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Significance The Orcadian Neolithic has been intensively studied and celebrated as a major center of cultural innovation, whereas the Bronze Age is less well known and often regarded as a time of stagnation and insularity. Here, we analyze ancient genomes from the Orcadian Bronze Age in the context of the variation in Neolithic Orkney and Bronze Age Europe. We find clear evidence for Early Bronze Age immigration into Orkney, but with an extraordinary pattern: continuity from the Neolithic on the male line of descent but immigration from continental Europe on the female side, echoed in the genome-wide picture. This suggests that despite substantial immigration, indigenous male lineages persisted for at least a thousand years after the end of the Neolithic.
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Ancient DNA at the edge of the world: Continental
immigration and the persistence of Neolithic male
lineages in Bronze Age Orkney
Katharina Dulias
a,b,c,1
, M. George B. Foody
a,1
, Pierre Justeau
a,1
, Marina Silva
a,2
, Rui Martiniano
d
,
Gonzalo Oteo-Garc
ıa
a
, Alessandro Fichera
a
, Sim~
ao Rodrigues
a
, Francesca Gandini
a
, Alison Meynert
e
,
Kevin Donnelly
e
, Timothy J. Aitman
f
, The Scottish Genomes Partnership
f
, Andrew Chamberlain
g
, Olivia Lelong
h
,
George Kozikowski
i,3
, Dominic Powlesland
a,j
, Clive Waddington
k
, Valeria Mattiangeli
l
, Daniel G. Bradley
l
,
Jaroslaw Bryk
a
, Pedro Soares
m
, James F. Wilson
e,n
, Graeme Wilson
o
, Hazel Moore
o
, Maria Pala
a
,
Ceiridwen J. Edwards
a,1,4
, and Martin B. Richards
a,1,4
a
Department of Biological and Geographical Sciences, School of Applied Sciences, University of Hudderseld, Hudderseld HD1 3DH, United Kingdom;
b
Department of Archaeology, University of York,York YO10 5DD, United Kingdom;
c
Institut f
ur Geosysteme und Bioindikation,Technische Universit
at
Braunschweig 38106 Braunschweig, Germany;
d
School of Biologicaland Environmental Sciences, Faculty of Science, Liverpool John Moores University,
Liverpool L3 3AF, United Kingdom;
e
Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4
2XU, United Kingdom;
f
Centre for Genomic andExperimental Medicine, Institute of Genetics and Cancer,University of Edinburgh, Edinburgh EH4 2XU, United
Kingdom;
g
Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UnitedKingdom;
h
Department of Research,
Business and Innovation, University of West England, Bristol, BS16 1QY, United Kingdom;
i
Private address, Broadford, Isle of Skye IV49 9BB, United Kingdom;
j
The Landscape Research Centre Ltd, Malton YO17 8SL, United Kingdom;
k
Archaeological Research Services Ltd, Bakewell DE45 1HB, United Kingdom;
l
Smurt
Institute of Genetics, Trinity College Dublin, Dublin D02 VF25,Ireland;
m
Centre of Molecular and Environmental Biology, Department of Biology, University of
Minho 4710-057 Braga, Portugal;
n
Centre for Global Health Research, UsherInstitute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom; and
o
Environment and Archaeology Services, Midbea Schoolhouse, Westray, Orkney KW172DP, United Kingdom
Edited by Anne Stone, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ; received May 11, 2021; accepted December 14,
2021
Orkney was a major cultural center during the Neolithic, 3800 to
2500 BC. Farming ourished, permanent stone settlements and
chambered tombs were constructed, and long-range contacts
were sustained. From 3200 BC, the number, density, and extrava-
gance of settlements increased, and new ceremonial monuments
and ceramic styles, possibly originating in Orkney, spread across
Britain and Ireland. By 2800 BC, this phenomenon was waning,
although Neolithic traditions persisted to at least 2500 BC. Unlike
elsewhere in Britain, there is little material evidence to suggest a
Beaker presence, suggesting that Orkney may have developed
along an insular trajectory during the second millennium BC. We
tested this by comparing new genomic evidence from 22 Bronze
Age and 3 Iron Age burials in northwest Orkney with Neolithic
burials from across the archipelago. We identied signals of
inward migration on a scale unsuspected from the archaeological
record: As elsewhere in Bronze Age Britain, much of the popula-
tion displayed signicant genome-wide ancestry deriving ulti-
mately from the Pontic-Caspian Steppe. However, uniquely in
northern and central Europe, most of the male lineages were
inherited from the local Neolithic. This suggests that some male
descendants of Neolithic Orkney may have remained distinct well
into the Bronze Age, although there are signs that this had dwin-
dled by the Iron Age. Furthermore, although the majority of mito-
chondrial DNA lineages evidently arrived afresh with the Bronze
Age, we also nd evidence for continuity in the female line of
descent from Mesolithic Britain into the Bronze Age and even to
the present day.
ancient DNA jOrkney jNeolithic jBronze Age jgenome-wide
Benefiting from the tail end of the Holocene climatic opti-
mum, the British Early Neolithic spread rapidly through
Britain and Ireland from the south over 300 to 400 y from
4050 BC (1–3). The settlers brought with them domesticated
wheat, barley, sheep, and cattle, as well as knowledge of cari-
nated bowl ceramics and causewayed enclosures (1–5), pointing
to a likely source in northern France or Belgium.
The Orkney Islands, lying to the north of the Scottish main-
land, flourished during the Neolithic (3800 to 2500 BC),
becoming a major cultural center (6–9). Underpinned by a
successful farming economy and long-range contacts, the earli-
est permanent settlements were constructed in wood, followed
by stone-built dwellings from 3300 cal. (calibrated) BC onward
(9, 10). The use of stone appears to have been a conscious
Signicance
The Orcadian Neolithic has been intensively studied and cel-
ebrated as a major center of cultural innovation, whereas
the Bronze Age is less well known and often regarded as a
time of stagnation and insularity. Here, we analyze ancient
genomes from the Orcadian Bronze Age in the context of
the variation in Neolithic Orkney and Bronze Age Europe.
We nd clear evidence for Early Bronze Age immigration
into Orkney, but with an extraordinary pattern: continuity
from the Neolithic on the male line of descent but immigra-
tion from continental Europe on the female side, echoed in
the genome-wide picture. This suggests that despite sub-
stantial immigration, indigenous male lineages persisted for
at least a thousand years after the end of the Neolithic.
Author contributions: J.F.W., G.W., H.M., M.P., C.J.E., and M.B.R. designed research; K.
Dulias, M.G.B.F., P.J., M.S., G.O.-G., A.F., S.R., F.G., A.M., K. Donnelly, T.J.A., T.S.G.P.,
V.M., P.S., J.F.W., M.P., C.J.E., and M.B.R. performed research; P.J., R.M., and D.G.B.
contributed new reagents/analytic tools; A.C., O.L., G.K., D.P., C.W., G.W., and H.M.
provided sample materials and information; and K. Dulias, M.G.B.F., P.J., M.S., R.M.,
J.B., P.S., J.F.W., G.W., H.M., M.P., C.J.E., and M.B.R. wrote the paper.
The authors declare no competing interest.
