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Friday, May 22, 2015

ESHG 2015 abstracts


Apart maybe from the first abstract below, I haven't been able to find anything jaw dropping yet. If anyone wants to help out, the abstract search engine is here.

Spatial variation of the Y-chromosome: The global patterns and correlations with other genetic systems, linguistic and geography

Balanovsky et al.

We developed the “Y-base” database, which includes frequencies of 500 Y-chromosomal haplogroups in 4200 populations worldwide, with total sample size 142,000. 130,000 Y-chromosomes came from 300 published papers and remaining 12,000 are our unpublished data.

Using this dataset we created the world spatial distribution maps of 230 haplogroups. This World Atlas of Y-chromosomal variation was created by GeneGeo software, which we developed for digital map analysis in gene geography. The zones of sharp changes in frequencies were interpreted as genetic boundaries; the main boundary crosses Eurasia and includes not only mountain (Himalayas and Caucasus) but also steppe segments.

The question arises to which degree patterns of Y-chromosomal variation agree with data on other genetic systems. To answer, we characterized all extant ethnic groups speaking Balto-Slavic languages by mitochondrial DNA (N=6,876), Y-chromosome (N=6,079) and genome-wide SNPs (N=296). We found that genetic distances, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography but slightly lower correlation (0.7) with the mitochondrial DNA and linguistic affiliation.

The high-throughput sequencing of the Y-chromosome reveals thousands phylogenetically informative SNPs. Population screening for these markers subdivides old haplogroups with subcontinental zones of spread into multiple young haplogroups with restricted areas - thus providing excellent tools for reconstructing population history. This approach allowed us successfully subdivide C2-M217, N1c-M178, and G1-M285 into 35 new subhaplogroups, to create their frequency distribution maps and estimate the SNP and STR mutation rate on the Y-chromosome.


Detection of mitochondrial haplogroups variability of small population living in 9th century based on analysis of ancient DNA

Šebest et al.

Introduction: Ancient DNA (aDNA) represents all types of DNA that can be recovered from archaeological and palaeontological material or museum specimens. Information from aDNA is very useful in phylogenetics, paleoanthropology or genealogy. The isolation and analysis of aDNA is accompanied by two major problems: low quality and quantity of aDNA and the risk of contamination with modern DNA. Therefore, several strict laboratory and methodological criteria must be followed. The aim of this study is to isolate and analyze aDNA from human remains of the small Avar-Slavic population living in 9th century and to determine mitochondrial haplogroups in order to estimate the ratio of haplogroups typical for these two ethnicities.

Material and methods: The 50 samples of human teeth and bones were used for the isolation of aDNA in this experiment. The samples were excavated from Avar-Slavic burial site located near Cífer-Pác (Slovakia). Isolation of aDNA were performed in recommended conditions. Mitochondrial haplogroups were determined by sequencing of the HVRI of mtDNA followed by analysis of polymorphisms in this region.

Results: Despite the fact that the graves of mentioned burial place contained Avar artefacts and some remains showed mongoloid cranial features, majority of detected mitochondrial haplogroups belong to the common lineages of the Slavic populations and only presence of haplogroup U7 (typical for region of Near East) indicate the Avar origin. Conclusion: Our results suggest that the assimilation between Avars and other neighbour ethnicities was too extensive in 9th century and, therefore the presence of haplogroups characteristic for Avars is very rare.


Analysis of the Y-chromosome in the Volga-Ural region populations from Russia

Trofimova et al.

We analyzed a sample of the Volga-Ural region, including 462 individuals from 8 populations: Udmurts, Komi, Mordvinians, Mari, Besermyans, Chuvashes, Tatars, Bashkirs. We have shown that the major proportion of Y-chromosome haplogroups in the studied populations accounted for the four branches (R1b-M269, R1a-M198, N1c1-Tat and N1c2-P43), which together make up from 51% to 100% of the patrilineal genetic diversity in the studied region.

We have shown that West Asian and Central Asian Y-chromosome haplogroup R1a-Z2125 in the Volga-Ural region occurs with the greatest frequency in Bashkirs (31%), which is the dominant subgroup of haplogroup R1a-M198 in this population despite the fact that in other populations Eastern European R1a-M558 and R1a-M458 are the dominant lines. This fact indicates that different haplogroup R1a-M198 lines in the populations of the Volga-Ural region have different sources.

The Eastern European influence in the population can be also seen in Tatars from Tuimasinsky district of Bashlortostan in which typical for Central Europe haplogroup R1b-M405 is the predominant line of the haplogroup R1b-M343. According to the PCA analysis based on the Y-chromosome haplogroups distribution, Bashkirs show the greatest separation from other populations of the region. The reason is the presence with the high frequency of Asian lineages in their gene pool.


Phylogeographic refinement of human Y chromosome haplogroup E provides new insights into the early dispersal of herders in sub-Saharan Africa

Trombetta et al.

Recently, a high number of Y chromosome SNPs has been discovered through next generation sequencing studies, but the geographic distribution for most of these variants remains largely unexplored.

Haplogroup E is the most common human Y chromosome clade within Africa and its internal branches have been linked to a wide range of human movements. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies and further dissected the E-M35 subclade by genotyping 62 informative markers in about 5000 samples from 118 worldwide populations.

