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Gravetto-Danubian
04-26-2016, 01:32 AM
Similar to preceding papers on Y chromosome, a new paper by Poznik et al. provides more perspectives and resolutions of some of the big Y haplogroup lineages.


We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

9013


In addition to again looking at European haplogroups like I1, it has delved into South Asia also, including a look at R1a-Z93 expansion.


In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring 4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the Western Steppe into the Indian subcontinent 27. There is a notable parallel with events in Europe, and future aDNA evidence may prove to be as informative as it has been in Europe

Link (http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3559.html)
Unfortunately, behind a Pay-Wall

J Man
04-26-2016, 01:49 AM
Any news about Y-DNA haplogroup J2a from this new study?

Gravetto-Danubian
04-26-2016, 01:56 AM
Any news about Y-DNA haplogroup J2a from this new study?

yes, apparently there is. But Im still trying to obtain access

ADD: ok look at Suppl material; eg page 21 & 82

ArmandoR1b
04-26-2016, 02:21 AM
There is a lot of information in the Supplementary Information

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3559.html#supplementary-information

Gravetto-Danubian
04-26-2016, 02:37 AM
Ok so some more :

""First, in the Americas, we observed expansion of Q1a-M3 (Supplementary Figs. 14e and 17) at ~15 kya, the time of the ini- tial colonization of the hemisphere. This correspondence, based on one of the most thoroughly examined dates in human prehistory, attests to the suitability of the calibration we have chosen.

Second, in sub-Saharan Africa, two independent E1b-M180 lineages expanded ~5 kya (Supplementary Fig. 14a), in a period before the numerical and geographical expansions of Bantu speakers, in whom E1b-M180 now predominates22. The presence of these lineages in non-Bantu speakers (for example, Yoruba and Esan) indicates an expansion predating the Bantu migrations, perhaps triggered by the develop- ment of ironworking.

Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe"

Most of the money is in Suppl data available freely

Agamemnon
04-26-2016, 02:38 AM
From the paper:


As the haplogroup expansions we report are among the most extreme yet observed in humans, we think it more likely than not that such events correspond to historical processes that have also left archaeological footprints. Therefore, in what follows, we propose links between genetic and historical or archaeological data. We caution that, especially in light of as yet imperfect calibration, these connections remain unproven. But they are testable, for example, using aDNA. First, in the Americas, we observed expansion of Q1a-M3 (Supplementary Figs. 14e and 17) at ~15 kya, the time of the initial colonization of the hemisphere21. This correspondence, based on one of the most thoroughly examined dates in human prehistory, attests to the suitability of the calibration we have chosen. Second, in sub-Saharan Africa, two independent E1b-M180 lineages expanded ~5 kya (Supplementary Fig. 14a), in a period before the numerical and geographical expansions of Bantu speakers, in whom E1b-M180 now predominates22. The presence of these lineages in non-Bantu speakers (for example, Yoruba and Esan) indicates an expansion predating the Bantu migrations, perhaps triggered by the development of ironworking23. Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe26. Potential correspondences between genetics and archeology in South and East Asia have not been investigated as extensively. In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring ~4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the Western Steppe into the Indian subcontinent27. There is a notable parallel with events in Europe, and future aDNA evidence may prove to be as informative as it has been in Europe. Finally, East Asia stands out from the rest of the Old World for its paucity of sudden expansions, perhaps reflecting a larger starting population or the coexistence of multiple prehistoric cultures wherein one lineage could rarely dominate. We observed just one notable expansion within each of the O2b-M176 and O3-M122 clades (Supplementary Fig. 14d).

[...]

Present day geographical distributions provide strong support for the correspondences we proposed for the initial peopling of most of Eurasia by fully modern humans ~50–55 kya and for the first colonization of the Americas ~15 kya. For later male-specific expansions, we should consider the consequences of alternative mutation rate estimates, as pedigree-based methods relying on variation from the most recent several centuries8,10,28 may be more relevant. The pedigree-based estimate from the largest set of mutations8 would lead to a ~15% decrease in expansion times, increasing the precision of the correspondences proposed for E1b and R1a. For R1b, a 15% decrease would suggest an expansion postdating the Yamnaya migration. Using either mutation rate estimate, the lineage expansions seem to have followed innovations that may have elicited increased variance in male reproductive success29, innovations such as metallurgy, wheeled transport, or social stratification and organized warfare. In each case, privileged male lineages could undergo preferential amplification for generations. We find that rapid expansions are not confined to extraordinary circumstances30,31 and that the Y chromosome resulting from these rapid expansions can predominate on a continental scale and do so in some of the populations most studied by medical geneticists. Inferences incorporating demography may benefit from taking these male–female differences into account.