A complete list of the Scottish Genomes Partnership can be found in the SI Appendix.
This article is a PNAS Direct Submission.
This open access article is distributed under Creative Commons Attribution License 4.0
(CC BY).
1
K. Dulias, M.G.B.F., P.J., C.J.E., and M.B.R. contributed equally to this work.
2
Present address: Ancient Genomics Laboratory, The Francis Crick Institute, London
NW1 1AT, United Kingdom.
3
Deceased December 25, 2020.
4
To whom correspondence may be addressed. Email: c.j.edwards@hud.ac.uk or m.b.
richards@hud.ac.uk.
This article contains supporting information online at http://www.pnas.org/lookup/
suppl/doi:10.1073/pnas.2108001119/-/DCSupplemental.
Published February 7, 2022.
PNAS 2022 Vol. 119 No. 8 e2108001119 https://doi.org/10.1073/pnas.2108001119 j
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ANTHROPOLOGY
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design choice (9, 11, 12) and has resulted in an extraordinary
level of archaeological preservation.
While recent genome-wide studies (13) have demonstrated
the extent and tempo of continental migration into Britain dur-
ing the Beaker period, after 2500 BC, there has so far been lit-
tle or no recognition of the archaeological implications of this
for Orkney. The paucity of Beakers and associated material cul-
ture in the archaeological record has been taken as an indica-
tion that the cultural and population shifts occurring elsewhere
in Britain at this time had little direct impact in Orkney (8,
14–18) and indeed may have been locally resisted (6). As a
result, Orkney has been seen to have developed along a largely
insular trajectory during the second millennium BC.
Significant changes in funerary practice did begin to emerge
at this time, and research has concentrated on funerary
remains. Barrow cemeteries, some of the largest in northern
Britain, appeared in Orkney around the end of the third millen-
nium BC. These earthen mounds contained multiple burials,
added sequentially and most frequently comprising cremated
remains in pits or stone-lined cists (18). Flat cist cemeteries
were also in use for both inhumation and cremation burials,
and often graves contained the remains of several individuals,
but grave goods were infrequent.
Until recently, the low visibility of settlement sites had led to
the idea that this was a period of environmental and cultural
recession (19). The balance has begun to be redressed through
focused environmental analyses (20) and reports on settlements
such as at Crossiecrown (9) and Tofts Ness (21). Opportunities
to correlate settlement and funerary remains are very rare, and
few sites extend across the Neolithic and Bronze Age (BA)
periods, making it difficult to draw a coherent picture of change
over time. In this respect, the ongoing investigations at the
Links of Noltland (LoN) are providing valuable new insights.
The LoN is located on Westray, the northwesterly most
island of the Orkney archipelago. The exceptional conditions
have preserved extensive settlement and cemetery remains dat-
ing from at least 3300 cal. BC up to about 500 BC (22–25).
While no direct overlap has yet been detected between Neo-
lithic and BA phases of settlement, there is no evidence for a
major hiatus in occupation. The BA settlement, distinguished
on architectural grounds and dating from 2500 to 1200 cal.
BC, includes three separate conglomerations of domestic and
ancillary buildings, which, like their Neolithic counterparts,
were spread across a contemporary farmed landscape. Built
from a mix of stone and earthen banks, often arranged in pairs,
they were in use until at least 1200 cal. BC. A cemetery located
among these settlements, used between at least 2150 BC and
850 BC, comprised >50 burials, including >100 individuals.
Both cremation and inhumation were practiced, at times con-
temporaneously, and multiple burials within a single grave were
common. Material evidence of the “Beaker complex,” seen
across mainland Britain, is scant in Orkney; a few sherds from
two Beaker vessels were recovered from the wider area (19),
dated to 2265 to1975 cal. BC, but no further pottery or recog-
nizable artifacts have been found in association with the ceme-
tery or settlement.
The study of ancient genomes has shown that across much of
Europe, including mainland Britain, the arrival of Metal Age
culture was accompanied by the introduction of new ancestry
from the Pontic-Caspian Steppe and a predominance of Y-
chromosomal haplogroup R1b-M269 (13, 26–31). We investi-
gated genomic variation in the Orkney archipelago within the
context of this framework. Genome-wide SNP (single–nucleo-
tide polymorphism) capture and shotgun data were available
from 21 Early Neolithic Orcadians (13, 32), but only one from
the BA (13). To investigate BA Orkney, we generated whole-
genome shotgun sequence data from 22 samples from the LoN
cemetery and analyzed them alongside these published data.
We also included new data from three Iron Age (IA) samples
from the multiperiod ritual complex and cemetery site of
Knowe of Skea (KoS), on the west coast of Westray, and 12 fur-
ther prehistoric samples from Scotland and northern England.
Results
We present shotgun genome data from 29 samples from prehis-
toric Scotland and eight from northern England: 22 from the
BA LoN in Westray, Orkney, dating to 1400 to 1700 BC
(LoN); three from the IA KoS in Westray, Orkney, dating to
the first two centuries AD; one from IA Milla Skerra (MS),
Unst, Shetland; one from IA High Pasture Cave (HPC), Isle of
Skye in the Hebrides (33); one from Neolithic Strath Glebe
(SG), also Skye; a Pictish sample from Rosemarkie Cave (RC),
Black Isle in northern Scotland, dating to 430 to 630 AD; a
Beaker burial sample from Low Hauxley (LH), Northumber-
land; three BA samples from West Heslerton (WH), North
Yorkshire; two IA samples from Knapton Wold (KW), North
Yorkshire; and two IA samples from Carsington Pasture Cave
(CPC), Derbyshire. Whole-genome coverage varied greatly
from 0.0007×to 0.8207×. We undertook genome-wide analysis
on samples above 0.009×, with samples averaging 0.194×. All
samples passed contamination tests (Table 1, SI Appendix, Table
S1, Dataset S1 Aand B, and SI Appendix, Fig. S1). We analyzed
these in the context of genome data from Early Neolithic Ork-
ney (n=21) (13, 32) and Neolithic, Chalcolithic (CA), and BA
Europe and 1,856 new mitogenomes from modern Orkney (n=
1,356) and Shetland (n=500) (Datasets S1Cand S2).
Genome-Wide Variation. ADMIXTURE analysis (Fig. 1A)
showed that the samples from BA Orkney closely resembled
other northern European BA people in their overall genome-
wide profiles and were highly distinct from Neolithic Orkney
samples, which resembled more our Neolithic sample from
Skye and other British and Irish Neolithic samples. Neolithic
samples all lacked the CHG (“Caucasus hunter-gatherer”)
component (in blue) that most clearly signals admixture from
Pontic-Caspian Steppe pastoralists (34). The CHG fraction in
Orkney (both BA and IA) is somewhat higher (40%) than in
other Scottish CA and EBA (Early Bronze Age) samples but
within the wide range of values for England (Fig. 1Aand SI
Appendix, Fig. S2A). Modern Orcadians have an even higher
fraction of the CHG component, reflecting medieval Norse set-
tlement, estimated from modern genome-wide surveys at 20
to 25% (35) and 25 to 30% of modern Y chromosomes (36,
37). Geographical and chronological trends are portrayed more
clearly in the PCA (principal component analysis) (Fig. 1Band
SI Appendix, Fig. S3). LoN BA samples broadly clustered with
northern and central European Bell Beaker, CA, and BA sam-
ples, and KoS IA samples fell within the same broad cluster.
