Imputed genomes and haplotype-based analyses of the Picts. Preprint.

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​Abstract

The origins and ancestry of the Picts of early medieval Scotland (ca. AD 300-900) has been traditionally seen as a problem, prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century AD resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the Pictish genomes within the Iron Age gene pool in Britain and demonstrate local biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-ByDescent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in the Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of female endogamy, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and presentday groups of the UK.



Allele frequency-based genomic affinities in ancient Britain155 To investigate population affinities of the individuals from Pictland, we performed Principal 156 Component Analysis (PCA) and ADMIXTURE analyses on a dataset comprising present-day Europeans, 157 the newly imputed genomes and the imputed ancient genomes from Margaryan et al. (9) (S7 Table). 158 The PCA shows that the ancient individuals from Britain broadly fit within present-day diversity (Fig 159 2A). However, we notice some variability among these individuals as BAL003 and LUN004 fall within 160 the modern Welsh cluster, but with BAL003 being notably closer to the present-day Scottish, 161 Orcadians, English and Northern Irish clusters, suggesting some degree of genetic differentiation162 amongst individuals from Pictland. The Iron Age and Roman period individuals from England are 163 spread across the modern English, Northern Irish, Scottish and Welsh clusters. Four ancient Orcadians 164 from the Iron and Viking Ages fit with present-day Welsh, Northern Irish and Scottish populations. 165 However, two Viking Age Orcadians (VK204 and VK205) are intermediates between the British and 166 Scandinavian clusters, consistent with previous results finding evidence of admixture in these 167 individuals between British-like and Scandinavian-like ancestries (9). The early medieval individuals 168 from England are intermediate between modern English people and Scandinavians, which is 169 consistent with various degrees of admixture between Iron Age groups from England and immigrants 170 from northern/central Europe (14,17). These results agree with the pseudo-haploid-based analyses of 171 the BAL003 and LUN004 genomes, showing a broad affinity to modern western Europeans (
Click to expand...
S1.3 Text, 172 S10, S12-S15 and S18 Figs), but with a much-improved resolution.




Haplotype-inferred genetic structure in early medieval Britain179 Haplotype-based methods have been shown to outperform conventional unlinked SNP approaches in 180 the detection of population substructure (41). To make use of the additional power provided by 181 linkage disequilibrium, we conducted a FineSTRUCTURE clustering analysis and Identity-By-Descent 182 (IBD) analysis on the imputed diploid dataset. Our analysis show that the genomes from Lundin Links 183 and Balintore form a genetic cluster together with genomes from the Iron Age and Roman period from 184 England (except 6DT3 - who instead show strong affinity to western/central Europe or Scandinavia185 based on the IBD analysis, Fig 3, S1.6 Text - and I0160), and from the Late Iron Age to Viking Age from 186 Orkney (except VK204 and VK205 who carried susbstantial Scandinavian-like ancestry; ‘Pop12’, S25187 Fig, Fig 3). Included in this cluster are also Viking Age individuals from Britain, Iceland and Scandinavia; 188 the latter likely corresponds to individuals buried in Scandinavia but whose parents were from a 189 British-like gene pool, consistent with results in Margaryan et al. (9). Based on outgroup-f3, the190 individuals from Orkney, Scotland, and England, dated from the Iron Age to medieval period are 191 symmetrically related to each other (S5 Fig). However, we also note that BAL003, but not LUN004,192 show multiple instances of IBD sharing >4 cM with early medieval individuals from England (S21 Fig),193 which is also reflected in their relative position in the PCA (Fig 2A), implying substantial shared 194 ancestry and possibly recent gene-flow from a source genetically similar to those samples. This implies 195 that we cannot consider individuals from Pictland a homogenous genetic group but instead a complex 196 mixture of contemporary genetic ancestries.197 The unlinked approach implemented in the ADMIXTURE analysis also reveals a minor but detectable 198 genetic structure consistent with results from the PCA (Fig 2A) but not evide