Heber
04-26-2016, 03:38 PM
It appears to be a follow up of the Wei, Xue, Jobling, Tyler Smith.. paper from 2013
A calibrated human Y-chromosomal phylogeny based on resequencing

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561879/#!po=30.8824

This article has several quotes from the authors

"Dr Yali Xue, lead author from the Wellcome Trust Sanger Institute, explained: "This pattern tells us that there was an explosive increase in the number of men carrying a certain type of Y chromosome, within just a few generations. We only observed this phenomenon in males, and only in a few groups of men."

The earliest explosive increases of male numbers occurred 50,000-55,000 years ago, across Asia and Europe, and 15,000 years ago in the Americas. There were also later expansions in sub-Saharan Africa, Western Europe, South Asia and East Asia, at times between 4,000 and 8,000 years ago. The team believes the earlier population increases resulted from the first peopling by modern humans of vast continents, where plenty of resources were available.

The later expansions are more enigmatic.

Dr Chris Tyler-Smith, from the Sanger Institute, added: "The best explanation is that they may have resulted from advances in technology that could be controlled by small groups of men. Wheeled transport, metal working and organised warfare are all candidate explanations that can now be investigated further."

https://www.sciencedaily.com/releases/2016/04/160425141808.htm

ADW_1981
04-26-2016, 04:45 PM
The Bantu expansion, whatever the exact timeframe, seems to have not involved R-V88.

Heber
04-26-2016, 05:25 PM
"Third, in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe26"

They seem to imply that the expansion of R1b-L11 is due to the Bell-Beaker culture in Western Europe.

9017

9018

Tomenable
04-26-2016, 06:17 PM
Nothing or not much about R1a-Z283.

Tomenable
04-26-2016, 06:26 PM
Aryan migration/invasion from the steppe to India:

"In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93 [5 out of 8 lineage expansions], occurring ~4.0–5.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the Western Steppe into the Indian subcontinent."

Tomenable
04-26-2016, 07:24 PM
It's about Amerindian (Q1a-M3), Aryan (R1a-Z93), Beaker (R1b-L11) and Bantu (E1b-M180) expansions.

But the paper is totally silent about R1a-M198(xZ93) and R1b-M269(xL11), which is rather disappointing.

rozenfeld
04-26-2016, 07:32 PM
But the paper is totally silent about R1a-M198(xZ93) and R1b-M269(xL11), which is rather disappointing.

Well, it's actually not surprising. This paper is a part of 1000 genomes project and they didn't have any samples from Eastern Europe, look at the map:

http://www.1000genomes.org/sites/1000genomes.org/files/images/1000g_map.png

ADW_1981
04-26-2016, 08:10 PM
It would be nice to have seen populations included from the Balkans and Eastern Europe to properly measure E-V13 and I2a2-M423 Dinaric branches.

rozenfeld
04-26-2016, 08:23 PM
It would be nice to have seen populations included from the Balkans and Eastern Europe to properly measure E-V13 and I2a2-M423 Dinaric branches.

Well, then one can wait for the publications of Simons Genome Diversity Project:

https://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project-dataset/

https://www.simonsfoundation.org/wp-content/uploads/2014/10/new-data-image-800x428.jpg

List of samples:

http://simonsfoundation.s3.amazonaws.com/share/SCDA/datasets/10_24_2014_SGDP_metainformation_update.txt

Shaikorth
04-26-2016, 08:26 PM
Well, then one can wait for the publications of Simons Genome Diversity Project:

https://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project-dataset/

https://www.simonsfoundation.org/wp-content/uploads/2014/10/new-data-image-800x428.jpg

List of samples:

http://simonsfoundation.s3.amazonaws.com/share/SCDA/datasets/10_24_2014_SGDP_metainformation_update.txt

Simon's genome project is more useful for autosomal stuff because all its samples are high coverage sequences but there's only about 1-3 from each population meaning many uniparental lines will go unsampled.