D-statistics quantify shared genetic drift among genomes and
can thus also be used to estimate the degree of similarity
among individuals. We calculated symmetry D-statistics by com-
paring potential outlier samples (as noted in the ADMIX-
TURE analysis) to the rest of the LoN using the form D(Mbuti,
Test; Potential Outlier, LoN). The LoN samples consistently
formed a clade, indicating that they were statistically indistin-
guishable from each other (SI Appendix, Fig. S4Aand Dataset
S1D). With D-statistics of the form D(Mbuti, LoN; European
BA, European BA), after closest matches to the slightly older
published Lop Ness BA sample from Sanday, Orkney, the most
common significant similarities were with British Bell Beaker
complex (BBC) samples, the Scottish BA, and Orkney KoS IA,
as well as to a few continental individuals such as French BBC
and the Dutch BA (SI Appendix, Fig. S4Band Dataset S1E).
Outgroup-f3 statistics showed a similar pattern, with LoN clos-
est to eastern British, Welsh, Irish, and northwest European
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https://doi.org/10.1073/pnas.2108001119 Ancient DNA at the edge of the world: Continental immigration and the
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BBC and BA samples, albeit with overlapping errors across
European BBC and BA samples (Fig. 1Cand SI Appendix, Fig.
S5A). This indicates that the Orkney BA was most likely settled
via the British mainland (possibly the eastern side) by people
who arrived in Britain during the Beaker period.
The software qpAdm (38) summarizes f
4
-statistics (which are
similar to D-statistics) in order to estimate the direction and
magnitude of gene flow, or admixture, from one population to
another. We modeled admixture fractions with qpAdm using
the three major components demonstrated by ADMIXTURE;
Steppe, “Anatolian Neolithic Farmer” (ANF), and “Western
Hunter-Gatherer” (WHG) (SI Appendix, Fig. S6 and Dataset
S1F). The LoN comprised 55% of their ancestry from the
Steppe, 33% from ANF, and 12% from WHG, broadly similar
to published BA samples from across Britain (13).
The populations that contributed to the LoN population
were likely admixtures of those three components. To identify
more proximal sources for the LoN, we modeled various poten-
tial Early Neolithic versus Late Neolithic/EBA source popula-
tions (Table 2). The Orcadian BA samples could be plausibly
modeled as 4 to 7% local Neolithic and 93 to 96% Scottish
BBC populations, but also as 1 to 5% local Neolithic and 95
to 99% French BBC populations or 1% local Neolithic and
99% Danish BA populations. Despite the uncertainty indi-
cated by the SEs, these results clearly imply very high levels of
replacement of the Neolithic people by people related to conti-
nental BBC immigrants by the EBA, with only 5% assimila-
tion at most of the local autosomal gene pool. However, by the
time the descendants of the BBC immigrants reached Orkney,
they appear to have lost their Beaker cultural affiliation, as
reflected in the dearth of Beaker-associated material culture in
Orkney (6).
Thus, the picture from the genome-wide analyses suggests a
substantial replacement of the Orcadian population between
the Late Neolithic and the BA, similar to that seen in mainland
Britain (13). However, there are striking and unexpected differ-
ences between the patterns displayed by the uniparental marker
systems, which can illuminate in more detail how this process
took place.
Mitochondrial DNA Variation. Early Neolithic Orkney (n=21)
includes mitochondrial DNAs (mtDNAs) characteristic of the
European Neolithic, suggesting predominantly settlement from
the western Neolithic but with a minor contribution from the
Danubian Neolithic (SI Appendix, Section S5). By contrast, the
BA LoN suite of lineages (n=20) is very different (Datasets
Table 1. Summary of ancient samples reported in this study
Sample Site Period Calibrated date to 2σSex mtDNA haplogroup Y-DNA haplogroup (2017 ISOGG nomenclature)
KD026 SG Scotland Neolithic - XY U5b2c I2a2b-FGC29562/Y10705
KD070 LH England EBA 24642209 cal. BC XY T2e1 R1b1a1a2a1a2c1a1n-BY575
KD003 WH England EBA - XX T2e n/a
KD040 WH England EBA - XY T2b4h R1b1a1a2a1a1e1b-FGC15048
KD041 WH England EBA - XY U5a1+@16192 R1b1a1a2a1a2c-S461/Z290
KD006 LoN Orkney MBA 16221498 cal. BC XY T2a1b1a I2a1b1a1b-A1150/Y13519
KD044 LoN Orkney MBA - XX U5b2a3b n/a
KD045 LoN Orkney MBA - XY J1c2a I2a1b-M423
KD046 LoN Orkney MBA - XY T2a1b1a Undetermined
KD047 LoN Orkney MBA 15011319 cal. BC XY H39 I2a1b1a1b-A1150/Y13519
KD048 LoN Orkney MBA 15091416 cal. BC ? H39 n/a
KD049 LoN Orkney MBA - XY H39 I2a1b1a1b1-A8742
KD050/65 LoN Orkney MBA 16091437 cal. BC XX H39 n/a
KD051 LoN Orkney MBA 17431543 cal. BC ? Undetermined n/a
KD052 LoN Orkney MBA - XX K1a29a n/a
KD053 LoN Orkney MBA - XY Undetermined Undetermined
KD055 LoN Orkney MBA - XX J1c2a n/a
KD057 LoN Orkney MBA - XY H1n1 I2a1b1-L161.1/S185.1
KD058 LoN Orkney MBA 16161456 cal. BC XX K1a3a n/a
KD059 LoN Orkney MBA 16201462 cal. BC XY T2b21 I2a1b1a1b-A1150/Y13519
KD060 LoN Orkney MBA - XY H1n1 I2a1b1-L161.1/S185.1
KD061 LoN Orkney MBA - XY K1c2 R1b1a1a2a1a2c1a-CTS24/DF13/S521
KD062 LoN Orkney MBA 15361425 cal. BC XX U5b2a3b n/a
KD063 LoN Orkney MBA - XX H58a n/a
KD064 LoN Orkney MBA - XY T2b21 I2a1b1a1b1-A8742
KD066 LoN Orkney MBA - XX T2a1b1a n/a
KD067 LoN Orkney MBA - XX H+195 n/a
KD071 KW England IA - XX H1b1+16362 n/a
KD072 KW England IA - XX H1b1+16362 n/a
CE003 CPC England IA 758416 cal. BC XX X2b4 n/a
CE004 CPC England IA 387205 cal. BC XY H10b R1b1a1a2a1a-L151/PF6542
KD004 KoS Orkney IA 340 cal. BCcal. AD 4 XY H1b R1b1a1a2a1a2c-S461/Z290
KD042 KoS Orkney IA - XX U5a1b1a n/a
KD043 KoS Orkney IA 25215 cal. AD XY H1b R1b1a1a2-M269/PF6517
KD005 HPC Scotland IA 46 cal. BCcal. AD 202 XX H7a1b n/a
KD073 MS Shetland IA 236402 cal. AD XY J1b1a1 Undetermined
KD001 RC Scotland IA/medieval 441641 cal. AD XY J1b1a1a R1b1a1a2a1a-L151/PF6542
CPC, Carsington Pasture Cave, Derbyshire; HPC, High Pasture Cave, Skye; KoS, Knowe of Skea, Westray, Orkney; KW, Knapton Wold, North Yorkshire;
LH, Low Hauxley, Northumberland; LoN, Links of Noltland, Westray, Orkney; MS, Milla Skerra, Unst, Shetland; RC, Rosemarkie Cave, Black Isle; SG, Strath
Glebe, Skye; WH, West Heslerton, North Yorkshire.
