A Genetic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory

[Grace O'Malley]

I'm presently reading this and will add as I go along. The paper can be retrieved from here. By Dr Lara Cassidy.

http://www.tara.tcd.ie/handle/2262/82960


Neolithic individuals were found to place overwhelmingly within haplogroup I2a (Electronic Data TableS5-7), one of the dominant lineages of the European Mesolithic and commonly observed in other western Neolithic populations (Haak et al. 2015; Mathieson et al. 2015; Olalde et al. 2017). 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.


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.

Irish mesolithic samples are indistinguishable from other European HGs.


However, a notable exception is the Palaeolithic sample from El Miron in Spain, belonging to the Magdalenian culture, who, within a majority “red” background, possesses a mosaic of components that dominate in diverse modern populations, such as Papuans, East Asians and Indians. This noisy signal is likely to represent deep pre-glacial population structure between Iberian refugia populations and those further east in Italy and the Balkans (Fu et al. 2016). The signature is also seen to a lesser extent in the earliest Mesolithic sample of the region, but disappears in later Spanish samples. Importantly, Irish Mesolithic individuals do not show any detectable level of this ancestry, displaying profiles more similar to Palaeolithic samples from Switzerland and Italy.

[Grace O'Malley]

Possible echoes of the Roman Empire here. Bedouin component present from Italy and the Balkans. Also present in France, Germany and was seen in Britain but absent by the Medieval period. Ireland bypassed as well as Scandinavia and also not seen in the Basque.


By modern times (Fig. 1.2E), a fourth component of ancestry (beige), found at highest levels in Bedouin populations, has left an impact on European populations, particularly those of Italy and the Balkans. This is most likely an effect of the Mediterranean civilisations that dominated the regions for many centuries, culminating in the Roman empire (27 BC – 395 AD), which saw much of the continent subsumed into this growing hegemony. Indeed, this component penetrates the more isolated northern regions to some degree, including France and Germany. Despite its absence in Medieval individuals, the component is also seen in Britain, where it decreases in scale from Southern England to Scotland. Ireland is bypassed almost entirely, as in Scandinavia. Intriguingly, in Iberia this component is also close to absent in the linguistically divergent Basque region, in sharp contrast to neighbouring populations.

[Grace O'Malley]

Irish Neolithic indistinguishable from Iberian. There is a dramatic eastward shift in the Bronze Age. The Bronze Age populations somewhat resemble present modern-day populations from the same region.


By the Iron Age (Fig. 1.3E) Irish genetic diversity appears to have homogenised, forming a tight cluster indistinguishable from contemporary British individuals, and placing close to modern populations from both islands.

[Grace O'Malley]

In terms of relationships to earlier hunter-gatherer groups, the Mesolithic Irish appear more similar to Italian and Swiss individuals from the Epigravettian and Azilian cultures, rather than the Iberian Magdalenian and later Mesolithic. This suggests the post-glacial colonisation of the island did not occur from a purely Iberian refugia, although these interpretations, based solely on PCA analysis, will be revisited in greater detail in Chapter Three. Importantly, no early Mesolithic samples from Ireland are available, and the possibility of demographic discontinuity within this period cannot be ruled out.

Interesting about the Neolithic population and I find this somewhat fascinating. The HG ydna 12a completely replacing the farmer ydna. This is the paragraph. It brings up the possibility of drift but not sure that is the case? Anyway it is very interesting.


Mitochondrial haplogroup frequencies mirror the autosomal patterns of population replacement with some indigenous input, showing a minority of Mesolithic U5 lineages observed among an abundance of west Asian haplogroups. However, in striking contrast, Y chromosomes show near complete continuity across the transition, with all but two male individuals belonging to the dominant Mesolithic lineage I2a. This may be indicative of unequal contribution by male and female hunter-gatherers to incoming farmer populations, though in a reverse of the usual trend witnessed across episodes of colonisation, that of female continuity and male replacement (Jobling & Tyler-Smith 2003). Alternatively the smaller effective population size and thus increased drift acting on the Y chromosome may be responsible for the differential patterns.

Apparently there is a lack of British and continental northwestern Neolithic samples to compare to.

[Grace O'Malley]

Like what was known previously the Chalcolithic and Early Bronze Age was what brought the biggest change. Ydna changed to R1b-L21 with Rathlin 1 showing inflated sharing to modern populations Irish, Scots and Welsh with somewhat lesser affinity to the English most likely due to Anglo-Saxon migrations. `

Interestingly:


Forthcoming research on the fine-scale population structure of modern Ireland, based on haplotypic analyses, also supports these conclusions. This demonstrates that, while some introgression of European and British haplotypes into Ireland is apparent at horizons of known historical migrations, it is more ancient Celtic population structure that remains the defining characteristic of the Irishpopulation (Byrne et al. submitted).



However, it must be noted that substantial prehistoric migration to the island post-dating the Early Bronze Age from closely related populations of similar genetic makeup, particularly those of Celtic Britain or indeed historic Gaul, may not be detectable. Indeed, the presence of shared tribe names across the various regions in Ptolemy's Geography, hint at such a possibility. Substantial demographic upheavals in Britain and the continent, such as those linked to the spread of Latin and Germanic languages, may have worked to reduce signals of haplotypic and Y chromosomal continuity with Early Bronze Age Ireland, that could have otherwise extended the affinities of Rathlin1 across a much wider region of western Europe. Indeed, for the population of England, as noted above, this is demonstrably the case.

[Grace O'Malley]

Regarding migration of Celts. Possibly from some closely related populations but obviously not answered here.