Tomenable
04-27-2016, 04:51 AM
Figure 4 and Supplementary Table 10 suggest that expansion of R1a-Z93 started ca. 5,500 (5,600-5,300) years ago, not 4,500 (maybe "4" is a typo?).

Figure 4 (I added red lines):

http://s32.postimg.org/rwptsogjp/czas_ekspansji.png

vettor
04-27-2016, 06:27 AM
It appears to be a follow up of the Wei, Xue, Jobling, Tyler Smith.. paper from 2013
A calibrated human Y-chromosomal phylogeny based on resequencing

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561879/#!po=30.8824

This article has several quotes from the authors

"Dr Yali Xue, lead author from the Wellcome Trust Sanger Institute, explained: "This pattern tells us that there was an explosive increase in the number of men carrying a certain type of Y chromosome, within just a few generations. We only observed this phenomenon in males, and only in a few groups of men."

The earliest explosive increases of male numbers occurred 50,000-55,000 years ago, across Asia and Europe, and 15,000 years ago in the Americas. There were also later expansions in sub-Saharan Africa, Western Europe, South Asia and East Asia, at times between 4,000 and 8,000 years ago. The team believes the earlier population increases resulted from the first peopling by modern humans of vast continents, where plenty of resources were available.

The later expansions are more enigmatic.

Dr Chris Tyler-Smith, from the Sanger Institute, added: "The best explanation is that they may have resulted from advances in technology that could be controlled by small groups of men. Wheeled transport, metal working and organised warfare are all candidate explanations that can now be investigated further."

https://www.sciencedaily.com/releases/2016/04/160425141808.htm

I thought this below had some part in it
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4327154/

lgmayka
04-27-2016, 02:16 PM
It would be nice to have seen populations included from the Balkans and Eastern Europe to properly measure E-V13 and I2a2-M423 Dinaric branches.
The 1000 Genomes project (http://www.1000genomes.org/) did not recognize the presence of modern humans anywhere between the Netherlands and China. No Germans, no Slavs, no Balts, no Balkans, no West Asians, no Central Asians, etc.

parasar
04-27-2016, 02:16 PM
Figure 4 and Supplementary Table 10 suggest that expansion of R1a-Z93 started ca. 5,500 (5,600-5,300) years ago, not 4,500 (maybe "4" is a typo?).

This is consistent with the other quote you posted:
"expansions within R1a-Z93 [5 out of 8 lineage expansions], occurring ~4.0–5.5 kya"

parasar
04-27-2016, 04:03 PM
The coverage of South Asia is good - all corners are represented - Lanka, Bangladesh, Pakistan, Gujarat.

Regarding their 1000Y.subtrees (page 5) in the Supplement for R1a-Z93.
1. Under M417 it shows a split to Z645 and CTS7083 (under CTS4385)
2. Under Z645 to Z282 and Z93.
3. Under Z93 the main South Asian branch seems to be L657 with about half of these being Y7. The others are F992, Z2123, Y57 (under Z2124), and CTS6 (under Z2124 and Y57). Some of the F992 share SNPs with Z2123 - I assume these are Z2124xZ2123. Other F992 are don't share any SNPs with Z2123, but are indeed share with others -these are Y40/ Y37 (eg. the HG03926 group) or Y40/Z96 (TSI). One is F992*xY40, xM780, xZ2124 (HG03705)

My branch Y2392 is shared with HG04098 who shares Y2353 with HG0399 and Y2351 with NA20904 consistent with YFull https://www.yfull.com/tree/R-Y2351/

MattL
04-27-2016, 07:21 PM
When the study refers to L11 are they referring to a branch in parallel with P312 or above P312? Searching the various online charts I get confused since some places talk about L11 being a different branch than P312, but then I see the chart here:
http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml

and it has L11 over P312.

Heber
04-27-2016, 07:52 PM
Debbie posted this on Facebook.

"This a newly published paper in the American Journal of Human Genetics: “Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates”. Authors: Thomas Willems, Melissa Gymrek, David Poznik, Chris Tyler-Smith, The 1000 Genomes Project Chromosome Y Group and Yaniv Erlich. It is a companion piece to the Poznik paper “Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences”.

Abstract
Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2–6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.

