Irish ancient DNA

This study was published just a few days ago but is already from the previous year, tricks of the calendar. It is a scheme-breaker in several aspects, so I hope to be able to reflect here the most important aspects of it.

Lara M. Cassidy, Rui Martiniano et al., Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PNAS 2015. Freely accessible → LINK [doi: 10.1073/pnas.1518445113]

Abstract

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

The two sample sites are from North Ireland, being the so-called Neolithic one from the interior (Co. Down, c. 3200 BCE) and the so-called Bronze Age ones are from a small island (Rathlin) north of the main island (Rathlin 1 and 2 from c. 1900 BCE, Rathlin 3 from c. 1600 BCE). 

I say "so-called" because I'm not really confident that the terms "Neolithic" and "Bronze Age" apply in fact to most of them (I'd rather use Chalcolithic, shorthand for "advanced Neolithic with social complexity, regardless of metals", for all but Rathlin 3). I think in any case that the divider here is not metallurgy as such but actually the Bell Beaker divide: before and after Bell Beaker.

Bell Beaker is becoming a key element to our understanding of the demographic changes in Northern Europe, more than I would have expected admittedly. In the case of Ireland (and to a lesser extent parts of Britain) the arrival of the Bell Beaker phenomenon is accompanied with striking demographic growth, which may (or not) imply new settlement from outside. For Ireland, it seems growingly clear now, it probably does, unless Rathlin is a very unusual site, what is not parsimonious as we will see. 

Enough with the intro, let's get to the substance.

 

Haploid genetics

Ballanyhatty (Co. Down), a woman, carried the mitochondrial haplogroup (matrilineage) HV0. Rathlin 1 carried U5a1b1e, Rathlin 2 U5b2a2 and Rathlin 3 carried J2b1a. The only thing remarkable here is the lack of haplogroup H, the most common one in Europe today and detected since the Magdalenian era in Iberia, but more commonly later on within Neolithic. It can be a fluke of course but the shallow impression is that the mtDNA pool is "pre-modern". However all the rest is very "modern" in Rathlin Island, so... let's assume it's a mere fluke.

The three Rathlin individuals are all men, and their Y-DNA haplogroup has been successfully sequenced: they all belong to R1b-M529, the most common patrilineage in Ireland (and much of Britain and also Brittany) to this day. There's some hints that some of them could belong to downstream subhaplogroups but, if you read the fine print (the supp. materials) this is quite unclear, so let's leave it at this. 

R1b-S116 structure per Valverde 2015

The implications of this data point are important: it clearly defines a terminus ante quem for all possible R1b-M529 and upstream haplogroups' chronologies. Whoever defended a shorter chronology was clearly wrong. Together with a German Bell Beaker individual, these are the oldest R1b-S116 known so far, what is hardly surprising considering the huge blank in aDNA sampling in Western Europe but also suggests that, at least in some areas, Bell Beaker was implicated in the expansion of this most important European patrilineage and in general in the formation of modern-like Western European populations.

There are many open questions here yet because we lack ancient DNA data from France, West Germany, Belgium, Britain, much of Iberia, etcetera. But, with these new data points, I am beginning to believe that Bell Beaker was, if not a general cause, at least a key pivot around which these demographic changes leading to modern populations took place. It was probably a cause in Ireland but it's truly hard to extrapolate to other regions, where aDNA information is missing and archaeological one suggests different patterns of change or continuity. 

Autosomal DNA

The most striking implication of the autosomal DNA of these two Irish sites is that Rathlin men are almost identical to modern Irish (also Scots, Welsh and Cornish), while the much older Ballanyhatty woman is only slightly similar to modern Irish (and Scots), being much more like Sardinians and some South Iberians (what is congruent with what happens to all other Neolithic samples through much of Europe). 

Selection from fig. 3

So we are before a clear-cut demographic change in Ireland (and maybe other regions) at some point in the third millennium BCE. The most plausible date for the beginning of this change is probably around 2500 BCE, when we see the start of significant demographic growth in Ireland and is also the approx. date for Bell Beaker arrival to the island and other parts of Northern Europe (several centuries older in the South however).