ANTHROPOLOGY
Dulias et al.
Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
PNAS j3of10
https://doi.org/10.1073/pnas.2108001119
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S1Gand S2). There are a number of minor H lineages, includ-
ing H39 (four individuals), H58a, H+195, and two individuals
with H1n1. There are also two with J1c2a, three with
T2a1b1a—matching the EBA individual from Lop Ness (the
only previously published BA Orkney sample) (13), two with
T2b21, two with U5b2a3, one with K1a3a, one with K1a29a,
Location
Anatolia
Britain−Ireland
Central Europe
Central Mediterranean
France−Iberia
North−east Europe
Scandinavia
South−east Europe
This study
CPC Iron Age
HPC Bronze Age
Knapton Wold Iron Age
Knowe of Skea Iron Age
Links of Noltland Bronze Age
Low Hauxley Bronze Age
Milla Skerra Iron Age
Rosemarkie Pictish
Strathglebe Neolithic
West Heslerton Bronze Age
Culture
Bronze Age
Bell Beaker
Chalcolithic
Corded Ware
Globular Amphora
Iron Age
LBK
modern
Neolithic
Central Europe
Beaker
Central
Europe LBK
Britain
Neoltihic
Britain Chalcolithic/
Beaker/Bronze Age
Central Europe
Corded Ware/Beaker
Modern Britain
Scandinavia
Anatolia
Neolithic
Near East
Natuan
Bronze Age
Steppe
Europe Mesolithic
England_MESO
Skye_Strathglebe_NEO
Orkney_NEO
England_BB
England_BA
Wales_BA
Ireland_BA
Scotland_BB
Scotland_BA
Orkney_BA
Orkney_LinksOfNoltland_BA
Orkney_KnoweOfSkea_IA
Shetland_MillaSkerra_IA
Skye_HPC_IA
Scotland_Rosemarkie_IA
CPC_IA
Low_Hauxley_BA
West_Heslerton_BA
Knapton_Wold_IA
England_IA
English_MOD
Scottish_MOD
Orcadian_MOD
0.0
0.2
0.4
0.6
0.8
1.0
A
B
Fig. 1A and B. Visualization of Orkney genome-wide data in context. (A) Unsupervised ADMIXTURE plot (K=7) of European Mesolithic, Neolithic, BA,
and IA samples. The red component maximizes in the WHG, green in the ANF, and blue in the CHG; proles to the right of each label are from the same
population. (B) PCA showing rst two principal components of European Mesolithic, Neolithic, and BA samples, projected on present-day European varia-
tion. The gure shows a zoom-in of the full plot (SI Appendix, Fig. S3), excluding outlier Yamnaya and Mesolithic samples. LBK, Linearbandkeramik.
4of10 jPNAS Dulias et al.
https://doi.org/10.1073/pnas.2108001119 Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
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and one with K1c2. Eight of these individuals (three of the H39
individuals, all three T2a1b individuals, one of the two U5b2a3
individuals, and the K1a3a individual) were part of a multiple
burial, of which two were related (see below). The males from
the multiple burial also all carried Y-chromosome haplogroup
I2a1b-M423/I2a1b1-S185.
The age and geographic distribution of the clusters to which
most of the BA LoN lineages belonged suggest that most of
them were not inherited from the local Neolithic but arrived
later. Many are associated in ancient DNA studies with conti-
nental Corded Ware Culture, BBC, or BA populations (SI
Appendix, Section S5). For example, T2a1b1 is seen in the Ger-
man Corded Ware, whereas T2b21 matches German and Czech
BBC lineages. While H39 and K1c2 lineages have not been
seen in published ancient DNA data, the modern lineages are
restricted to northern Europe and date to 3000 BC and 2600
BC, respectively, again suggesting a source in the Corded Ware
expansion across northern Europe at 2500 to 3000 BC. Several
lineages, such as J1c2*, K1a3a, H1n1, H58a, and H+195, are
harder to resolve, but their distribution is in each case consis-
tent with a BBC arrival, although we cannot currently conclu-
sively rule out a local Neolithic source. The IA KoS remains
(n=3) include two identical H1b lineages and one U5a1b1a,
both of which can be attributed to either the BBC or the
Corded Ware on the Continent.
The lineage most likely to date to before the Beaker Age in
Orkney, seen in two LoN individuals, is U5b2a3 +16319, which
we name here U5b2a3b (Dataset S3). U5b2a3 dates to 8500
BC and is seen in Early Neolithic individuals from both Scot-
land (13) and Wales (39), and so the Orkney individuals
represent potential continuity from the British Neolithic into
the BA. Intriguingly, U5b2a3b is also seen in one modern indi-
vidual from the British Isles (40), as well as an individual from
Virginia, United States (founded as a British colony), indicating
potential continuity through to the present day. Indeed, with
U5b2a* found in Neolithic Orkney (32) and Scotland (13) and,
notably, Mesolithic Ireland (41) and U5b2a3 itself also seen in
Neolithic Ireland (41), along with the presence of U5b2 line-
ages in modern Orkney and Shetland (Dataset S2), it is possi-
ble that some U5b2 lineages, including U5b2a3b, may signal
some of the most ancient lineages surviving in present-day Brit-
ain and Ireland, potentially even from the local Mesolithic.
Y-Chromosome Variation. There are 16 known Y-chromosome
(Y-DNA) haplotypes from Neolithic Orkney, of which 14
appear to be well resolved (13, 32). All 14 belong to hap-
logroup I2a, of which seven are I2a1b-M423, four are I2a1b1-
S185, one is I2a2-S33, one is I2a2a1b-CTS10057, and one is
I2a2a1a2-Y3679 (the remaining two are poorly resolved I and
I2). In BA LoN, even though the majority of genome-wide and
female lineages most likely arrived in Britain and Orkney with
the BBC or BA, all but one of the nine Y-DNA lineages belong
to haplogroup I2a1b-M423, with just one belonging to R1b-
M269 (SI Appendix, Section S6 and Dataset S1H). We found
four distinct haplotypes within I2a1b: I2a1b-M423, I2a1b1-
S185, and the more derived I2a1b1a1b-A1150 and
I2a1b1a1b1-A8742.