The only exception may be mass migration from a closely related group, as noted above. Indeed, the most recent expansions of Goidelic from Ireland to Scotland and Brittonic from Cornwall to Brittany, both involving some population migration, are a testament to how regularly such phenomena could occur. Future contributions of ancient genomics to linguistic models will involve the demonstration or disqualification of such events across the Bronze and Iron Ages, a task which demands both denser regional sampling and deeper genome sequencing of ancient individuals.

[J. Ketch]

Apparently R-M222 was found in Iron Age NW Ireland, although I guess that was expected.

[Grace O'Malley]

Still getting to the Iron Age. Was reading about the HGs and then just skipped over a lot of it. (Not greatly interested). Taking a lot of breaks reading.


Northeastern France (Calais-Picardy) provides the most popular candidate homeland for Ireland andBritain’s first farmers (Cunliffe 2013; Mallory 2013). Strong parallels are seen between the Neolithic of southeastern Britain and the continental Michelsberg and Chasséen cultures across the channel (Fig. 3.1C), which share similar round-bottom Carinated Bowl pottery, domesticated faunal assemblages and flint leaf-shaped arrowheads (Whittle 2007; Cunliffe 2013). Carinated Bowls are most abundant along the eastern seaboard of Britain, though they are ubiquitous across the Neolithic of both islands, as are the characteristic arrowheads. Another component of the Neolithic package in Britain and Ireland that has clear connections with northern continental traditions are the large rectangular timber houses that first appear a few generations after pottery and domesticates in southeast England (Sheridan 2013; Cummings 2017). In Ireland, this so-called ‘housing horizon’ begins no earlier than 3,720–3,680 cal BC (Whitehouse et al. 2014; McLaughlin et al. 2016), accompanied by the appearance of cereals. Together, such material culture has been grouped under the the blanket term ‘Carinated Bowl Neolithic’ (Sheridan 2010), and is proposed to have spread along the east coast of Britain, before penetrating into Scotland and crossing over to Northern Ireland, where it travelled southwards down the east and west coasts.

Second strand of Neolithisation from Brittany.


Importantly, later Iberian samples show increased haplotypic and allelic input from the Spanish EN, relative to Irish individuals. This, together with the clear lack of Spanish HG ancestry in the Irish Neolithic (though again potential outliers, such as MillinBay6 exist) argues against any large-scale direct contribution from Iberian populations to the island, via the Atlantic. From an archaeological perspective it is more likely that the Mediterranean-type ancestry within the Irish Neolithic diverged from Spanish groups at the Golfe du Lion, where it spread both inland via the Rhône and westwards toward the coast. Furthermore, admixture with LBK and derivative groups in the north most probably took place,
suggested by the increased haplotype and allele sharing seen with LBK individuals for some Irish samples. The extent of such admixture cannot at present be estimated, but it may be partially responsible for the overall dilution of Cardial ancestry in Irish samples relative to Iberians.

[Grace O'Malley]

The demographic effects of historical and proto-historical migrations on the modern populations of Ireland and Britain have recently been explored using novel haplotypic methods (Leslie et al. 2015, Byrne et al. submitted), revealing the impact of both continental movements into the islands (Anglo-Saxons, Viking, Normans) and movements between the islands, which have have left particularly strong signatures in the east and north of Ireland, as well as in Scotland. Furthermore, Byrne et al. (submitted) have demonstrated that haplotypic clustering methods loosely separate the modern Irish population on the basis of the historical provinces of Ireland (Ulster in the north, Leinster in the east, Munster in the south and Connacht in the west), whose boundaries, typically incorporating geographical barriers such as the Shannon river, have existed in some form since the very beginning of Irish written history. These records also indicate a society which was feudal and dynastic in nature, with great emphasis put male line descent. Indeed, patronyms are still the most common surname type in Ireland, and emerged early in Medieval records. Warfare was common between kingdoms, of which cattle-raiding constituted a key part, given their value as a key economic and sustenance source (O’Connell et al. 2016). It is perhaps remarkable that the modern Irish population has some of the highest incidences of lactase persistence in the world (Gerbault et al. 2011), alongside other variants with possible selective advantages, including mutations involved in iron-retention (Distante et al. 2004) and skin pigmentation (Rajeevan et al. 2012).

[Peterski]

"Byrne et al. (submitted)" - which study is that?


Irish Neolithic indistinguishable from Iberian.

This is what I was telling long ago, that Irish (and British in general) Neolithic was more like Iberian Neolithic than like Italian Neolithic.

[Grace O'Malley]

"Byrne et al. (submitted)" - which study is that?



This is what I was telling long ago, that Irish (and British in general) Neolithic was more like Iberian Neolithic than like Italian Neolithic.

Haha but you haven't read the paper or noted the quotes above. The Irish and British Neolithic's homeland is mostly Northeastern France with a secondary flow from Brittany. Irish Neolithic lacks the Spanish HG ancestry that is in Spain and in their Farmer population. So as the paper says "this, together with the clear lack of Spanish HG ancestry in the Irish Neolithic (though again potential outliers, such as MillinBay6 exist) argues against any large-scale direct contribution from Iberian populations to the island, via the Atlantic."

But all Western Farmer populations are similar to Sardinians.

I'm reading now about the Bell Beakers and R1b which appeared in both Ireland and Britain in the late Chalcolithic and Early Bronze Age while R1b did not start appearing in the Iberian Peninsula until the Late Bronze Age. Also Ireland and Britain L21. So again no direct population movement from Iberia.

I'll add anything else that I find interesting later on.

[Grace O'Malley]

"Byrne et al. (submitted)" - which study is that?