Analysis of genetic continuity across Britain

The Pictish data allow us to obtain a transect of Iron Age/early medieval genomes across Britain and 234 directly look at the pattern of haplotype sharing between them and present-day genomes. The Iron 235 Age and Roman period (except 6DT3) individuals from England and Scotland share more IBD segments 236 >1 cM (both in terms of number and length) with present-day individuals from Scotland (including 237 Orkney), Northern Ireland and Wales than with any other European populations included in our 238 analyses (Fig 3, S20 Fig), consistent with the structure observed in the PCA analysis (Fig 2A). We also 239 show that all early medieval individuals (excluding I0777) share more IBD with modern Danish than 240 with any other present-day population (Fig 3), suggesting genetic continuity between modern-day 241 Danish and the ancestors of these individuals (S1.6 Text).242 The analysis also revealed high IBD sharing between early medieval individuals from England and 243 present-day people across Britain following a southeast/northwest cline (Fig 4 and S22 Fig). This 244 pattern suggests that Anglo-Saxon ancestry expanded out of south-eastern England followed by 245 admixture with local populations, which is a scenario consistent with previous research 246 (11,14,17,42,43). BAL003 and LUN004 share a high proportion of IBD segments with present-day 247 people from western Scotland, Wales and Northern Ireland, similar to the individuals from Late Iron 248 Age Orkney and England (Fig 4 and S22 Fig). However, unlike these individuals, LUN004, and to a lesser 249 extent BAL003, shares relatively few IBD segments with the present-day eastern Scottish population made available under aCC-BY 4.0 International license.(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is bioRxiv preprint doi:........ Byrne et al. (43) and Gilbert et al. (42) previously suggested that the genetic 251 structure between western and eastern Scotland could result from the divide between the kingdoms 252 of the Gaelic-speaking Dál Riata in the west and Picts in the east, which is seemingly in contradiction253 with the results presented here. Instead, the present-day genetic structure in Scotland likely results254 from more complex demographic processes that cannot be reduced to a single model.255 We propose two non-exclusive processes that might explain the observed pattern of IBD sharing 256 between the Iron Age and early medieval populations and the present-day Scottish population. The 257 first is substantial admixture from immigrants that brought Iron Age Orcadian-, and England-like258 ancestries (likely independently), which partially replaced the eastern Scottish early medieval gene 259 pool. Indeed, in the following centuries (AD 1,100-1,300), eastern Scotland received substantial260 immigration, such as settlers from Britain south of the Forth, France, and the Low Countries (44–46).261 Under this scenario, BAL003 and LUN004 are good representatives of the broader ancestry present in 262 Scotland during the Pictish period. Alternatively, the ancestors of BAL003 and LUN004 share more IBD 263 segments with present-day people from western Scotland, Wales, and Northern Ireland because they264 (or their direct ancestors) migrated from these regions but did not contribute substantially to later 265 generations via admixture with local groups in eastern Scotland. This scenario is consistent with an 266 emerging picture of west-east lifetime mobility of both males and females in the early medieval period 267 in Scotland (47,48). Under such a model, it may be feasible that there are indeed still undiscovered268 ‘pockets’ of eastern Pictish-period ancestry, likely similar to that observed in Iron Age Orcadians, that 269 was differentiated from ancestry carried by BAL003 and LUN004 and which contributed significantly 270 to present-day populations from eastern Scotland. Oxygen and strontium isotope analysis of teeth 271 from these individuals holds promise to characterise this further. Importantly, we also emphasise that 272 stochasticity likely affected the pattern of IBD sharing in such a small sample size. Indeed, high 273 variability in IBD sharing is observed amongst individuals from the early medieval and Iron Age groups, 274 and to some extent between BAL003 and LUN004 (S22 Fig). made available under aCC-BY 4.0 ...............

Fig 3. Shared Identity-By-Descent (IBD) segments >1 cM between the ancient genomes from Britain 277 and present-day European populations. IA, Iron Age. VA, Viking Age.278279 Fig 4. Average IBD sharing >1 cM between present-day and ancient groups from the UK. IBD sharing 280 between each of the ancient genomes and modern samples is illustrated in S22 Fig. Ancient individuals 281 are indicated with coloured symbols. The black dots represent the geographic location of present-day 282 people from 35 regions of the UK (11,49), by the county town.283284 Our results also show substantial IBD sharing between Iron Age, Viking Age and present-day 285 Orcadians, supporting our observations using allele-frequency based methods of strong genetic 286 continuity in this region over time (Fig 2, 4 and S22 Fig). Therefore, the marked genetic differentiation 287 between the Orkney and mainland Britain is not only a result of Scandinavian admixture, as previously 288 hypothesised (11,42,50–53) but also pronounced genetic continuity that persisted for at least 2,000 289 years. The relatively low IBD sharing between BAL003 and LUN004 and modern-day Orcadians (Fig 4) 290 suggest the emergence of Pictish culture in Orkney (21,22,36) was not associated with population 291 replacement but largely due to cultural diffusion and connections.292 IBD segments in Iron Age individuals from south-eastern England are widespread throughout western 293 and northern Britain compared to the more recent Romano-British individuals from northern England; 294 the latter, however, do not share substantial IBD with any present-day people of the British Isles (Fig 295 4 and S22 Fig). The only exceptions is 6DT3 who was from the same genetic population as two early 296 medieval individuals (I0159 and I0773) with Scandinavian-, and northern European-like ancestry 297 (‘pop12’, S22 Fig, S1.6 Text). 6DT3 also share relatively more IBD segments >1 cM with the present day population from Scandinavia, Belgium and the UK (Fig 3), suggesting that Scandinavian-like299 ancestry could have spread to the British Isles before the Anglo-Saxon period.
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preprint pdf text, p. 8-14.