The paper is behind a paywall: http://www.cell.com/ajhg/abstract/S0002-9297(16)30093-3

However, it was previously made available as a preprint under a slightly different title:

http://biorxiv.org/content/early/2016/01/15/036590

Heber
04-27-2016, 08:07 PM
When the study refers to L11 are they referring to a branch in parallel with P312 or above P312? Searching the various online charts I get confused since some places talk about L11 being a different branch than P312, but then I see the chart here:
http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml

and it has L11 over P312.

L11 is over P312 and U106.
L51 is over L11.
L23 is over L51.
M269 is over L51.

https://www.familytreedna.com/groups/r1b/about/results#/RTREE

9051

Heber
04-27-2016, 08:09 PM
........

jesus
04-27-2016, 09:20 PM
Figure 4 and Supplementary Table 10 suggest that expansion of R1a-Z93 started ca. 5,500 (5,600-5,300) years ago, not 4,500 (maybe "4" is a typo?).

Figure 4 (I added red lines):

http://s32.postimg.org/rwptsogjp/czas_ekspansji.png

The L expansion is interesting. Probably related to natives from BMAC accompanying R1a Indo Iranians.

evon
04-27-2016, 09:22 PM
Link (http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3559.html)
Unfortunately, behind a Pay-Wall

Voila, magic!

Try sci hub, free access :)

;)

Gravetto-Danubian
04-27-2016, 10:34 PM
It would be nice to have seen populations included from the Balkans and Eastern Europe to properly measure E-V13 and I2a2-M423 Dinaric branches.

These might have to come from the Citizen Scientist body ?

Tomenable
04-27-2016, 11:17 PM
Such a quotation from the study:


in Western Europe, related lineages within R1b-L11 expanded ~4.8–5.9 kya (Supplementary Fig. 14e), most markedly around 4.8 and 5.5 kya. The earlier of these times, 5.5 kya, is associated with the origin of the Bronze Age Yamnaya culture. The Yamnaya have been linked by aDNA evidence to a massive migration from the Eurasian Steppe, which may have replaced much of the previous European population24,25; however, the six Yamnaya with informative genotypes did not bear lineages descending from or ancestral to R1b-L11, so a Y-chromosome connection has not been established. The later time, 4.8 kya, coincides with the origins of the Corded Ware (Battle Axe) culture in Eastern Europe and the Bell–Beaker culture in Western Europe26.

ATP3 from Iberian Copper Age is ~5.3–5.5 kya*, well within the range of expansion of R1b-L11 according to this new paper.

In case if you don't remember, ATP3 is a low-quality sample that is suspected of being R1b-M269+ (possibly also R1b-L11+):

http://www.anthrogenica.com/showthread.php?3474-Bell-Beakers-Gimbutas-and-R1b&p=107965&viewfull=1#post107965

*ATP3 is dated to 5466 - 5312 years ago (cal BP). ATP3's autosomal DNA also has indications of partially eastern origin:

http://www.eupedia.com/forum/threads/31558-Analysis-of-Chalcolithic-El-Portalon-samples-(Günther-at-al-2015)?p=466264&viewfull=1#post466264


ATP3 (3516–3362 BCE) stands out from other samples thanks to its high Northern Middle Eastern ancestry (31.97%) against 0% for ATP20, 11% for ATP17 and between 0% and 8% for other samples. What Genetiker calls Northern Middle Eastern is what we typically referred on this forum as Caucaso-Gedrosian admixture - the same as in the "Armenian-like admixture" in Yamna samples.

With its 32% of Caucaso-Gedrosian, 14% of Northern European ancestry, 6% of European Hunter-Gatherer and 3.8% of Veddoid, it does indeed look as if ATP3 has a bit over half of Steppe ancestry, but with a higher proportion of northern Middle Eastern and Veddoid than Yamna samples. In other words it could be descended to the pre-Indo-European Anatolian R1b-M269, the group of cattle herders that would cross the Caucasus and settle in the Pontic-Caspian Steppe. So could it be an offshoot of cattle herders that directly migrated from Anatolia to Iberia during the Neolithic period.

So we can't rule out that pre-L11 or L11+ came to Iberia long before Yamnaya expansion, and then expanded from Iberia.

Tomenable
04-27-2016, 11:46 PM
According to Maciamo R1b-M269 were originally Non-Indo-European cattle herders who lived to the south of Caucasus.

Later one group of them (L23* and Z2103) migrated to the Steppe and mixed with Indo-Europeans, forming Yamna culture.

Another group of them, however (R1b-L51 - predecessor to R1b-L11) migrated directly to Europe from Eastern Anatolia.