Not published yet. Woohoo something else for me to look forward to. :)

[Grace O'Malley]

Just to add to what I said earlier about the earlier Bell Beaker arrival in Britain and Ireland.


The majority of R1b-M269 lineages seen in Bell Beaker and Bronze Age populations from France, the Netherlands, Britain and Ireland belong to P312, which shows a modern distribution focused west of the Rhine Basin (Myres et al. 2011). The relatively late (post-Beaker) appearance of this marker in Iberia, in comparison to Ireland and Britain, suggests the arrival of R1b haplogroups to the islands was not catalysed by direct population movement from Iberia, but instead via a more northern Beaker group.
Notably, while absent in contemporaneous individuals from Iberia, R1b-P312 lineages are observed in Beaker samples from southern France and northern Italy (dating to circa 2,500-1,900 BC), indicating the haplogroup was not just restricted to the very north of Europe, but also areas associated with Mediterranean Beaker networks.

[Grace O'Malley]

The paper noted that only the subclade of R1b L21 is only observed in British and Irish samples and also commented on the continuity from this time to the present day Irish population. Britain does not show the same level of continuity with non-P312 subclades of R1b and the only male Anglo-Saxon sample available being I1 widespread in Nordic countries today.

And now M222.


Within Ireland a large diversity in R1b-DF13 subclades is seen in both the Bronze and Iron Ages, with an expectedly higher number of downstream mutations observed for Iron Age samples (See Electronic Data Table S5). Notably, all northwestern Irish Iron Age individuals sampled (Ballyglass44, Derrynamanagh08 and Derrynamanagh09) were seen to belong to the R1b-M222 subclade or a lineage leading directly to it. This haplogroup peaks in northwestern Ireland today and has been previously associated with the early Medieval Uí Néill dynasty of the region (Moore et al. 2006). Intriguingly, the two southern Iron Age individuals sampled, Courtmacsherry37 and Ballybunnion54, also both share a subclade, R1b-CTS3087. Given the known emphasis placed on patrilineal descent in Gaelic Ireland, denser surveys of Iron Age Y chromosomal variation on the island may contribute greatly to the understanding of territorial boundaries and patronymic surname distributions that were recorded during the early historical period.

[Grace O'Malley]

These paragraphs about mtdna are interesting. The Eastern HG mtdna brought to Ireland obviously were brought in by Bell Beaker females.



Most noticeably, in northwestern and central Europe, Ireland included, a small increase in Mesolithic U lineages is seen between the Neolithic and Bronze Age, including previously unobserved U5a1, U2e and U4 haplogroups, common in Latvian, Ukrainian and Russian HG individuals, as well as later steppe cultures (Figs. 2.1 and 4.3). In Iberia, an increase in U lineages is also seen across the transition, although these do not show any particular eastern affiliations. Remarkably, no U lineages are observed in Late Neolithic and Bronze Age samples from Scandinavia, nor have they been yet observed in individuals (n=6) from the preceding Neolithic TRB culture of Sweden (Skoglund et al. 2014; Mittnik et al. 2017), despite their prevalence in Mesolithic and Neolithic hunter-gatherer groups of the region.


Increased frequencies of mtDNA haplogroup I are also seen in several post-Neolithic populations from northern and central Europe, including Bronze Age individuals from Britain, Ireland, Denmark and Germany. Interestingly, high incidences of the lineage are seen in Hungarian Bell Beaker samples,although in other Bell Beaker populations the haplogroup is absent or extremely rare. The heterogenous nature of Bell Beaker culture is also seen in the distribution of haplogroup X, present in Atlantic Beaker populations, but absent in groups further east, and haplogroup H, seen at substantial frequencies in all Beaker groups with the exception of the British cohort. In this respect, the British Beaker population also displays remarkable discontinuity with the preceding Neolithic and succeeding Bronze Age of the island.

[Grace O'Malley]

Measuring the amount of Steppe ancestry


This method gives a range of 78-85% steppe-derived ancestry in the Corded Ware population, close to the value of 75%, reported in Haak et al. 2015. The majority of Irish Chalcolithic and Bronze Age samples fall between the range 48% and 64%, with highest values (>58%), observed for a number of northern (Rathlin1, Rathlin3, Pollnagollum90, Grange10) and eastern samples (Keenoge3, Blackhill32). This pattern can be visualised in Fig. 4.4D and will be discussed further in the following section. Similar ranges were observed for Únětice (53-65%) and Bell Beaker (42-56%) groups, again matching previously published estimates (Haak et al. 2015). This suggests Ireland, despite its peripheral position, did not receive a diluted level of steppe ancestry relative to populations within the Corded Ware contact zone, again emphasising the extensive nature of the migrations that occurred into the island at this horizon. In contrast, the lowest levels of steppe ancestry were calculated for another peripheral Atlantic population, the Portuguese Bronze Age (Martiniano et al. 2016), where it featured at a proportion of only 14-16% (Fig. 1.2C).

Reduced Steppe ancestry was seen in several southwestern individuals. for whom substantially reduced steppe ancestry was estimated (24% in Labbacallee212 and 36-39% in RoughanHill468, Killuragh1 and Poulnabrone01), a phenomenon that is apparent in both ADMIXTURE (Figs. 1.2C and 4.4D) and PCA (Fig. 1.3D) plots.

[J. Ketch]

The overall suggestion in the paper seems to be that there's overwhelming continuity in Ireland between the Early Bronze Age and Present, although it's a little light on details or answers about the levels or potential sources of post-Bronze Age admixture.

[Peterski]

(...)

I haven't read the paper yet, I was relying on your post ("Irish Neolithic indistinguishable from Iberian").

Is Irish Neolithic distinguishable from Italian or Swedish Neolithic? I guess it is if they mentioned Iberian.

