Tuesday, April 4, 2017

Waiting for Ancient DNA Data

The world is waiting for results from three important ancient DNA studies that could address longstanding open questions in historical population genetics, but limited to arguments around the edges using mostly existing information, until then.

* One is a huge dataset of ancient Bell Beaker DNA and related samples that would cast light on the Bell Beaker ancient DNA.

* One is a report on ancient Harappan DNA, the first major ancient DNA result from South Asia. Rumors have purported to leak one of the study's main findings.

* One, which will be longer in coming, is a major Minoan ancient DNA study.

While on their surface these are ancient DNA studies related to archaeological cultures, important historical linguistic issues are related to each. If you know the genetic source of a prehistoric culture, there are fewer uncertainties involved in making inferences about it linguistically.

Further Analysis

One of today's less notable than anticipated pair of papers is closed access, but some interesting points from other papers are found in the comments at Eurogenes' post on them linked above (edited for formatting and punctuation, emphasis mine) provide some interesting commentary on them:

We now know from whole Y chromosome sequencing studies of modern samples that the coalescent time of the most common European sub-clade of R1b-M269 is shallow, 5–7 thousand years (Batini et al. 2015; Hallast et al. 2015; Karmin et al. 2015; Poznik et al. 2016). 
From the aDNA studies we have learned that the oldest R1b-M343 lineages, including 14 KYA Villabruna Man from Italy (Fu et al. 2016) and three European hunter-gatherers and three early farmer samples (Fig. 7), did not belong to the R1b- M269 sub-clade According to the ancient DNA evidence, affinity in their autosomal genes to the early farmers of Atapuerca from Spain (Gunther et . . . 

Late Neolithic, Early Bronze Age and Iron Age samples from Central and Western Europe have typically the R1b-L11, R1a1-Z283 and R1a-M417 (xZ645) affiliation while the samples from the Yamnaya and Samara neighbourhood are different and belong to sub-clades R1b11-Z2105 and R1a2-Z93 (Allentoft et al. 2015; Cassidy et al. 2016; Haak et al. 2015; Mathieson et al. 2015; Schiffels et al. 2016). 
The R1b11-Z2015 lineage is today common in the Caucasus and Volga-Uralic region while being virtually absent in Central and Western Europe (Broushaki et al. 2016). 
Interestingly, the earliest offshoot of extant haplogroup R1b-M343 variation, the V88 subclade, which is currently most common in Fulani speaking populations in Africa (Cruciani et al. 2010) has distant relatives in Early Neolithic samples from across wide geographic area from Iberia, Germany to Samara (Fig. 7). In a similar way, early offshoots of the R1b and R1a phylogenies, including R1b lineages derived at P297 and ancestral at M269, and R1a lineages which are derived at M459.
To digest this, you need a program explaining how the Y-DNA R1a and R1b clades are related to each other.

On the R1a side:

*R1a-M459 (a.k.a. R1a1) is very basal and includes essentially all extant Y-DNA R1a although there are a few intermediate clades with very few representatives between R1a-M420 at the root of R1a and R1a-M459.

* R1a2-Z93 (a.k.a. R1a1a1b2) found mostly in Asia, is a sister clade to R1a1-Z282 (a.k.a. R1a1a1b1a) found mostly in Eastern Europe, and is not ancestral to the Eastern European clade. Both of these are clades within both R1a-M417 (a.k.a. R1a1a1) and R-Z645 (a.k.a. R1a1a1b).

*R1a-M417 (xZ645) (a.k.a. R1a1a1) is the same branch of R1a that includes the Eastern European and Asian clades minus the subclade (R1a1a1b) that includes both of those clades that make up the lion's share of R1a in West Eurasia.

The key point is that the European steppe ancient Y-DNA R1a individuals come are part of an already differentiated Asian clade of R1a (now found mostly in Central Asia and South Asia) which is a sister clade to the European clades rather than being ancestral to them. Likewise outlier pro-Corded Ware ancient Y-DNA R1a in Europe is from a distantly related basal clade of R1a that is not ancestral to the currently predominant clades of Y-DNA R1a found there. 

On the R1b side:

* R1b-M343 (a.k.a. R1b*) is the most basal root of Y-DNA R1b.

* R1b-V88 is a very basal branch of R1b on a different branch than R1b-M269.

* R1b-M269 (a.k.a. R1b1a1a2) is a quite derived branch found mostly in Western Europe.

* R1b-L11 (a.k.a. R-P310/L11* a.ka. R1b1a2a1a1*) is a derived version of R1b-M269 which a paraclade of R1b-L151/P310 that has three sister clades including two common sister clades:R-U106 (a.k.a. R1b1a2a1a1a) found in Germanic Europe, and R-P312 (a.k.a. R1b1a2a1a1b) found in Iberia, British Isles, Italy and France.

* R1b11-Z2105 appears to be a typo or obsolete classification because R1b-Z2105 is actually R1b1a1a2a2, which is the a2 subbranch of R1b-M269, which is a sister clade to R1b-L151/P310. It appears that this may be the same clade or much more closely related to the clade R-Z2103 (a.k.a. R1b1a2a2) which is found in the Balkans and Turkey.

The key point is that the Y-DNA R1b clades found in the ancient DNA of the Yamnaya and Samara are closely related sister clades of those found in Western Europe, rather than being ancestral to them. Likewise, the early outlier instances of ancient Y-DNA R1b in ancient DNA from Europe involves basal sister clades to the predominant R1b-M269 rather than ancestral clades of Y-DNA R1b.

The bottom line is that modern Europeans while related fairly closely to people bearing Y-DNA R1a and R1b on the European steppe identified to date, and in old outlier samples from Europe, and in modern Y-DNA R1b-V88 people mostly in North Africa, are not direct descendants of any of these populations and their clades expanded much more recently and very rapidly.

Another comment states:
Archaeological part (CWC) is actually quite good.
Here is a hint what will BBB show: 
"Bell Beaker groups had by now also emerged on the scene, introducing metallurgy, and they further complicated the mix of cultures and people." 
There are two key-words here - emerged and metallurgy. The first one suggest a rather local development. The second a connection to an originally non-IE way of life, as in this sentence: 
"Extensive exchange systems linked different groups together and secured access to products outside the pastoral economy, such as metal." 
Now we can connect this with the old-new slide about mobility, which also showed that CE BB were less mobile than CWC (you can't be more mobile than shepherds if you're "introducing metallurgy", because metal deposits don't have legs like cows; you can eventually jump from one ore mine to another). 
Another interesting thing is about pottery:

"Corded Ware pottery appeared later in Northern Europe, and we may suggest that this did not happen until women with ceramic skills married into this culture and started to copy wooden, leather and woven containers in clay."

1 comment:

andrew said...

Two of the three rumored papers are not out and blogged. The Harappan paper is still awaiting publication and reportedly will be out around September.