This predominance of I2a1b-M423 is surprising because it is
completely absent elsewhere in CA/BA Europe, where the Y-
DNA landscape is heavily dominated by R1b-M269 (Figs. 2–4
30
40
50
60
70
02040
0.2600
0.2605
0.2610
0.2615
0.2620
0.2625
0.2630
0.2635
0.2640
0.2645
0.2650
0.2655
0.2660
0.2665
0.2670
0.2675
0.2680
0.2685
0.2690
0.2695
0.2700
0.2705
0.2710
0.2715
0.2720
0.2725
0.2730
0.2735
0.2740
0.2745
0.2750
0.2800
f3
Period
Bell Beaker
EBA
LBA
MBA
Unetice
Links of Noltland outgroup−f3
C
Fig. 1C. (C) Map displaying outgroup-f3 statistics for the LoN samples, showing the close relationship with Bell Beaker and BA samples from the British
and Irish mainland and northwestern continental Europe.
ANTHROPOLOGY
Dulias et al.
Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
PNAS j5of10
https://doi.org/10.1073/pnas.2108001119
Downloaded by guest on February 7, 2022
and SI Appendix, Figs. S13–S15). For example, in a dataset of
21 BBC males from Britain, 20 carry the R1b-M269 lineage
and only one I2a, which is on the distinct I2a2a-M223 lineage.
If we include CA and EBA Britain and Ireland, 41 out of 43
males carried R1b-M269, two I2a2a-M223, and none I2a1b-
M423.
Thus, except for the single R1b-M269 lineage, all sampled
LoN BA males carried a subset of the Neolithic Y-DNA pool.
These are very unlikely to have been brought to Orkney by
BBC or BA migrants from further south in Britain. Not only
has I2a1b-M423 not been seen in the European BBC or BA,
but it was a minority lineage even during the European Neo-
lithic. Among 389 published male genomes from the European
Neolithic, only 12% (47 of them) carry I2a1b-M423, of which
40% (19/47) are from Britain or Ireland (42), and most of those
in Britain are from Orkney (Figs. 3 and 4). Even in Britain and
Ireland, outside of Orkney most Neolithic Y-DNA lineages
belong to haplogroup I2a2-S33 or I2a2a-M223 (Fig. 3),
although, curiously, our Neolithic individual from Skye belongs
to the very rare I2a2b-S154, seen elsewhere only in Middle
Neolithic France (43). I2a1b-M423 seems to be largely
restricted to western Neolithic Britain and Ireland, where it
occurs rarely alongside I2a2a-M223, as well as I2a1a-CTS595
(41), which has not yet been found in Neolithic Britain. This
perhaps suggests a relict distribution, shared by Orkney, Ire-
land, and western and northern Britain.
A consequence is that not only was the assimilation of Neo-
lithic male lineages very rare during the BBC spread in Britain,
but assimilation of I2a1b-M423, which formed a small minority
of Neolithic British mainland lineages, must have been even
rarer, if it ever happened at all. We conclude that the I2a1b-
M423 lineages at BA LoN had most likely persisted from the
local Orcadian Neolithic and were not contributed to this popu-
lation by mainland British Neolithic groups. By contrast, the
two sampled males at the IA KoS site, also on Westray,
belonged to the R1b-M269 lineage.
I2a1b-M423 likely arrived in Orkney with the first farmers.
In the Neolithic, I2a1b-M423 was largely distributed in an arc
around the Atlantic fac¸ade of Europe, from the western Medi-
terranean to the Baltic. Outside Britain, most I2a1b-M423 line-
ages are from Middle/Late Neolithic Spain and France, with
one from Germany and a small number from Sweden, where,
at a megalithic site on Gotland, all four genotyped males
belonged to I2a1b-M423 (Fig. 4) (32). It is also present in sev-
eral hunter-gatherers in northern and central Europe, including
Mesolithic Ireland. This distribution, the molecular-clock age
of the two major subclades (I2a1b1-S185 and I2a1b2-S392 both
date to 7 ka) (YFull YTree version 8.06.01, 27 June 2020;
https://www.yfull.com/tree/), and evidence that the ancestral lin-
eage survives today only in Iberia (YFull tree) suggest assimila-
tion from hunter-gatherers during the spread of the Neolithic
into southwest Europe, followed by Neolithic dispersal into
northwest and northern Europe, although some further assimi-
lation in northern Europe is also possible.
Runs of Homozygosity and Kinship. We assessed runs of homozy-
gosity (ROH) using the program hapROH (44). ROH profiles
of BA LoN samples indicate a small effective population size
but give no evidence for recent consanguinity, up to third
cousin unions (SI Appendix, Fig. S7). HapROH estimated the
effective population size to be 400. This is a large decrease
from Neolithic Orkney and also much lower than elsewhere in
Neolithic, BBC, or BA Britain and northwest Europe (SI
Appendix, Table S2). These results suggest a small, endoga-
mous population.
We estimated kinship using Relationship Estimation from
Ancient DNA (READ) software (45), coupled with uniparental
markers and the age-at-death osteoarchaeological profile. The
READ analysis identified almost no evidence for close kinship.
Even among the seven individuals in the multiple inhumation
who passed the criteria for DNA analysis (out of 11), the only
first- or second-degree relationship involved two full siblings: a
brother and sister, where the former died in adolescence and
the latter soon after birth. The siblings shared an identical, rare
mtDNA haplotype (within H39), and the male carried the most
common Y-DNA haplotype at the cemetery (I2a1b1-S185). An
infant from outside of the multiple burial carried a slightly dis-
tinct lineage of mtDNA H39, but we could find no evidence of
close kinship using READ (SI Appendix, Fig. S8A).
The low Y-DNA diversity and multiple sharing of rare
mtDNA haplotypes both suggest a small, close-knit community,
notwithstanding the relatively recent arrival (within the previ-
ous millennium) of most of the mtDNAs from overseas.
European Mesolithic/Neolithic hunter-gatherer
European Neolithic/Chalcolithic
Orkney Neolithic
Orkney Bronze Age
L161/S185
M423
I2a1b2
I2a1b1
I2a1b
L621/S392
LUX
MES
NOR
NEO
SWE
NEO
LIT
NEO
IRE
MES
14x IBE
MLN/CA
9x FRA
MLN
FRA
EN
ENG
NEO
SCO
NEO
SWE
MN
7x ORC
NEO
ORC
BA
IBE
NEO
2x FRA
MN
GER
MN
4x ORC
NEO
7x ORC
BA
3x SWE
MN
2x SCO
NEO
4x IRE
NEO
SWE
NEO
Fig. 2. Schematic phylochronology of Y-chromosome haplogroup I2a1b-
M423. For detailed branching at the tips, see SI Appendix, Fig. S15.
Table 2. Putative BA and Neolithic ancestry of LoN MBA and Lop Ness EBA (13) samples modeled with qpAdm
Target Neolithic population Neolithic proportion Late Neolithic/BA population BA proportion SE Pvalue
LoN British Neolithic 0.039 Scotland BBC 0.961 0.032 0.079759
LoN Orkney Neolithic 0.038 Scotland BBC 0.962 0.031 0.080413
Lop Ness Orkney Neolithic 0.075 Scotland BBC 0.925 0.045 0.151044
LoN British Neolithic 0.005 France BBC 0.995 0.031 0.124343
LoN Orkney Neolithic 0.006 France BBC 0.994 0.031 0.124541
Lop Ness Orkney Neolithic 0.052 France BBC 0.948 0.046 0.066244
Lop Ness Orkney Neolithic 0.013 Denmark BA 0.987 0.032 0.284911
Only feasible and signicant results are displayed. The strong apparent similarity between the Orkney MBA LoN samples and the southern France BBC
samples is likely not due to common ancestry but possibly due to the higher levels of Neolithic assimilation in the latter (SI Appendix, Fig. S2B); the reason
for the similarity with the Danish BA is unclear.