And that group settled in Iberia (see: ATP3), where it expanded demographically, and later geographically as Bell Beakers.

Of course that group originally expanded as Non-Indo-Europeans, and became Indo-Europeanized in Central Europe by CWC.

=====================================

We must wait for Iberian Bell Beaker DNA - it will tell us whether R1b-L11 expanded directly from the Steppe or from Iberia.

Tomenable
04-27-2016, 11:48 PM
Hmm, Perhaps U106 expanded to the Steppe and became IE Western Yamna, while only P312 were originally Non-IE Beakers?

This would also explain my theory that U106 were dolichocephalic Proto-Celts (see: Hallstatt Nordid anthropological type of Hallstatt culture), who Celticized brachycephalic-mesocephalic P312 Beaker Folks. As was believed by Old School anthropologists.

See the "U106 were the True Celts" thread: http://www.anthrogenica.com/showthread.php?6939-R1b-U106-were-the-True-Celts-and-Belgae-(my-opinion)

Hallstatt type is now most common in Scandinavia, but is associated with (and named after) Celtic-speaking Hallstatt culture:

http://www.theapricity.com/snpa/rg-hallstatt.html


(...) Hallstatt is the name of an Austrian village and a nearby archaeological site where extensive human remains [of Iron Age Celtic Hallstatt culture], corresponding skeletally to the classic Nordid type, were discovered. The Hallstatt Nordic is the 'classic' Nordid type, and metrically identical to the original central European Nordid type preserved in Iron Age skeletal material. (...)

But modern distribution is different from its original Iron Age distribution:


(...) The Hallstatt Nordid type is found in its greatest concentration on the southern Swedish plain and in the adjacent long valleys and lowlands of southeastern Norway. Outside of this kernel, which Carleton Coon described as "a refuge of the classic Nordic race", non-Nordid (mostly Cro-Magnoid) admixture increases rapidly, and no true predominantly Hallstatt Nordid population may be found. The type has blended with broader-featured, more robust Cro-Magnids in Denmark, northern Germany and the Be-Ne-Lux countries (Dalo-Falid, Borreby), and is present at lower levels in the British Isles, where the related Keltic type is more common. (...)

"On the Physical Anthropology of Ancient Celts" (mostly round-headed like Beaker Folks, but partly long-headed "Nordic" too):

https://periklisdeligiannis.wordpress.com/2013/12/30/on-the-physical-anthropology-of-the-ancient-celts/

=============================

PS: I know, I know, physical anthropology doesn't really correlate with genetics (or at least not always). :P

Heber
04-28-2016, 08:22 AM
Well, then one can wait for the publications of Simons Genome Diversity Project:

https://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project-dataset/

https://www.simonsfoundation.org/wp-content/uploads/2014/10/new-data-image-800x428.jpg

List of samples:

http://simonsfoundation.s3.amazonaws.com/share/SCDA/datasets/10_24_2014_SGDP_metainformation_update.txt


The companion paper by Willems uses the Simons Genome Diversity Project. Does anyone know if it was used for the Poznik paper.

"This a newly published paper in the American Journal of Human Genetics: “Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates”. Authors: Thomas Willems, Melissa Gymrek, David Poznik, Chris Tyler-Smith, The 1000 Genomes Project Chromosome Y Group and Yaniv Erlich. It is a companion piece to the Poznik paper “Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences”.


Abstract
Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2–6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.


The paper is behind a paywall: http://www.cell.com/ajhg/abstract/S0002-9297(16)30093-3

However, it was previously made available as a preprint under a slightly different title:

http://biorxiv.org/content/early/2016/01/15/036590

http://biorxiv.org/content/early/2016/04/09/036590.figures-only

Tomenable
05-01-2016, 10:17 AM
R1b-L51* is mostly confined to South-Western Europe (and I think that it is even more so with R1b-L11*):

Map of unresolved paragroup R1b-L51*: http://secherbernard.blog.free.fr/public/.L51_Map_with_Neolithic_Path_003_m.jpg

Considering that it is non-existent in "the East", IMO R1b-L51 was never part of Yamna, but moved West before Yamna:

http://secherbernard.blog.free.fr/public/.L51_Map_with_Neolithic_Path_003_m.jpg

If Iberian Chalcolithic ATP3 was indeed R1b-L51, then the presence of ancestors of R1b-L51 in Yamna must be ruled out.

