Tracing Y dna sequences

[Angela]

This is a massive new paper. See:

[h=1]Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences[/h]http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3559.html

"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."

The supplement:
http://www.nature.com/ng/journal/vaop/ncurrent/extref/ng.3559-S1.pdf

 

[Tomenable]

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.

 

[Tomenable]

Figure 4 and Supplementary Table 10 show that expansion of R1a-Z93 started ca. 5,500 (5,600-5,300) years ago.

OTOH, the text says that it started 4,500 years ago, maybe "4" is a typo or this refers to expansion in India only?

 

[Angela]

Figure 4 and Supplementary Table 10 show that expansion of R1a-Z93 started ca. 5,500 (5,600-5,300) years ago.

OTOH, the text says that it started 4,500 years ago, maybe "4" is a typo or this refers to expansion in India only?

I think the latter probably refers only to India.

The holes in the results are explained by the fact that they're using only 1000 Genomes data, which is too bad.

Also too bad that it's behind a pay wall, but from the Supplement they're confirming much of what we've all been thinking for a very long time.

I don't quite understand what it means when they say that R1b expanded after Yamnaya. I know they're tying R1b L11 to Beaker, but where did they come from, and when?

 

[Tomenable]

The holes in the results are explained by the fact that they're using only 1000 Genomes data

Yes, in this study they were not researching Central, Northern or Eastern Europe.

This map shows from which regions they got samples (India and Atlantic Europe):

I know they're tying R1b L11 to Beaker, but where did they come from, and when?

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.

ATP3 is that low-quality sample which is suspected of being R1b-M269+ (possibly also R1b-L11+), but it isn't certain if it was:

http://www.eupedia.com/forum/thread...cy-of-I1-and-not-much-R1b?p=479118#post479118

El Portalon cave is located near a pass between the Douro and Ebro basins, maybe the kind of place traders and travellers might wash up?

We can say R1b-M269 is more likely [for ATP3 sample] than the others because the others have contradictory calls - in most cases lots of contradictory calls.

E1b1b1a1-L547+, but E1b1b1a-PF2108-, E1b1b-PF1689-, E1b1-P180-, E-PF1561- (besides it is F+)
I2a2a1b2a2-something-Y16447+ (not old enough anyway according to Y-Full), but I-CTS1006-, IJ-F1450, IJ-Y1943-
J2a1b-S18476+, but J2a-M410-, J2-PF4926-, J-PF4562-, and the 2 IJ-
O3a2c1c1-F1835+, but NO-F415-, NO-M2335-
Q1b-Y1109+, but Q1b-Y1254- (to be fair this might not be equivalent)
Q1a2b2a2-Y1618+, but Q1a2-Y750-
R2(a?)-Y3545+, but R2(a?)-Y3385-, Y3402-, FGC22606-, Y4689-, FGC12636-
R1b1a2-PF6518+, R1b1a-Y97+ (albeit this one is likely spurious), R1-M748+, K-PF5501+, GHIJK-M3773 , F-Y1811+, F-PF2756+.

If it is actually R1b-M269 then it has 6 contradictory calls scattered randomly through a very large number of called SNPs (and these could even be genuine private SNPs for all we know), and a neat unbroken sequence of positive SNPs.
If it was another one then there are more contradictory calls, including negative SNPs upstream in their own lineages, and the R ones just happen to form an unbroken sequence.
So M269 *is* more likely than any of the others, due to that crazy little thing called math.

It could still be just a fluke, or more plausibly contamination (though from what Ted Kandell was saying the R1 SNP sounds genuine). I wouldn't take it as solid proof of early Iberian M269. But I certainly wouldn't bet against finding more either.

*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/thread...er-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.

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

 

[Goga]

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

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

No, Maykop & Yamnaya Horizon are much older than Bell Beaker. And they found R1b in Yamnaya Horizon even before Bell Beaker was born. So R1b in Yamnaya CAN'T be from Bell beakers, beause at that time Bell Beaker didn't exist.

There were many different waves of R1b and R1a into Europe & the Eurasian Steppes


It is possible that one of those early non-Indo-European R1b waves entered Europe at the same time when R1b entered Africa from West Asia (via Levant).

Remember that not all R1b is Indo-European. Only R1b ancestral to Yamnaya R1b or the same as can be Indo-European that entered Europe..

 

[Tomenable]

And they found R1b in Yamnaya Horizon even before Bell Beaker was born.

In Yamnaya they found only Eastern R1b (Z2103), not Western R1b (L11).

 

[Goga]

In Yamnaya they found only Eastern R1b (Z2103), not Western R1b (L11).

Ok, but I thought that R1b-L23 is ancestral to both (Z2103 & L11) and that R1b-L23 is also very 'Eastern' like it predecessors: M269, P297, L278 etc..

And since Z2103 and L11 are not chronologically related to each other they couldn't evolve from each other.

https://en.wikipedia.org/wiki/Haplogroup_R1b


But, it is indeed possible that L11 evolved from L23 in Iberia or something. If that's the case then L11 can't be part of late PIE migration into Europe from Yamnaya, and therefore L11 is originally not Indo-European at all. But that would also make R1b-L23* originally not Indo-European that could migrate into Europe even before Yamnaya (, what I doubt). Because it has been said that late PIE speakers in Europe came from Yamnaya.

It is also possible that Yamnaya was not only Z2103, but also L23* and some other R1b-'brother' lineages. Just 1 lineage for a culture is impossible, there has to be more lineages than only Z2103 in Yamnaya Horizon.

 

[elghund]

Could L23 have emerged from the Dnieper-Donets culture? That was just west of the Yamnaya culture, close enough for acculturation. BTW, kudos to Maciamo for the timeline-haplogroup graphic in 2013 (click above). You saw it here first.