6of10 jPNAS Dulias et al.
https://doi.org/10.1073/pnas.2108001119 Ancient DNA at the edge of the world: Continental immigration and the
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However, the most significant signal remains the contrast
between the autochthonous male lineages versus higher-diver-
sity nonlocal female lineages, pointing to ongoing patrilocal
marriage patterns, not only in the BA but, by inference from
the persistence of I2a1b-M423, at the end of the Neolithic too.
We note that although the contrast between the largely indige-
nous Y-DNA and the largely continental mtDNA and autoso-
mal fraction is very striking, a level of 95% continental
genome-wide ancestry could be achieved by the marrying out of
indigenous men with immigrant women in only five genera-
tions, or 100 to 150 y, which the results suggest were followed
by isolation and endogamy (SI Appendix, Section S3.10).
Discussion
We have investigated genomic variation in BA and IA Orkney
and compared it with the available evidence for the preceding
Orcadian Neolithic, in the context of Mesolithic, Neolithic, BA,
and IA variation from across Europe. Both the mtDNA and Y-
DNA variation of Neolithic Orkney point to settlement primar-
ily from the Mediterranean/Rh^
one/Atlantic dispersal route, via
the British mainland, in line with genome-wide analyses for
Neolithic Britain as a whole (13, 39). Although this process was
largely one of colonization, we find some evidence for potential
assimilation and survival of indigenous Mesolithic maternal lin-
eages. The presence of an apparently ancient local branch of
mtDNA haplogroup U5b complements genome-wide observa-
tions of hunter-gatherer assimilation in western Scotland (39)
and Ireland (41).
This study confirms that the drastic shift in the British popu-
lation in the BA, evident in both the genome-wide (13) and
mtDNA patterns, also occurred in Orkney. Orkney was largely
resettled from the British mainland by people of substantially
recent continental ancestry. Although this demographic shift
may have taken place over centuries, it was likely sustained rel-
atively unchanged into the IA; although we have analyzed only
three IA samples, they all show a similar pattern.
Unexpectedly, despite this wave of immigration, local Neo-
lithic male lineages persisted well into the BA, at least in West-
ray. While we do see evidence for male newcomers, in the
presence of a single R1b-M269 Y-DNA lineage (in an infant
burial), the other males all carry the indigenous I2a1b-M423
lineage. This lineage survived in a single fifth or sixth century
Pictish sample from Birsay, northwest Mainland (46), but is
only seen in a single family (among 407 males tested) in Orkney
today.
The I2a1b-M423 lineage almost vanished elsewhere in west-
ern Europe after the end of the Neolithic. None are seen in
post-Neolithic European archaeological remains. It is seen at
only 1% in modern Britain and is almost absent in most of
modern western Europe, although one recent subclade of
I2a1b2-S392 has undergone dramatic expansion with Slavic
populations in the Balkans (Figs. 2–4 and SI Appendix, Fig.
S13) (47).
A possible explanation can be found in the continuity, stabil-
ity, and self-sufficiency of farming settlements, such as LoN.
These successful household groups, while undoubtedly partici-
pating in an Orkney-wide Neolithic society, also developed
strong local identities, manifested in locally variant art styles,
material culture, architecture, and ritual activity. They may, for
example, have pursued their own long-range contacts, as sug-
gested, for example, by the importation of aurochs and local
tomb art, distinctive within Orkney and most directly compara-
ble with that found at Br
unaB
oinne in Ireland, where
I2a1a-CTS595
I2a1b-M423
I2a2*-S33/I2a2b-S154
I2a2a-M223
H2a
Bronze Age
Neolithic/Chalcolithic
Mesolithic/Neolithic
hunter-gatherer
Mainland
Rousay
Westray
Holm of Papa Westray
Sanday
Hoy South
Ronaldsay
North
Ronaldsay
Stronsay
Shapinsay
Eday
Papa Westray
Burray
I2a1b-M423
I2a2*-S33/I2a2b-S154
I2a2a-M223
Neolithic/Chalcolithic
Bronze Age
AB
Fig. 3. Distribution of Mesolithic and Neolithic Y-chromosome lineages, and their Bronze Age descendants. (A) Britain and Ireland with (B) zoom in on
Orkney. Colors represent different Y-chromosome lineages, and distinct outlines represent the time period of the sample. Each circle represents one indi-
vidual, except for Trumpington Meadows, Cambridgeshire (66), where two brothers are represented by a single circle. Maps prepared with GADM tools
(https://gadm.org/data.html) (67) using data from SRTM (68).
ANTHROPOLOGY
Dulias et al.
Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
PNAS j7of10
https://doi.org/10.1073/pnas.2108001119
Downloaded by guest on February 7, 2022
patrilineal descent has recently also been inferred from genetic
data (41). From a position of strength during the Neolithic,
such settlements may have been better placed to mediate
inward migration and to make specific choices with regards to
the management of lineage.
We propose that we may be seeing the surviving remnants of
well-established Neolithic household groups in BA Orkney: a
number of distinct male lineages that have persisted when
almost the whole of the rest of the population (and genome)
has been replaced. While the archaeological signs of these
groups may not have been especially ostentatious, the persis-
tence of their lineages for at least a thousand years beyond the
point when the vast majority of male lineages elsewhere in Brit-
ain were replaced by newcomers might imply a more protracted
and perhaps more negotiated process of assimilation than else-
where, as well as pointing to much less insularity than has often
been assumed for the Orcadian BA (25).
There are several caveats to this suggestion. Firstly, we are
describing the situation in one of the most remote parts of the
Orkney archipelago and at a particular moment in time. It is a
snapshot and may not be representative of Orkney as a whole.
While the single Lop Ness sample (from another island in the
archipelago) confirms the overall pattern of continental immi-
gration, the individual is female and therefore provides no
information on the male lineage. Further investigations can
help to fill out the picture.
Secondly, there are numerous cremation burials at the site
for which DNA analysis cannot be carried out. Is it possible
that newcomer R1b-M269 males were mostly cremated? This
seems unlikely; substantial numbers of BBC and EBA inhuma-
tion burials have been analyzed from England and Scotland,
and the males carried almost exclusively R1b-M269 Y-DNA
lineages. However, even if this were the case, the persistence in
inhumations of the I2a1b-M423 lineage, in the face of an
almost 95% replacement at the genome-wide (and probably
also the mtDNA) level, remains extraordinary.
Within the European context, the Orkney BA stands in stark
contrast as a location, at the northwestern extreme of the conti-
nent, where the majority of the genome was overwritten
between the Late Neolithic and the end of the EBA but the
male lineages somehow persisted. Even so, we can understand
this phenomenon in terms of the same patrilocal marriage prac-
tices that we see throughout west Eurasia. The ancestral distri-
bution in Orkney demonstrates deliberate marriage patterns
involving local men and incoming women. This process of pref-
erential assimilation seems likely to have continued for many
generations, given the extent of replacement of the remainder
of the Orcadian Neolithic genome.