====

It looks like a sort of Atlantic Neolithic that was a similar population from British Isles - France - Iberia.

Later, it was replaced by Steppe ancestry to a larger degree in the north and to a lesser in the south.


Reduced Steppe ancestry was seen in several southwestern individuals. for whom substantially reduced steppe ancestry was estimated (24% in Labbacallee212 and 36-39% in RoughanHill468, Killuragh1 and Poulnabrone01), a phenomenon that is apparent in both ADMIXTURE (Figs. 1.2C and 4.4D) and PCA (Fig. 1.3D) plots.

So these Bronze Age "reduced Steppe outliers" have as much as 61-76% (!) Neolithic Irish ancestry?

They are going to score like modern Spanish people, or even more southern, in G25 and GEDmatch.

====

Edit:

Wait, this is about % of Steppe, not % of Bell Beaker. OK, they will probably score like modern French people.

Is there an estimate showing what % of Bell Beaker + what % of Irish Neolithic these 4 outliers samples had?

[Grace O'Malley]

Yes there does seem to be continuity in the Irish. Bolded bit is intriguing.


Irish Iron Age samples extend the entire range of Irish variation on PC2, suggesting substantial continuity with the modern population. Irish Early Bronze Age samples show a more constricted distribution closer to the center of the plot, but still exhibit a systemic shift towards Irish Iron Age and modern populations, particularly those from individualised burials. The most parsimonious explanation for such observations is direct continuity between the Chalcolithic/Early Bronze Age and modern period in Ireland, with much of the haplotypic variation explained by PC2 forming in the intervening millennia, in a similar manner as suggested for Wales in PC3. While migration may be partially responsible for this structure, it is worth noting that the Irish Iron Age and modern population typically extends away, rather than towards, any potential external sources of variation in the dataset, including a contemporary Iron Age population from Britain, the most likely source of migration into Ireland between the Bronze Age and Early Christian periods. However, several exceptional Irish Iron Age samples exist, returned to in later sections.

[Grace O'Malley]

So these Bronze Age "reduced Steppe outliers" have as much as 61-76% (!) Neolithic Irish ancestry?

They are going to score like modern Spanish people, or even more southern, in G25 and GEDmatch.

====

Edit:

Wait, this is about % of Steppe, not % of Bell Beaker. OK, they will probably score like modern French people.

Is there an estimate showing what % of Bell Beaker + what % of Irish Neolithic these 4 outliers samples had?

I'll see later. Very large paper and just trying to get through all of it. :) To be honest I feel like a drink now. :p

[Peterski]

These low Steppe samples are all from Munster right?:
(this would imply SW Ireland was Neolithic refugium)

Labbacallee212
RoughanHill468
Killuragh1
Poulnabrone01

Did they model them as Dutch Beaker + Irish Neolithic mix?

Also, did French Beakers settle Ireland, or Dutch Beakers?


I'll see later. Very large paper and just trying to get through all of it. :) To be honest I feel like a drink now. :p

OK keep reading & posting! I don't have time to read it now.

[Grace O'Malley]

These low Steppe samples are all from Munster right?:
(this would imply SW Ireland was Neolithic refugium)

Labbacallee212
RoughanHill468
Killuragh1
Poulnabrone01

Did they model them as Dutch Beaker + Irish Neolithic mix?

Also, did French Beakers settle Ireland, or Dutch Beakers?

Yes Munster SW Ireland so some Neolithic survival but later genomes more Steppe. I'll continue with the paper but they say a bi-modal entry into Ireland so I'd say yes both groups.

[J. Ketch]

These low Steppe samples are all from Munster right?:
(this would imply SW Ireland was Neolithic refugium)

Labbacallee212
RoughanHill468
Killuragh1
Poulnabrone01

Did they model them as Dutch Beaker + Irish Neolithic mix?

Also, did French Beakers settle Ireland, or Dutch Beakers?



OK keep reading & posting! I don't have time to read it now.
It alluded to Ireland being suggested as a mix of Atlantic Beakers from Brittany and Dutch Beakers, or Atlantic Beaker influenced first, which was then supplanted by a wave of Dutch Beakers from the North/East (via Britain, which was wholly Dutch Beaker influenced). That's something I didn't know about.

[Grace O'Malley]

More about Britain.


In contrast to the gentle gradient of ancient Irish variation, British and continental individuals show a more punctuated distribution along PC2 (Fig. 4.6B-C), forming two clear clusters at both ends of modern British variation. Anglo-Saxons fall with southeastern English variation in this and all other PC considered, alongside a Nordic Iron Age sample, reflecting the large genetic contribution of Germanic migrations to this part of the island (Leslie et al. 2015; Schiffels et al. 2016). Iron Age Britons comprise another tight grouping at the opposite end of British variation, emphasising the admixed nature of the modern population (Leslie et al. 2015; Martiniano et al. 2016; Schiffels et al. 2016). Early snapshots of continental introgression events may be represented by two samples that fall midway between the two groups, one from an Anglo-Saxon context (O3), which was reported as admixed in the original study (Schiffels et al. 2016), and the second from a Roman British population (6DT23), another member of which was demonstrated to be of likely Middle Eastern origin (Martiniano et al. 2016). Notably, no Irish Iron Age samples are seen to fall into this region of the PC space.

https://i.imgur.com/ZMSBsK1.png
https://i.imgur.com/6rt9WH1.png
Figure 4.6. PCA of haplotypic similarity of ancient and modern individuals from Britain and Ireland. Modern individuals are coloured by geographical region (labelled in panel B), based on fineSTRUCTURE clustering assignments from Byrne et al. (submitted) Ancient individuals are outlined in black and coloured following the same geographical key. Six continental ancient samples are also included in grey. A) plots PC1 and PC3, which segregate the modern populations of Orkney and Wales from the remained of the dataset. A magnified image of ancient individuals is also shown. B) plots PC2 and PC6, which provide the most accurate geographical representation of the two islands. C) plots PC2 and PC4, the latter of which serves to distinguish Chalcolithic and Bronze Age samples from the remainder of the dataset.

