant signals of association with SNPs at 8 different genomic regions including a novel candidate region associated with skin pigmentation. We found that the associated SNP had a higher derived allele frequency in East Asians compared to Europeans and that it showed strong signals of positive selection in East Asians, consistent with the independent evolution of light skin in Eastern Eurasians. " - P18.035C - The Irish DNA Atlas - a Study of Genetic Diversity in Ireland - " To date we have recruited 211 participants. An analysis of dense genotyping data from 142 participants shows that the Atlas participants present affinity with British individuals in ADMIXTURE analysis, but analysis at higher values of k resolves a component that appears enriched in Ireland, but also found in neighbouring counties. fineStructure analysis identifies geographically aligned genetic substructure within Ireland, and can clearly identify Irish with British ‘Planter’ ancestry." - Irish version of the POBI - P18.002B - Genetic signals of adaptation to climate in native populations of North Eurasia - "28 SNP in genes and genomic regions demonstrating positive signals of natural selection in recent genome-wide studies and involved in pathways and processes potentially implicated in adaptation to cold or resistance to low temperatures (thermoregulation, response to temperature stress, energy metabolism, regulation of muscle constriction etc.) were selected for the study" - P18.009A - Ancient DNA study of a mysterious lake of Himalaya - the "Roopkund deads" again, with better translation.

But now to actually read the more interesting news for today...

Shaikorth said...

That 20k divergence estimate is large enough to make me think they mean divergence from some East Eurasians when they talk about Eurasians, or they have run MSMC in some really weird way unlike that in Wong et al or the Kalash paper for all its flaws.

Grey said...


"Other ESHG of of potential interest to various posters"

cool stuff