Among 1204 Sardinians there were 57 R1b other than U152 (128 samples), including some basal clades::

- 10 x R1b-M269*
- 9 x R1b-L23*
- 3 x R1b-L151*
- 25 x R1b-P312*

- 4 x R1b-DF27
- 2 x R1b-L21
- 2 x R1b-L513
- 2 x R1b-U106

Source: Francalacci 2013

R1b-M269 was also found in aDNA of Aboriginals of Canary Islands, who spoke a Berber-related language.

==============================

Here is my view on the subject - we will IMO never find R1b-L11 in Yamnaya, because it was not there:

http://s32.postimg.org/6j3mdu7v9/R1b_expansions.png

For "some" (caugh, caugh) reason, R1b is very numerous in Pre-Arabic, Semitic populations of the Middle East:

http://www.anthrogenica.com/showthread.php?615-Assyrian-Y-DNA-Distribution&p=3654&viewfull=1#post3654

Non-Indo-European (Non-Arabic Semitic, Akkadian-Aramaic) Assyrians have 23% of R1b (!):

http://i1096.photobucket.com/albums/g326/dok101/chart_1.png

Six major haplogroups among them are J1, J2, E1b, T, G and R1b. IMO this is all Pre-IE Near East.

Prediction 1:

Western Yamnaya will turn out to be full of R1a-M417 - and directly ancestral to Corded Ware males.

Prediction 2:

Early Bell Beaker culture (in Iberia and France) will turn out to be full of R1b-L11, or at least R1b-P312.

ADW_1981
05-01-2016, 02:15 PM
R1b-L51* is mostly confined to South-Western Europe (and I think that it is even more so with R1b-L11*):

Map of unresolved paragroup R1b-L51*: http://secherbernard.blog.free.fr/public/.L51_Map_with_Neolithic_Path_003_m.jpg

Considering that it is non-existent in "the East", IMO R1b-L51 was never part of Yamna, but moved West before Yamna:

http://secherbernard.blog.free.fr/public/.L51_Map_with_Neolithic_Path_003_m.jpg

If Iberian Chalcolithic ATP3 was indeed R1b-L51, then the presence of ancestors of R1b-L51 in Yamna must be ruled out.

Among 1204 Sardinians there were 57 R1b other than U152 (128 samples), including some basal clades::

- 10 x R1b-M269*
- 9 x R1b-L23*
- 3 x R1b-L151*
- 25 x R1b-P312*

- 4 x R1b-DF27
- 2 x R1b-L21
- 2 x R1b-L513
- 2 x R1b-U106

Source: Francalacci 2013

R1b-M269 was also found in aDNA of Aboriginals of Canary Islands, who spoke a Berber-related language.

==============================

Here is my view on the subject - we will IMO never find R1b-L11 in Yamnaya, because it was not there:

http://s32.postimg.org/6j3mdu7v9/R1b_expansions.png

For "some" (caugh, caugh) reason, R1b is very numerous in Pre-Arabic, Semitic populations of the Middle East:

http://www.anthrogenica.com/showthread.php?615-Assyrian-Y-DNA-Distribution&p=3654&viewfull=1#post3654

Non-Indo-European (Non-Arabic Semitic, Akkadian-Aramaic) Assyrians have 23% of R1b (!):

http://i1096.photobucket.com/albums/g326/dok101/chart_1.png

Six major haplogroups among them are J1, J2, E1b, T, G and R1b. IMO this is all Pre-IE Near East.

Prediction 1:

Western Yamnaya will turn out to be full of R1a-M417 - and directly ancestral to Corded Ware males.

Prediction 2:

Early Bell Beaker culture (in Iberia and France) will turn out to be full of R1b-L11, or at least R1b-P312.

Some Assyrian diaspora groups have even higher R1b, such as 40% in Iran. I can't cite the study off hand though. I don't believe your L51 (xL11) is terribly accurate though. It seems to peak in Central Europe (yet seems vacant in Germany) and Italy, and L11(xU106, xP312) has a very north-west European frequency.

Tomenable
05-01-2016, 03:35 PM
Let's confine this discussion about the origins of R1b-L11 to just one thread:

http://www.anthrogenica.com/showthread.php?7006-ANCIENT-DNA-AND-HUMAN-EVOLUTION&p=154122&viewfull=1#post154122