[J. Ketch]

This part was most interesting to me.

Haplotypic exploration of ancient and modern populations from Britain and Ireland

Recent studies have utilised patterns of haplotypic sharing among modern British and Irish individuals to great effect, in order to explore finescale population structure within the islands (Leslie et al. 2015), Byrne et al. submitted). A similar analysis is performed on the same datasets here, with the novel addition of imputed genotypes from ancient Irish, British and northern European samples. The resulting components of variation, reveal not only spatial, but temporal trends in haplotypic affinity from the Irish Chalcolithic period onwards (Fig. 4.6). These are used here to visualise the ancestral similarities and differences found between and within Ireland’s Early Bronze Age, Iron Age and modern populations.

Isolation at the British Peripheries

Several of the major principal components (PCs) identified explain little of the variation present in the ancient dataset. This includes the first and third PCs (Fig. 4.6A), which respectively segregate the populations of Orkney and Wales, while compressing the remainder of modern and ancient variation. The presence of strong haplotypic differentiation between these populations and the rest of Britain was reported in the original publication of the dataset (Leslie et al. 2015), and, in the case of Orkney, has been explained as the result of isolation and of Norse settlement. Notably, PC5 also solely describes Orcadian variation, and, alongside PC1, is not considered in further results and discussion.
The driving factor behind haplotypic divergence of Welsh populations is less clear. However, we note here that, alongside modern individuals from the border regions of Wales, the entire Irish Early Bronze Age population (several southwestern samples excluded) is also pulled away from the main cluster and in the direction of Welsh individuals on PC3 (Fig. 4.6A), suggesting they possess some haplotypic variation found in Wales that is absent in the remainder of the dataset. Surprisingly, the same increased affinity is not seen for the Iron Age Britons of Yorkshire and southeastern England, as may have been expected given both the persistence of Brittonic Language and culture in Wales after the Anglo-Saxon migrations, and the previously demonstrated affinity of the Yorkshire individuals to the modern Welsh population (Martiniano et al. 2016). This could indicate that the prolonged regional isolation of Wales, aided by its mountainous geography, stretches into the Bronze Age period, allowing the build up of the extensive haplotypic diversity seen in PC3.

The Establishment of Irish Haplotypic Diversity

The second component of variation (Fig. 4.6B-C) is unique in that it explains a large amount of variation present in both ancient and modern individuals. This corresponds to the primary split seen in fineSTRUCTURE analysis by Byrne et al. (submitted), which segregates Ireland and Britain into two distinct genetic islands, capturing what is defined as an Anglo-Celtic cline. Western Ireland and southeastern Britain form the two extremes of this component, with the Scottish population bridging the gap between the two clusters. Strikingly, ancient samples also separate out along this axis, with Irish individuals from both the Early Bronze Age and Iron Age periods falling further towards modern Irish variation than their British and continental counterparts (Fig. 4.6B-C).
Irish Iron Age samples extend the entire range of Irish variation on PC2, suggesting substantial continuity with the modern population. Irish Early Bronze Age samples show a more constricted distribution closer to the center of the plot, but still exhibit a systemic shift towards Irish Iron Age and modern populations, particularly those from individualised burials. The most parsimonious explanation for such observations is direct continuity between the Chalcolithic/Early Bronze Age and modern period in Ireland, with much of the haplotypic variation explained by PC2 forming in the intervening millennia, in a similar manner as suggested for Wales in PC3. While migration may be partially responsible for this structure, it is worth noting that the Irish Iron Age and modern population typically extends away, rather than towards, any potential external sources of variation in the dataset, including a contemporary Iron Age population from Britain, the most likely source of migration into Ireland between the Bronze Age and Early Christian periods. However, several exceptional Irish Iron Age samples exist, returned to in later sections.

The homogenisation of British population structure through admixture

In contrast to the gentle gradient of ancient Irish variation, British and continental individuals show a more punctuated distribution along PC2 (Fig. 4.6B-C), forming two clear clusters at both ends of modern British variation. Anglo-Saxons fall with southeastern English variation in this and all other PCs considered, alongside a Nordic Iron Age sample, reflecting the large genetic contribution of Germanic migrations to this part of the island (Leslie et al. 2015; Schiffels et al. 2016). Iron Age Britons comprise another tight grouping at the opposite end of British variation, emphasising the admixed nature of the modern population (Leslie et al. 2015; Martiniano et al. 2016; Schiffels et al. 2016). Early snapshots of continental introgression events may be represented by two samples that fall midway between the two groups, one from an Anglo-Saxon context (O3), which was reported as admixed in the original study (Schiffels et al. 2016), and the second from a Roman British population (6DT23), another member of which was demonstrated to be of likely Middle Eastern origin (Martiniano et al. 2016). Notably, no Irish Iron Age samples are seen to fall into this region of the PC space.
The compression of Iron Age British haplotypic variation close to the zero coordinate, relative to that of Ireland, suggests that PC2 may not effectively explain the majority of diversity present within this group, possibly due to their lack of representation within the larger admixed modern British cohort. In this respect, PC2 is perhaps best considered as explaining the distribution of Irish-related haplotypic variation in both modern and ancient individuals, which acts as somewhat of an imperfect proxy for Celtic ancestry in the neighbouring island of Britain, counterbalancing the Anglo-Saxon input. We caution that such a phenomenon may cause similar placement of individuals for unrelated demographic reasons. For example, the placement of Northern Irish and Scottish individuals between the two islands is proposed to be the result of numerous migrations in both directions, including the Gaelicisation of Scotland circa 600 AD and the later Ulster plantations (Byrne et al. submitted). It is notable that no PC segregates Scotland from the rest of the dataset, suggesting the modern population has been mainly borne from admixture, rather than isolation, the reverse of what is proposed for Wales. Indeed, the more muted and systematic shift towards Irish variation of Welsh populations, whose diversity is better captured in PC3 and PC6, may represent more ancient shared Celtic ancestry between the groups. The tight clustering of three German Late Neolithic and Bronze Age individuals at the edge of ancient Irish variation, alongside the Iron Age British population, could also be due to a similar effect of older shared ancestry. Such an interpretation may find some temporal grounding in the differential placement of a Nordic Late Neolithic individual further towards the Germanic extreme of the plot.

