The Population Genetic History Of Ireland

A new PhD thesis examining ancient DNA from Ireland largely reproduces the paradigm expectation set firmly in place in May 2017 with a major paper known sometimes as the Bell Beaker Behemoth. This paradigm provides that major population genetic change driven by mass migration occurred at the dawn of the Neolithic era (with substantial Mesolithic introgression), and again in the Bronze Age, at which point the modern Irish gene pool (and the gene pool of most of Europe) was largely established and primarily diversified internally through gradual evolution and selective effects, after that point.

The possibility that there was a Mediterranean as opposed to Danubian Neolithic source for Ireland's Neolithic Revolution (this could be nothing if the author considers all Anatolian ancestry to be Mediterranean - the author does not do this and distinguishes continental ancestry from direct Mediterranean ancestry based upon trace continental hunter-gatherer components present in LBK derived first farmers, but not found in Mediterranean route first farmers) is interesting if that is indeed what was found.

Also notable is the possibility that the Bronze Age migration may have had two roughly contemporaneous separate sources, one Northern European and one Atlantic, focusing on different parts of the Emerald Isle.

This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. 

ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time.

The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH).

Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population.Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies.

Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. 

Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time.

Cassidy, Lara, A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory, Trinity College Dublin.School of Genetics & Microbiology. GENETICS, 201 (PhD thesis October 2017) via Eurogenes. Supplementary material reproduced here.

Cassidy was also lead author of a January 2016 study on Irish ancient DNA at PNAS together with Mallory and others involving a much smaller sample.

With regard to the last point highlighted in the abstract, a comment at Eurogenes notes that:

Page 196 shows phenotype allele frequencies in Mesolithic, Neolithic, Bronze, iron age Ireland. 

Lactose persistent allele (rs4988235-A)
Neolithic=0%
Bronze age=5%
Iron age=50%
Modern=80%  

Light skin allele (rs16891982-G)
Neolithic=30%
Bronze age=70%
Iron age=100%
Modern=100%

The same individual, Samuel Andrews, also observes that: "I wish they tested for red hair SNPs. Because, modern Northwest Europe has around 10x higher frequency of red hair alleles than Bell Beaker did believe it or not. Red hair is rare today, but used to be 10x more rare in the Bronze age."

Query if the Iron Age shift could be due to demic replacement by Celtic speakers who were otherwise genetically very similar to Bronze Age Bell Beaker people who led to population replacement from the Neolithic population of Ireland, rather than by pure fitness based selection.

A comment from Rob at Eurogenes notes this quote from the paper: ''it is perhaps noteworthy that none of the four Early Cardial Neolithic individuals so far sampled (Croatia and Spain) belong to G2. Indeed, two possess haplogroups rare or absent in Balkans and Hungarian Neolithic (R and E1b1).''

A comment from Romulus at Eurogenes notes that: 

Neolithic British and Irish Y-DNA is far from extinct. I can say this for a fact, I'm part of the I2a P37.2 project on FTDNA and those subclades are plentiful, in particular I2a1b-L161.1. This subclade has been known about for a very long time. 

Haplogroup I2a1b-L161.1 

Commonly known in genetic genealogy circles as I2-M423-Isles, L161.1 is found at highest frequencies in western Ireland (5-10%) and the Scottish Highlands (1-5%), but is also found at low frequencies (> 1%) throughout Central and Western Europe, from Latvia, Lithuania and Belarus to the British Isles, and from Scandinavia to north-western Spain. It has also been found in Albania, northern Greece, Bulgaria and Romania. 

British Isles I2a2 as well is Neolithic derived. 

As expected, Mesolithic samples show more basal lineages with respect to the Neolithic cohort, a significant number of whom placed within the subclade I2a2a1-M284, found almost exclusively in Britain today (International Society of Genetic Genealogy 2017; FamilyTreeDNA 2017). ***A near complete*** turnover is then witnessed in the Chalcolithic and Early Bronze Age, with virtually all samples from this time onwards belonging to the R1b-L151 haplogroup, associated with the Atlantic Modal Haplotype. This lineage forms a downstream branch of R1b-M269, the most prevalent haplogroup in western Europe today (Myres et al. 2011). It was possible to place a further majority of samples (81.8%) into the subclade R1b-L21, a haplogroup whose distribution shows a steep and somewhat restricted peak in modern Ireland, where it accounts for almost half of male lineages (Myres et al. 2011). Only one Y chromosome examined fell outside R1b-M269 after the Neolithic period, belonging to an Early Bronze Age individual from the southwest, Killuragh1, who placed within I2a2a1-M284. 

Most likely *all* of British I2 is Neolithic derived.

Bell Beaker Blogger considers the linguistic implications of the study, and in particular, the Afro-Asiatic substratum hypothesis.

The mainstream view is that the Celtic entered the Islands in the LBA with the IA representing its cultural apex. Population movements certainly spread this language, but genetic continuity would suggest that Bronze Age natives would have learned Celtic (as a new dialect or a new language)

Before the Celtic invasion, the Island of Britain probably spoke a number of languages related to those of the Low Countries (certainly some kind of LLPIE, possibly the speculative Nordwestblok). But Ireland may be another story as its ethnic enclaves were more choppy, with strange menages of new lifeways and ancient craft traditions. (food vessels as one example). . . .

If Late Neolithic Irish tended toward the more Levantine variety of Farmer, and if they survived in any significant numbers to the MBA in Ireland, then it is well possible that portions of the LBA Irish population were learning (or mangling) Continental Celtic from the aspect of an Afro-Asiatic thinker.