The existence of a powerful and likely strongly hierarchical
strand in Neolithic society has been proposed on the basis of the
discovery of an incestuous first-degree union at Newgrange in Ire-
land (41) and was prefigured by earlier analyses of Ireland and
Mesolithic/Neolithic hunter-gatherer
Neolithic/Chalcolithic
Bronze Age
Fig. 4. Distribution of prehistoric I2a1b-M423 Y-chromosome lineages in Europe. Each circle represents one individual carrying I2a1b. Map modied
from Mapswire.com (https://mapswire.com/), which is licensed under CC BY 4.0.
8of10 jPNAS Dulias et al.
https://doi.org/10.1073/pnas.2108001119 Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
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other megalithic cultures in both northwest and central Europe
(32, 48). Cassidy et al. (41) argue that it encompassed the whole
of Ireland, adding that it may have incorporated the similar mega-
lithic communities of Wales and Orkney, most likely originating in
Brittany (1, 49). I2a1b-M423 is seen in both Mesolithic and Neo-
lithic Ireland, and the main cluster seen in Late Neolithic Ireland,
I2a2a1a1-M284—found in the putative elite lineage at Newgran-
ge—matches an Orcadian Neolithic lineage from the Isbister
Chambered Cairn (“Tomb of the Eagles”) on South Ronaldsay
(Fig. 3 and SI Appendix,Fig.S13) (13). Both our data from
BA Orkney and the Neolithic circumcoastal distribution of the
Y-chromosome I2a1b-M423 haplogroup lend further support to
this suggestion. European Neolithic society, at one extreme (but
hardly peripheral) edge of its distribution, may have been patrilin-
eal, patrilocal, and hierarchical long before the arrival of the
Beaker complex and (most likely) Indo-European speech (27, 28,
31, 50).
Our data suggest that Neolithic lineages persisted within par-
ticular farming households, which, although not obviously elite,
appear to have retained control of specific landholdings over
many generations. This linkage of lineage with specific place is
strongly suggestive of preferential inheritance along the male
line. The continuity which this engendered is likely to have con-
tributed significantly to the longevity of settlements between
the third and first millennia BC. The indigenous male lineages
remained in place while their people, their culture, their lan-
guage, and even their genomes were transformed to resemble
more and more those of the European mainland from which
the newcomers had come.
Our findings both demonstrate EBA migration into Orkney
and amplify the recognition that “the expansion of the Beaker
complex cannot be described by a simple one-to-one mapping
of an archaeologically defined material culture to a genetically
homogenous population” (51). They also highlight that popula-
tion influx may have occurred even where few archaeological
traces have been identified. This prompts a critical reassess-
ment of the origins of Orcadian BA practices, which have hith-
erto been viewed either as insular development, imitative of
distant elites, or the result of gradual filtering-in of influences.
The circumstances surrounding the emergence of novel monu-
ment types such as barrows and burnt mounds, for example,
will need to be reconsidered.
If more widely borne out, these findings suggest that BA
Orkney is likely to have seen regular and sustained migration,
engaged in long-distance exchange networks, and adopted
novel practices. The perseverance of Neolithic lineages—and,
potentially, identities—into this period adds a further layer of
cultural complexity, the implications of which remain to be fully
explored.
Materials and Methods
We describe the archaeological samples and materials and methods fully in SI
Appendix. Briey, weextracted DNA from 37 samples using existing protocols
(33, 52, 53). We constructed and UDG (uracilDNA glycosylase) treated next-
generation sequencing libraries (42, 54, 55), pooled equimolarly, and
sequenced all libraries on an Illumina HiSeq4000 (100-bp, paired-end sequenc-
ing; Macr ogen). We trimmed sequence reads of adapter sequences and merged
them using AdapterRemoval (version 2.1.7) (56). We mapped reads to the
human reference genome (UCSC [University of California Santa Cruz] hg19) and
the human mitochondrial reference genome (the revised Cambridge reference
sequence or rCRS, NC_012920.1) (57) using BWA aln (BurrowsWheeler align-
ment tool) (version 0.7.12-r1039) (58) and ltered for mapping quality (56, 59).
We examined molecular damage patterns to establish data authenticity and lev-
els of mtDNA and whole-genome contamination. As expected from UDG-
treated samples, observed damage patterns were minor (SI Appendix,Fig.S9).
We carried out uniparental marker analysis and molecular sex determination
(60) following established methods. We used GATK (version 3.8) to call pseudo-
haploid genotypes at known SNP positions, which were then merged with the
Human Origins dataset (61), the 1000 Genomes Project data, and realigned pub-
lished ancient samples (SI Appendix). We investigated population relationships
between newly reported samples and other ancient and modern individuals
using smartPCA and ADMIXTURE (version 1.3) (62), with Dand fstatistics calcu-
lated using ADMIXTOOLS (63) to formally conrm relationships, and quantied
admixture using qpAdm (34). A list of published samples we used in analyses is
in Dataset S1I. We inferred kinship relationships using READ (45) and assessed
ROH and effective population size with hapROH (44). We describe construction
of Y-chromosome phylochronology for I2a and R1b-M269 in SI Appendix,
Section S6 and Figs. S10S16. We extracted the modern mitogenomes from the
whole-genome Orkney Complex Disease Study (ORCADES) for Orkney (64) and
the VIKING study for Shetland (65).
Data Availability. Raw sequencing reads of ancient samples produced for this
study have been deposited in the European Nucleotide Archive under acces-
sion no. PRJEB46830. Modern mitochondrial genomes generated as part of
this study have been deposited in GenBank, accession nos. MZ846240
to MZ848095.
ACKNOWLEDGMENTS. We thank Steve Birch, Jenny Murray, and Sue Black
for help with samples; Harald Ringbauer for advice on hapROH; and Joyce
Richards for comments on an early draft. Excavations at LoN and KoS are
directed by H.M. and G.W., EASE (Environment and Archaeology Services),
grant funded by Historic Environment Scotland. M. Ni Challanain, M. McCor-
mick, and D. Gooney undertook osteological identications and sample
selection. K.D., M.G.B.F, P.J., M.S., G.O.-G, A.F., and S.R. were supported by a
Leverhulme Trust Doctoral Scholarship program awarded to M.B.R. and M.P.