Haplotypic diversification after the Iron Age

PC6 shows the reverse trend to PC4, compressing ancient variation along the zero line, while allowing modern variation from all populations to fan out across the axis (Fig. 4.6B). This spread of modern haplotypic diversity shows something of a north-south trend, as identified in Byrne et al. (submitted). South Welsh and Cornish populations exhibit the largest amount of haplotypic variation and are followed on the axis by populations from southern Ireland, Devon and Border regions of Wales. Populations from the northern regions of Wales, England and Ireland, as well as Scottish groups, form the other extreme of PC6, with compression of the eastern populations of both islands apparent due to the homogenising effects of Anglo-related admixture (Byrne et al. submitted).
The clustering of ancient samples along the zero line suggests that, in Ireland at least, the majority of the geographical variation captured by PC6 postdates the Iron Age period. That said, a subtle shift towards northern groups is apparent in the Irish Iron Age, relative to both the preceding Bronze Age and British Iron Age. This is particularly apparent for individuals falling further towards Irish modern variation on PC2, and suggests some of the diversification captured by PC6 was already underway at this point in time. Two early modern Irish individuals from the Plantation period, postdating the Late Iron Age by roughly a millennia, are also plotted here and show extremely similar placement to modern individuals from the same regions, falling further ‘north’ and ‘south’ of the preceding axis of Iron Age samples. Further sampling of the British Iron Age and Medieval periods, specifically in Wales, will be required to interpret how such patterns are related to the clear divergence of northern and southern Celtic-speaking populations on the neighbouring island of Britain. Indeed, this novel preliminary analysis highlights the powerful temporal anchors ancient genomes can provide to spatial trends of regional genetic variation.

[Grace O'Malley]

https://i.imgur.com/HkI53PF.png
https://i.imgur.com/G1jq4v6.png
https://i.imgur.com/WuXFlIe.png

[Grace O'Malley]

Still going through this. Apparently these two from close to Drogheda are possibly from Britain.


The most likely candidate migrants from an archaeological perspective are two eastern individuals from Knowth (175-50 cal BC; 86-252 cal AD), whose burial rites are common in Britain and almost unknown in Ireland during the period (McGarry 2010). This interpretation is supported by their placement away from the main distributions of Irish Iron Age and modern variation. However, it must be noted that a number of other Irish Iron Age individuals place even further towards the British cluster, including three unrelated samples from Ballyglass Middle, the only Irish Iron Age site sampled that shows clear ancestral homogeneity among burials. The site itself is unusual in the relatively early date retrieved from unburnt bone (80-420 cal AD), at a time cremation was ubiquitous in Ireland. Two individuals from Derrynamanagh also show increased British affinities, but again the site shows wide differentiation on PCs 2 and 4, despite the close kinship among a number of samples (not included here). Previously undetected relatedness is also seen here between Derrynamanagh04 and Derrynamanagh05, later confirmed through IBD kinship analysis, which revealed the pair to be fourth degree relatives (Appendix II).

[Grace O'Malley]

Supplementary sheets are here.

https://docs.google.com/spreadsheets/d/1mk9pMMUbChzyW8CwVUYgokVL4iv83WBAKdIf3pWXJnw/edit#gid=833626537

I hope some of these will get into the G25 or be uploaded somewhere so that we can have a better look.

[Grace O'Malley]

As these three streams successively swept into Europe, one clear recurring is the persistence of older ancestries in the peripheral regions. For example, in Iberia and Scandinavia, Mesolithic and Neolithic ancestries and material cultures are seen to survive and contribute substantially to the later populations. Remarkably, Ireland appears to represent a microcosm of this phenomenon, with the remote southwest seemingly harbouring Irish Mesolithic ancestry long into the Neolithic period, as well as inflated levels of Neolithic ancestry together with megalithic traditions many centuries after the arrival of metallurgy, individualised burial and steppe-related populations. This apparent isolation of the western regions in prehistoric times follows closely with what we observe across written Irish history and indeed in the modern day country, where the west coast represents one of the last bastions of Celtic languages. Haplotypic analyses of the modern population also reveal similar trends of western diversity through isolation and eastern homogenisation through migration, mainly from Britain. Importantly, the archaeological identification of isolated relic populations in Ireland throughout the prehistoric periods may be hindered by small population sizes and lack of surviving material culture, but could be uncovered through large-scale genomic surveys. Indeed, more visible archaeological populations may yield individuals with a recent ancestor belonging to the ghost population, as appears to be the case for Parknabinnia675.