The phylogeny of haplogroup E showed novel features compared to the previous topology, including a new basal clade. Within haplogroup E-M35, we resolved basal polytomies and assigned all the E-M35* chromosomes to different new monophyletic clades. Through a Bayesian phylogeographic analysis, we associated each node of the tree to specific geographic areas. By this analysis, we identified a new E-M35 sub-Saharan clade, which originated about 11 kya in the northern part of the Horn of Africa. SNP-based dating, phylogenetic structuring and geographic distribution of this clade (and its sub-clades) are consistent with a multi-step dispersal of herders within eastern Africa and its subsequent diffusion to sub-equatorial areas.

Our results provide new insights into the evolutionary hypotheses about the spread of pastoralism in Africa and increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry informative markers.

11 comments:

Romulus said...

I am curious how they gathered such a massive amount of y dna samples from 300 existing papers when most sampling done on existing countries typically sits around n=1000.

alobrix said...

What do you think about this?

http://www.abstractsonline.com/Plan/ViewAbstract.aspx?mID=3753&sKey=72f5e563-6ac0-4bd2-bd37-628ba5104183&cKey=c1e79ccc-345f-4286-ad2f-843301998ffb&mKey=cabdedda-497c-457e-8481-34a866ab3681

Davidski said...

It looks like they discovered less than what we already knew.

Vincent said...

Finally a new study on haplogroup E! This was needed so much.

Krefter said...

Check this out...

https://docs.google.com/spreadsheets/d/1rCs_wKZp1XYSHEU8619lxxyYDXUPaSXJqXTwQ_ml_OA/edit#gid=0

I've been using 4mix a lot today on West Euros, and it's confirmed what I've always thought....

West Europeans are Bronze age Central European+Middle Neolithic West European+Middle Eastern.

I exhausted pretty much every possibility. And the one above creates the best fits and makes the most sense historically.

Everywhere in West Europe except the North Sea have recent West Asian ancestry(according to ANE K8). In England there's probably some, but it's pretty small.

I've got lots of notes and evidence as to why this model works best for West Europe if anyone wants to see it. I didn't put all French samples because many were German-like, Italian-like, North Sea-like, and Basque-like.

I'll add Italy later. East Europe looks more complicated. I don't have enough ancient East European genomes to get historically realistic fits. But obviously most East Euros are mostly from LN/BA-types.

Davidski said...

Have you tried modeling Middle Neolithic admixture as Stuttgart + Loschbour?

I think you should, because even based on the small number of Middle Neolithic samples we have, it looks like there was quite a bit of diversity in Europe at the time in terms of WHG/ENF ratios.

So if you're using the available Middle Neolithic samples, you're making some big assumptions about who was around when the steppe people crashed into Europe. On the other hand, if you use Stuttgart + Loschbour (or KO1) then you're eliminating a lot of the unknowns.

I reckon the algorithm should still be able to pick up post Neolithic gene flow from the Near East based on the ANE/ASE/ENF/SSA/WHG ratios.

Krefter said...

Stuttgart doesn't erase West Asian ancestry for most West Euros. He does lower it though.

If they are modeled as LN/BA+Stuttgart+MN or WHG, the only ancestor with ANE is LN/BA. If LN/BA is raised as high as it needs to explain West Euro ANE there isn't enough room for Stuttgart to raise ENF to the right level.

Most West Euros need an ancestor who raises ENF but also keeps ANE high. West Asians are the only people who can do this.

For example look at these results.

French6=0% WHG + 23% Stuttgart + 67% Bell_Beaker_LN + 10% Cypriot @ D = 0.0077

French7=12% WHG + 5% Stuttgart + 57% Bell_Beaker_LN + 26% Cypriot @ D = 0.0151

German13=4% WHG + 0% Stuttgart + 71% Bell_Beaker_LN + 25% Cypriot @ D = 0.0085

Chad Rohlfsen said...

You have to drop the bell beaker thing. It's far too complicated to make it one pop, when there are so many Bronze and Iron Age groups. Keep it with extreme samples, as David said.

Krefter said...

CHad,

I understand. But the combined average of BBC is similar to Unetice. If I just use one or the other the scores don't differ very much.

Alberstedt, Corded Ware, HungaryBA, and some of the BBCs look like Yamnaya+MN, while the other LN/BAs look like North Europeans(Yamnaya+MN+HG). My guess is the later was much more popular, because we see them today.

I also did tests with Yamnaya, MN, WAs and of EEFs, HGs, and WAs.

Krefter said...

I'm starting to try to solve the problem of LN/BA diversity and finding the right LN/BA ancestor.

I created 7 "MNs" to represent Pre-Yamnaya ancestry. They vary from 35/65 WHG/ENF to 65/35 WHG/ENF. The Steppe source is one of the CWC individuals who scored 0% in South Eurasian. Most high-ANE LN/BA Euros score in South Eurasian which makes it hard to get good fits.

It'll confirm West Asian ancestry.

Krefter said...

For all West Euros it's possible doing Corded Ware(or Yamnaya)+MN to get 0% West Asian and a very good fit.

But for some the "MN" side has to be like 65% ENF, while all our MN genomes score less than 60%.

Some LN/BAs had MN ancestors like Gok2 and some had MN ancestors who were over 60% WHG. So, I agree with Chad that I shouldn't have assumed all LN/BAs who went into West Europe had mostly WHG MN ancestors. Although looking at North Euros today, it isn't crazy to say most were WHG-rich.

But, seriously, what are the chances any MNs were still 60+ ENF? Based on ANE K8, there's probably recent West Asian ancestry in most of West Europe.