Putting these samples in the wider context the authors get this:

Fig. 1. Genetic affinities of ancient Irish individuals. (A and B) Genotypes from 82 ancient samples are projected onto the first two principal components defined by a set of 354,212 SNPs from Eurasian populations in the Human Origins dataset (29) (SI Appendix, Section S9.1 and S10). (A) This PCA projects ancient Eurasian Hunter–Gatherers and Neolithic Farmers, where they separate clearly into Early Neolithic, MN (including the Irish Ballynahatty genome), and several hunter–gatherer groups. (B) PCA projection of Late Neolithic, Copper, and Bronze Age individuals where the three Rathlin genomes adopt a central position within a large clustering of European Bronze Age individuals. (C) A plot of ADMIXTURE ancestry components (K = 11) of these same ancient genomes. In West and Central Europe, ancient individuals are composed almost entirely of two dominant strands of ancestry, linked to hunter–gatherer (red) and early farmer (orange) populations, until the Late Neolithic. At this point, a third (green) Caucasus component features. Previously, this component was only seen in ancient Steppe and Siberian populations such as the Yamnaya. The three Rathlin genomes each display this Caucasus strand of ancestry whereas the Irish Neolithic does not.

Sure: a key element here is the "teal" Caucasus-related component, which is a tell-tale signature of the Indoeuropean or Kurgan expansion into Europe. As exercise to get a rough estimate of how much Indoeuropean (Yamna-like) ancestry there is in each sample, I propose you to get a ruler and a calculator, measure it for each sample and find the resulting fraction. You can also do the same for the early Neolithic (EEF) ancestry, using the "orange" component. There is an interesting substantial leftover fraction that can only be extra "hunter-gatherer" (HG), wherever it comes from. 

My own estimates are as follows:

• Late Neolithic (LN) samples: 80% EEF + 20% extra HG.
• German LN (early Kurgans) = 23% IE + 40% EEF + 37% HG → 27% extra HG relative to LN
• Corded Ware = 64% IE + 21% EEF + 15 HG → 10% extra HG rel. to LN
• Elbe Bell Beaker (avg.) = 13% IE + 44% EEF + 43% HG} → 32% extra HG rel. to LN
• Irish BA = 25% IE + 34% EEF + 41% HG} → 32% extra HG rel. to LN

There is some data in the supp. materials (S12.2.2) which is roughly consistent with this, although their fraction of extra HG (using Lochsbour as reference) is smaller than mine, while their Yamna or IE one is larger instead (no idea why this lesser contradiction, honestly, although they almost overlap once we include error margins). 

Where does this extra HG fraction comes from? It is quite apparent that the currently available samples do not include its source. As I have mentioned many times, there is a huge "Atlantic" blank in the autosomal samples, including nearly all France and many areas around it: Switzerland, West Germany, Low Countries, Britain and about 3/4 of the Iberian Peninsula. 

In this study however we get a hint in the supp. materials: KO1, an Epi-Magdalenian sample from Hungary, stands out like a sore thumb in the f3 analyses of all three Rathlin samples:

Figure S12.1. Outgroup f3-Statistics for each ancient Irish Individual. Tests in the form f3(Mbuti; IA, X), where IA is an Irish ancient genome and X is any other ancient individual or population. Data points are coloured by archaeological context.

Obviously the origin of the extra HG cannot be KO1 as such but there must be one or several populations, as of yet unsampled, in which this extra HG (most akin to KO1) was notorious. My best candidates as of now are the following cultures:

• Michelsberg, which replaced LBK in most of Germany, North France, Belgium, Switzerland, etc. prior to the Corded Ware shockwave. It's part of the wider Funnelbeaker and Megalithic phenomena and one of the ancient cultures I really want to see sampled in some depth. 
• Artenac, which replaced previous layers in all West France and Belgium and is part of the wider Megalithic and Bell Beaker phenomena. It originated around Dordogne and is usually considered proto-Aquitanian, i.e. proto-Basque.
• The major civilization of Zambujal or Vila Nova de Sao Pedro in Portuguese Estremadura, which was a key pivot in the Megalithic and particularly the Bell Beaker phenomenon.

And in general I'd complement these with samples from all the Atlantic facade of Europe, including Britain, the Basque Country (a lot was going on in the Chalcolithic here in spite of the small size), West France, Belgium, the Rhône valley and Switzerland, etc. If we'd have data points for all these areas in the Chalcolithic period, we'd surely have a much more clear picture of what was going on in Europe in this critical period of demographic change. Definitely it's not just Corded Ware and the Elbe basin can only give us so much information anyhow. 

This is also important regarding the origins and spread of R1b-S116 and its "brother" haplogroup U106, no kidding. Let's sample the West, it's about time.