DNA sequencing was also supported by the UK Natural Environment Research
Council Biomolecular Analysis Facility (NBAF) at the University of Liverpool,
under NBAF Pilot Scheme NBAF685, awarded to C.J.E. whilst at the University
of Oxford. P.S., M.P., and M.B.R. acknowledge FCT (Fundac¸~
aoparaaCi
^
encia e
a Tecnologia) support through project PTDC/EPH-ARQ/4164/2014, partially
funded by FEDER (Fundo Europeu de Desenvolvimento Regional) funds
(COMPETE 2020 project 016899). PS was supported by FCT, European Social
Fund, Programa Operacional Potencial Humano, and the FCT Investigator Pro-
gramme and acknowledges FCT/MEC (Minist
erio da Educac¸~
ao e Ci^
encia) for
support to CBMA through Portuguese funds (PIDDAC: Programa de Investi-
mentos e Despesas de Desenvolvimento da Administrac¸~
ao Central)PEst-OE/
BIA/UI4050/2014. V.M. and D.G.B. acknowledge the Science Foundation Ire-
land/Health Research Board/Wellcome Trust Biomedical Research Partnership
Investigator Award No. 205072 to D.G.B., Ancient Genomics and the Atlantic
Burden.The ORCADES was supported by the Chief Scientist Ofce of theScot-
tish Government (CZB/4/276, CZB/4/710), a Royal Society University Research
Fellowship to J.F.W., the MRC (Medical Research Council) Human Genetics Unit
quinquennial programme QTLinHealthandDisease,Arthritis Research UK,
and the EU FP6 EUROSPAN project (contract no. LSHG-CT-2006-018947). The
Edinburgh Clinical Research Facility, University of Edinburgh, performed DNA
extractions and the Sanger Institute performed whole-genome sequencing.
The Viking Health StudyShetland (VIKING) was supported by the MRC Human
Genetics Unit quinquennial programme grant QTL in Health and Disease.
DNA extractions were performed at the Edinburgh Clinical Research Facility,
University of Edinburgh. Whole genome sequencing was supported by the
Scottish Genomes Partnership award from the Chief Scientist Ofce of the
Scottish Government and the MRC (grant reference SGP/1) and the MRC Whole
Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). We
acknowledge Wellcome Trust funding (098051) for the ORCADES whole-
genome sequencing. J.F.W. acknowledges support from the MRC Human
Genetics Unit programme grant, Quantitative traits in health and disease
(U. MC_UU_00007/10). We also acknowledge the invaluable contributions of
the research nurses in Orkney and Shetland, the administrative team in Edin-
burgh, and the people of Orkney and Shetland.
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ANTHROPOLOGY
Dulias et al.
Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
PNAS j9of10
https://doi.org/10.1073/pnas.2108001119
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https://doi.org/10.1073/pnas.2108001119 Ancient DNA at the edge of the world: Continental immigration and the
persistence of Neolithic male lineages in Bronze Age Orkney
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... We used the Pileup tool from GATK software (v.3.7.0) 69 to extract base calls over single-nucleotide polymorphism (SNP) sites in the 1,240k panel 75 for relevant genomes and selected one base call at random (base quality >30) for each site to generate pseudo-haploid genotypes. We merged 1,240k genotypes for 534 Iron Age individuals [17][18][19]41,61,[76][77][78][79][80] with a dataset of 5,326 modern individuals from western Europe 38,81 and, using approximately 266,000 sites common to both datasets, projected ancient genomes onto a PCA plot of modern variation using smartpca (version 16000) from EIGENSOFT 82 . We quantified EEF ancestry in British Iron Age genomes following a previously described procedure 17 . ...
... We used a dataset of 697 individuals [17][18][19]41,[76][77][78][99][100][101][102][103][104][105][106] from the European Bronze Age to medieval period for ChromoPainter 36 analysis (Supplementary Table 12). This dataset had been previously subjected to Beagle5 imputation and phasing. ...
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Roman writers found the relative empowerment of Celtic women remarkable¹. In southern Britain, the Late Iron Age Durotriges tribe often buried women with substantial grave goods². Here we analyse 57 ancient genomes from Durotrigian burial sites and find an extended kin group centred around a single maternal lineage, with unrelated (presumably inward migrating) burials being predominantly male. Such a matrilocal pattern is undescribed in European prehistory, but when we compare mitochondrial haplotype variation among European archaeological sites spanning six millennia, British Iron Age cemeteries stand out as having marked reductions in diversity driven by the presence of dominant matrilines. Patterns of haplotype sharing reveal that British Iron Age populations form fine-grained geographical clusters with southern links extending across the channel to the continent. Indeed, whereas most of Britain shows majority genomic continuity from the Early Bronze Age to the Iron Age, this is markedly reduced in a southern coastal core region with persistent cross-channel cultural exchange³. This southern core has evidence of population influx in the Middle Bronze Age but also during the Iron Age. This is asynchronous with the rest of the island and points towards a staged, geographically granular absorption of continental influence, possibly including the acquisition of Celtic languages.
... Conversely, a lack of admixture in Scotland is observed in the wake of the Middle to Late Bronze Age genetic turnover in Britain, suggesting that contact between Celtic speakers and now-unknown non-Celtic speakers could persist well into later prehistory (Patterson et al. 2022). In Orkney, Neolithic farmer lineages survived well into the Iron Age along the male line, and influx of Steppederived lineages mainly occurred along the female line (Dulias et al. 2022). ...
... A third possibility is to identify the Insular Celtic substrate with the few people descending from Neolithic farmers holding out in northern Britain and in Orkney (Dulias et al. 2022), but these holdouts seem rather peripheral to the more southerly location where Brittonic and Goidelic must have formed. ...
... Studies (GWAS). In practice, the median c 2 statistic (squared Z-score for number of standard 94 errors s is from zero) is inflated by 5.26-fold relative to a c 2 distribution with one degree of 95 freedom. In human genetics studies, such inflation can arise due to a variety of factors such as 96 uncorrected population structure, and is often addressed by rescaling c 2 statistics by the 97 median inflation across the genome 21,22 . ...
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We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ∼0% to ∼20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1 ; a rise from ∼0% to ∼8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ∼2% to ∼9% from ∼5500 to ∼3000 years ago before dropping to ∼3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the “Thrifty Gene” hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
... Further aDNA studies have confirmed that the Late Iron Age Irish and northern British tribes, some of whom were later referred to as the Picts, were the direct descendants of these Beaker immigrants (Dulias et al., 2022;Margaryan et al., 2020). The Beaker Culture existed in Britain from 2500 BC until around 1800 BC (Bradley, 2007, p. 14), bracketing the constructions of Holme I and II. ...
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... Bentley et al., 2002Bentley et al., , 2012Knipper et al., 2017), from aDNA analyses (cf. Schroeder et al., 2019;Dulias et al., 2022;Villalba-Mouco et al., 2022), or from a combination the two (Sjögren et al., 2020). At times these interpretations of female migration as evidence of patrilocality (residence) are linked to patrilineality (descent) and may even be seen as indications of patriarchy (power) (Mittnik et al., 2019;Sjögren et al., 2020). ...
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Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.
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Human remains from the Iron Age in Atlantic Scotland are rare, which makes the assemblage of an adult female and numerous foetal bones at High Pasture Cave, on the Isle of Skye, particularly noteworthy. Archaeological evidence suggests that the female had been deposited as an articulated skeleton when the cave entrance was blocked off, marking the end of use of the site. Particularly intriguing is the deposition of disarticulated remains from a foetus and perinate close to the adult female, which opens the possibility that the female might have been the mother of both of the infants. We used shotgun genome sequencing in order to analyse the mitochondrial genomes of all three individuals and investigate their maternal relationship, and we report here, for the first time, complete ancient mitogenomes from foetal-aged bone fragments. While we could not exclude the possibility that the female was the mother of, or maternally related to, the foetus, we could definitely say that she was not the mother of the perinate buried alongside her. This finding is contrary to the standard archaeological interpretation, that women in such burials most likely died in childbirth and were buried together with their foetuses.