Noteworthy: Present-day Eastern Scottish people share much less ancestry with the Pictish samples from Scotland, who share more ancestry with Western Britain - Wales, West Scotland - and Northern Ireland.
 
I don't quite follow the authors' interpretations of the PCA plot and K=4 ADMIXTURE chart, where they write

Moreover, although modern Orcadians are differentiated from the rest of the British Isles due to extensive admixture with Scandinavians, recent genomic research shows that genetic drift also played an important role.
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The ADMIXTURE chart for modern Orcadians shows the lowest level of the grey "Scandinavia" component in the British Isles. Orcadians seem more like a two-way admixture between the red "Isles" component and the blue "France" component, with minor levels of the grey "Scandinavia" component and the green "Central Europe" component.

There seems to be a suggestion by the authors that the red component could be Orcadian-specific, where they write

The Iron Age and unadmixed Viking Age Orcadians also show the highest degree of a red ancestry component , which is inconsistent with having originated from direct gene flow from any population included in this study and instead likely reflects retention of a less diverse pre-Iron Age ancestry in Orkney and/or strong genetic drift (such as a bottleneck or founder effect).
Click to expand...

Whereas I see the red component as a feature of all British Isles and British Isles-admixed populations (e.g. Norwegians).

I would also like to know more about the green component, present in England since at least the Iron Age. I don't believe this ancestral stream is native to Scandinavia but rather Central Europe, perhaps entering Scandinavia during the Bronze Age.

The authors write

[...] the grey and green ancestry components, likely first introduced by Scandinavian migrants as they are first observed in VK204 and VK205 and then in modern Orcadians. These components are also carried at a high proportion in modern Norwegians and Danes.
Click to expand...
 
;)

BAL003- Balintore-419-538 AD-XX-H2a1e

LUN001-Lundin Links-416-545 AD-XX-T2a1a

LUN002-Lundin Links-563-653 AD-unidentified sex-H1c20

LUN003-Lundin Links-384-562 AD-XX-T2b11

LUN004-Lundin Links- -XY-J1c3g/ R1b-L52

LUN005-Lundin Links- -XY-K1c2 ( this is the second male they didn't mention the y haplogroup of this individual)

LUN006-Lundin Links- -unidentified sex -J1c3b1

LUN009-Lundin Links-430-590 AD-XX-J1c3b
 
real expert said:
​Abstract

The origins and ancestry of the Picts of early medieval Scotland (ca. AD 300-900) has been traditionally seen as a problem, prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century AD resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the Pictish genomes within the Iron Age gene pool in Britain and demonstrate local biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-ByDescent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in the Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of female endogamy, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and presentday groups of the UK.





preprint pdf text, p. 8-14.



Noteworthy: Present-day Eastern Scottish people share much less ancestry with the Pictish samples from Scotland, who share more ancestry with Western Britain - Wales, West Scotland - and Northern Ireland.
Click to expand...

Very interesting indeed. I'm going to read it very carefully. Thanks for posting.
 
Broadly understood, it would show Picts of High Middle Ages were akin enough to IA British before Romans and Saxons. Not too surprising, I think. I don't know enough about Scotland history to can date their arriving but I know today eastern Scot people are physyially a bit different from the people of the western neo-Celtic fringes, and bear a high percentage of English or Norman surnames not to be confused with the englicized surnames of the previous Highlanders or with the handful of norman surnames pertaining to clans chiefs.
 
MOESAN said:
Broadly understood, it would show Picts of High Middle Ages were akin enough to IA British before Romans and Saxons. Not too surprising, I think. I don't know enough about Scotland history to can date their arriving but I know today eastern Scot people are physyially a bit different from the people of the western neo-Celtic fringes, and bear a high percentage of English or Norman surnames not to be confused with the englicized surnames of the previous Highlanders or with the handful of norman surnames pertaining to clans chiefs.
Click to expand...

A good percentage of Flemish surnames too, from Flemings who came over with the Normans.
 
I think there is a good degree of homogenization though, the variance in physical type is probably Neolithic-> BA transition rather than anything related to Norman or Scandinavian IMHO. The Picts were reputably pretty tall according to the Romans, but also I think the BB settlers were taller than the Neolithic inhabitants. This is the case pretty much everywhere in Europe though and likely partly related to diet.

I was actually unaware that a stocky body type is quite common in Scotland, in particular among females until I saw it myself as my daughter was a former competitive dancer. While the long limbed stereotype does occur, it predates the Germanic speaking settlers if we consider Roman accounts. I haven't visited UK enough to know if certain regions are different, but from what I can tell it's pretty homogenous as people have moved around a lot within the country in the last 500 years.
 