[Imperator Biff]

Fucking cunts rembargoed the thesis until 2023.


Are these people for real? What a pisstake. We’ve been waiting since 2017 for this.

[Imperator Biff]

https://pdfhost.io/search?text=Lara%20Cassidy

Anyone who wishes to read the pdf can do so here.


Also, and it has to be said, fuck trinity college. :cool:

[Leto]

Just tell me guys — are the Irish really Bronze Age Celts? :D

[Jana]

Just tell me guys — are the Irish really Bronze Age Celts? :D

Celts migrated to British Isles in Iron Age as far as I know.

[Leto]

Celts migrated to British Isles in Iron Age as far as I know.
So they weren't the first Indo-Europeans over there?

[Jana]

So they weren't the first Indo-Europeans over there?

Exactly. Bell Beakers came before them and left biggest genetic imprint in Irish. I suppose they spoke arhaic NW Euro languages, something older than Celtic and Germanic.

[Grace O'Malley]

Fucking cunts rembargoed the thesis until 2023.


Are these people for real? What a pisstake. We’ve been waiting since 2017 for this.

You're joking. Does all this have to be deleted?

Just checked and it is now embargoed until 2023. How crazy is that?

[Grace O'Malley]

Anyway this conclusion by alan from Anthrogenica is very good. The big problem is missing samples from France and Britain when this thesis was published.


I saved it before it was embargoed :0) Its actually a very good read. Took me many hours to read it as im a sort of slow chewing it over as it goes reader who pauses for thought a lot. Only shame is it was written before that French data was available. Author was very cautious and didnt overextend in terms of conclusions. If the data wasnt available and no firm conclusions were possible, it was stated. Nevertheless I think her conclusions are right. Most interesting.

1. The Irish Mesolithic population probably came via Britain across the dry channel from a NW European Mesolithic microlithic groups (guess likely northern France or Low Countries) who probably derived from late palaeolithic groups around Switzerland who in turn derived mostly from western Gravettian roots (similar to Villabruna) not Magdellanian ones as usually presumed. It differs from both Iberian WHG and north-eastern WHG dominated groups. Author actually has a lot of v interesting things to say about this period.

2. The Irish farmers probably came from France where there was a melting pot between Cardial elements who came up to the Loire and LBK inputs who reached the Norman-Breton border. They were mixing for a long period prior to migration with the Cardial element apparently dominating genetically despite no cardial pottery in the north of France. The detail of this is still to be teased out because French data wasnt available. Seems to suggest (as archaeology does) that it mostly came from Britain although doesnt rule out the possibility that some came direct from NW France. Male lines similar to Mesolithic (as is true in the UK and France).

3. As expected it shows a big influx of steppe genes with the beaker and early bronze age. Total turnover of yDNA to P312 (almost all proven L21). There was for some time a difference between most of the island and the SW corner which retained more farmer DNA. Lack of samples from likely Irish beaker sources in Britain and northern France etc hampered working out actual percentage of displacement as the percentage of farmer in them was unknown. Seems to think at least a small percentage of the farmer was local but cannot be sure.

4. Modern genetic bedrock and yDNA largely set by the early bronze age but there is a little change towards British direction in the Iron Age and some individuals who probably migrated from there. Again, its impossible to work out how much continuity v migration when there is no comparable data from western Britain to work with. However, if there was a significant Iron Age incursion then it would have had to come from a population that was very like the existing Irish one. Problem is, it is strongly to be suspected that western seaboard populations in Iron Age Britain would have been very similar.

Basic lesson. Need a bigger sample and need to have big samples from Britain and France to progress further.

[Grace O'Malley]

Just tell me guys — are the Irish really Bronze Age Celts? :D

Basically Bronze Age Bell Beakers and highly likely some Celtic input at a later date. I'd say Northern France, Britain need to be studied to get all the pieces of the puzzle.

[Grace O'Malley]

As large amounts of text from the thesis are here and it has now been embargoed until 2023 does anyone know if this thread has to be deleted?

[Grace O'Malley]

Just tell me guys — are the Irish really Bronze Age Celts? :D

Someone on Eurogenes posted this. It's most likely very accurate.

So, a trickle from Hallstatt(indirectly), and a sprinkle of Viking, apart from that modern Irish are essentially Rathlin island. Love it.

[Grace O'Malley]

Eurogenes post linked here if anyone wants to read it.

http://eurogenes.blogspot.com/2020/05/genetic-continuity-and-change-in.html

[J. Ketch]

The Irish are almost certainly majority descended from Early Bronze Age Irish/British (quite comfortably), but I still think the continental Celtic + Germanic admixture since that point is fairly significant.

[Grace O'Malley]

The Irish are almost certainly majority descended from Early Bronze Age Irish/British (quite comfortably), but I still think the continental Celtic + Germanic admixture since that point is fairly significant.

With the way this embargo stuff is going what's the chance of getting a good study from Cassidy on the later periods i.e. late Bronze up to Late Medieval? Apparently it is mostly likely to do with unpublished studies from what Generalismmo is saying. So that's the only positive I can take that there are some studies coming out.