The historical linguistic puzzle in the case of the Celtic languages is that by linguistic measures and when correlated with archaeology associated with Celtic culture, this language family looks like it ought to be relatively young, dating to the Iron Age, as Bell Beaker Blogger indicates the conventional wisdom suggests.

But, the ancient DNA points strongly to a dramatic population shift approaching replacement levels in the early Bronze Age across the Celtic region, largely by the Bell Beaker culture, without much population genetic change thereafter. Population replacement at Bronze Age levels almost surely brought about language shift as well, and the Bell Beaker culture's geographic extent is a decedent match for areas that were historically Celtic linguistically.

If the Bell Beaker culture was linguistically proto-Celtic, why does the language family look so young and why do distinctively Celtic cultural items not appear until the Iron Age?

But, if the Celtic language spread in the Iron Age, what languages were spoken before then by the Bell Beaker people, and, how and why did it spread so broadly with so little population genetic change?

Then again, the Iron Age spread of the Celtic languages was quite a phenomena, with the Continental Celtic languages spreading very far including to Anatolia where the Continental Celtic Galatian language "was spoken in the region of Ankara of what is now central Turkey. Classical writers say that the language is similar to that of Gaul. There is also evidence of invasion and settlement of the Ankara area by Celts from Europe." 

We know from place names and historical accounts that the Galatian language was "once spoken by the Galatians in Galatia mainly in the north central lands of Asia Minor (modern Turkey) from the 3rd century BC up to at least the 4th century AD, although ancient sources suggest it was still spoken in the 6th century. Galatian was contemporary with and perhaps closely related to the Gaulish language." But, no historical texts in that language are known. This community was best known for the Epistle directed to their Christian community by the Apostle Paul which is including in the Bible.

This Iron Age expansion of Celtic languages could also explain some of the otherwise seemingly mysterious correspondences between Celtic Irish culture and language and that of Serbia that is noted at the Old European Culture blog in the sidebar on a regular basis.

The table of contents of the paper is as follows:

Acknowledgements i

Summary v  

1. Introduction 1 

Overview 1 

A Brief Prehistory of Genetics 2 

The Initial Genetic Scaffolding of Human Evolutionary History 3 

What’s in a Genome? 6 

Detecting Human Population Structure in Genomic Data 7 

Next Generation Sequencing and the Genomics Era 10 

Ancient DNA:  The Early Years 13 

A Palaeogenomic Revolution 15 

References 19  

2. The  Takings  of  Ireland:  Punctuated  population  replacement  followed  by  long  term  continuity on Europe’s Atlantic edge 26 

Overview 26 

Introduction 27 

Methods 38 

Results 41 

Conclusions 52 

References 52  

3. The First Arrivals: A genetic insight into Ireland’s Mesolithic inhabitants  61 

Overview 61 

Introduction 62 

Methods 70 

Results 76 

Conclusions 93 

References 98  

4. The Genomics of Megaliths: Origins and structure of Irish Neolithic societies 101 

Overview 101 

Introduction 102 

Methods113 

Results 120 

Conclusions 140 

References 147  

5. Bronze Age Beginnings: Signals of continuity across the Irish Metal Ages and theestablishment of the Insular Atlantic Genome 150 

Overview 150 

Introduction 151 

Methods165 

Results 172 

Conclusions197 

References 201  

6. Final Discussion 205  

Appendix I: Archaeological Contexts and Sampling Information. 209  

Appendix II: Molecular and Bioinformatic Methodology 273 

Electronic Data Tables S1-S7 are available athttps://docs.google.com/spreadsheets/d/1mk9pMMUbChzyW8CwVUYgokVL4iv83WBAKdIf3pWXJnw/edit?usp=sharing

The summary of the paper states:

The thesis submitted here concerns the palaeogenomic analysis of 140 ancient individuals from all periods of Irish prehistory, with a view to providing a working demographic framework for the entirety of the island’s human occupation. This was achieved through the use of Illumina next generation sequencing (NGS) technology, which when combined with skeletal sampling of the petrous temporal bone gives unprecedented access to the surviving endogenous DNA present in archaeological remains. The 93 successful samples were sequenced to an average of 1X coverage, and data was processed following standard NGS pipelines adapted for aDNA research. Diploid genotype calls were imputed for all samples and utilised alongside pseudo-haploid calls for population genetic analyses.

Chapter Two creates an initial demographic scaffold for Irish prehistory based on this data set, established with respect to the larger palaeogenomic narrative that has emerged for the European continent. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. Chapters Three, Four and Five respectively provide more detailed analysis of the Mesolithic, Neolithic and Chalcolithic to Iron Age periods.

Chapter Three uses D-and f-statistics to demonstrate high shared genetic drift between Irish hunter-gatherers and contemporaries from France and Luxembourg. Allelic affinities further suggest that these northwestern hunter-gatherer populations find their origins in more eastern glacial refugia, such as Italy, rather than Iberia. Runs of Homozygosity (ROH) analysis demonstrate the Irish population underwent a severe inbreeding bottleneck, indicating some level of demographic isolation occurred after initial colonisation of the island. Phenotypic and polygenic trait analyses were also carried out, revealing the individuals studied to be dark-skinned and blue-eyed, with relatively inflated estimates of genomic height.

Chapter Four utilises both allelic and haplotypic-sharing methods to establish substantial contributions from both Mediterranean farming groups, whose origins lie in Anatolia, and northwestern hunter-gatherers to the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests that the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies.

Chapter Five addresses the nature of the Chalcolithic and Early Bronze Age transitions in Ireland. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time.