Angela said:
A good percentage of Flemish surnames too, from Flemings who came over with the Normans.
Click to expand...
Yes.
Many so-called Norman families invited into Scotland by various Scottish kings were actually Flemish.

William the Conqueror's wife Matilda/Maud was Flemish.

Soldiering aside, Flemings proved to be excellent artisans and merchants who boosted the economies of east-coast Scottish burghs.
 
Angela said:
A good percentage of Flemish surnames too, from Flemings who came over with the Normans.
Click to expand...

Yes, but I'm short here.
evidently, the surnames Fleming, Bremner ('brabender') speak by themselves.
I heard some of the Flemings came from French speaking areas of Flanders, so their names were not too easy to distinguish. I read too some Belgians or Flemings took foot in S-W Wales, but maybe not at the same time..
I have to read more on this specific aspect.
 
Aaron1981 said:
I think there is a good degree of homogenization though, the variance in physical type is probably Neolithic-> BA transition rather than anything related to Norman or Scandinavian IMHO. The Picts were reputably pretty tall according to the Romans, but also I think the BB settlers were taller than the Neolithic inhabitants. This is the case pretty much everywhere in Europe though and likely partly related to diet.

I was actually unaware that a stocky body type is quite common in Scotland, in particular among females until I saw it myself as my daughter was a former competitive dancer. While the long limbed stereotype does occur, it predates the Germanic speaking settlers if we consider Roman accounts. I haven't visited UK enough to know if certain regions are different, but from what I can tell it's pretty homogenous as people have moved around a lot within the country in the last 500 years.
Click to expand...

Tallness has nothing to do with long or short limbs, or so few... (only a very slight mechanical link non-genetical but in response to mesological individual influences); a common feature (not the only one) among British people is high stature but short legs and long back, not the true 'mediter' nor the 'nordic' look. And sturdy is not by force associated with short limbs: too much pseudo-science among the 'fans' of amateur typology (I don't say you're concerned, here!). IMO Scandinavian and Saxons settlers had modified the distribution of certain phenotypes, but their have not been an overwhelming flood anywhere, spite heavier in Shetlands, supposedly, an they were not so homogenous yet. The individual heterogeneity of British inhabitants for external phenotypes is old and was reinforced during BA; since that, I think the IA and later "invasions" or osmosis have not modified too much the inhabitants aspects, what is not to say eveything stayed stable. That said, some slight differences are still seen between regions of the Great Isles. Different history (foreign inputs here and there) and drifting pockets of pop's (look at Wales, even for auDNA!)
But the topic speaks more of auDNA than of physical aspect as a whole, for I have read.
 
Concerning Flemish origins in Scotland, I think it had been overrated; as often, in their multifolds genealogies of feudal period, some families put forwards one of their origin now and another origin later. The most of the noble men come with and after William the Bastard, were interallied between families spanning from eastern Brittany (no more Celtic speaking for the most) until FLanders (French speaking very often, I think). A complication is the fact they often left their personal names or the name of their lineage to took a placename granted to them by the Power*. It's what make British anthroponymy so hard. These placenames can be of diverse Celtic(s), Anglo-Saxon or "Norman" origin, linguistically speaking. I foind this link
 
Sorry: I found this link
https://flemish.wp.st-andrews.ac.uk/2013/09/27/an-introduction-to-flemish-names-in-scotland/
I find not too precise.
example: Cameron: in Lowlands it depends on one of three placenames, when in Highlands it's gaelic family name (cam shrôn : hooked nose or wry nose) for descendants of MacDhomhnuill Duibh fils de Donal(d) le noir.
At least one of the so called Flemish Families were already settled in Normandy before going to England.
the site mentions also Campbell (cam-beul wry mouth, maybe curved lips, maybe moral: lyer?) an other wellknown Gaelic clan...

It mentions too: Balliol (+ Bell, Beal, Beale, le Bel, Bailey etc. from Bell Roots by J. E and F. J. Bell), but I personally see very much evident a link with the France Flanders town (ture this time!) of Bailleul between Lille and the French Westhoek Flemish speaking before.
Other doubius things: Abernethy as of Flemish origin; in fact a placenmae occupied more surely by a Celtic lineage, not even Saxon.
Bruce (of Brix in Normandy): I 'm not aware of any Flemish origin?)
So, concerning linguistic origin of names: no certainty - surely overrated; concerning auDNA, yes, some input not visible by names, through the wives.
 
Sorry again: the site I criticize cites names as of Flemish origin: the contradicting details are of mine (about Cameron, Campbell, Abernethy, Bruce) are based on serious works, among whom, "The surnames of Scotland" of George F. Black.
 
I have still to look at the lower layer people names and input, it's true. Not so easy, not so many works as for the gentry.
 
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