[Aren]

I'm puzzled by the "Bedouin-like" component that pops up in modern day Europeans, even in France, Germany and Britain. She argues that it's related to Roman admixture which might be true but earlier in the paper she mentions this


Strikingly, while a gradual increase in European hunter-gatherer ancestry (red) can be seen through time in the Hungarian Middle and Late Neolithic, this is not mirrored in Linearbandkeramik (LBK) populations who expanded further North via the Danubian route. Instead these culturally homogenous groups, show minor components of ancestry present in West Asia at the time (coloured teal and beige). These west Asian components also appear as larger minority contributions in the Greek Late Neolithic and to a lesser extent in Hungarians. In contrast, the earliest Spanish Neolithic individual, descended from populations who followed a Mediterranean route of expansion, is devoid of these smaller ancestries, presenting a majority early European farmer genome in orange, with marked European hunter-gatherer introgression. Overall, this heterogeneity suggest persistent contacts with West Asia after the initial colonisation of the Balkans, as well as differential interactions with local hunter-gatherer populations among Neolithic groups in Europe

It's very plausible that this West Asian shift actually made its way to Northern/Western Europe through Central European farmers, probably indirectly via La Tene/Hallstatt. And in the case of Britain probably due to conact with the continent much later on during the modern era.

[Grace O'Malley]

I'm puzzled by the "Bedouin-like" component that pops up in modern day Europeans, even in France, Germany and Britain. She argues that it's related to Roman admixture which might be true but earlier in the paper she mentions this



It's very plausible that this West Asian shift actually made its way to Northern/Western Europe through Central European farmers, probably indirectly via La Tene/Hallstatt. And in the case of Britain probably due to conact with the continent much later on during the modern era.

Just putting that paragraph here.


Possible echoes of the Roman Empire here. Bedouin component present from Italy and the Balkans. Also present in France, Germany and was seen in Britain but absent by the Medieval period. Ireland bypassed as well as Scandinavia and also not seen in the Basque.


By modern times (Fig. 1.2E), a fourth component of ancestry (beige), found at highest levels in Bedouin populations, has left an impact on European populations, particularly those of Italy and the Balkans. This is most likely an effect of the Mediterranean civilisations that dominated the regions for many centuries, culminating in the Roman empire (27 BC – 395 AD), which saw much of the continent subsumed into this growing hegemony. Indeed, this component penetrates the more isolated northern regions to some degree, including France and Germany. Despite its absence in Medieval individuals, the component is also seen in Britain, where it decreases in scale from Southern England to Scotland. Ireland is bypassed almost entirely, as in Scandinavia. Intriguingly, in Iberia this component is also close to absent in the linguistically divergent Basque region, in sharp contrast to neighbouring populations.

But why is it not in Irish, Scandinavians and Basque? That's why it is intriguing and she specifically mentions a "Bedouin" component not West Asian.

Wouldn't those populations you mentioned have had some impact on Irish, Basque and Scandinavians also?

Edit: Bedouin component not seen in Medieval individuals and reading it again it looks like she is saying this component is in today's populations but not in Irish, Scandinavian and Basque.

[Imperator Biff]

https://irishgenomics.blogspot.com/2020/05/a-genomic-compendium-of-island.html?m=0

For anyone who is interested in downloading or reading the paper in case other links get taken down.

[Aren]

Just putting that paragraph here.





But why is it not in Irish, Scandinavians and Basque? That's why it is intriguing and she specifically mentions a "Bedouin" component not West Asian.

Wouldn't those populations you mentioned have had some impact on Irish, Basque and Scandinavians also?

Edit: Bedouin component not seen in Medieval individuals and reading it again it looks like she is saying this component is in today's populations but not in Irish, Scandinavian and Basque.

I think David answered that to you on another forum, admixture runs are simply not that reliable.

I'm not gonna look more into this it seems completely pointless.

[Grace O'Malley]

It's largely an artifact of the ADMIXTURE method.

What often happens is that the program creates clusters based on the most isolated/drifted populations, and then the other, more outbred groups are given membership in near and far related clusters to compensate for this problem.

So you really have to check properly whether the appearance of some Middle Eastern or even South Asian admixture reflects recent gene flow. Remember that bullshit with Dienekes' Gedrosia cluster? Same thing.

Very interesting and I think this applies to the commercial companies also.

[Coastal Elite]

"A 2,000 year delay occurred between the Mesolithic occupations of Britain and Ireland. Requirement of seafaring knowledge may have been the main hurdle for any new arrivals, though the island’s dense forest cover and impoverished array of post-glacial flora and fauna may not have encouraged permanent settlement (Woodman 2015). When Ireland was eventually colonised, it was most probably from a British source, with the earliest Irish stone toolkits, geometric microliths (Fig. 1.1C), broadly resembling those that emerged in the Britain during its Later Mesolithic period. An accidental colonisation event is unlikely, given the seemingly deliberate introduction of wild boar to the island at the time (Mallory 2013). A suggested origin of these immigrants is the now submerged landscape surrounding the current Isle of Man, visible from Ireland, where rising sea levels would have forced population relocations. Continued communication between new colonies and their flooding homelands may have been compromised, which could provide explanation for the lack of parallel development between the Irish Early Mesolithic and any contemporary British population (Mallory 2013), although outside contacts cannot be ruled out."

Does anyone else agree with the Isle of Man origin for the first inhabitants of Ireland during the Mesolithic period? It quotes from Mallory 2013 but this is also mentioned in his 2018 reprint of Origins of the Irish so I assume it is the mainstream view. Isle of Mann, Scotland, and Wales have similar toolkits to Ireland from the era so all are probable origin locations.

[tipirneni]

The Megalithic period seems to be connected with similar monuments all over the world in Malta, Italy, Egypt, India etc.. There is presence of I2a and H2a haplogroup. Even H1/3 were present in Wales probably will show up in Ireland in this period upon further digging. These show the Mesolithic and Neolithic people were connected to world wide movement not just some local variation until the arrival of R1b Steppe group.

Cassidy showed these samples in the latest paper which I showed in another post
https://www.theapricity.com/forum/showthread.php?345560-Was-Newgrange-Neolithic-site-an-ancient-Hindu-shrine