Article

100 ancient genomes show repeated

population turnovers in Neolithic Denmark

https://doi.org/10.1038/s41586-023-06862-3 Major migration events in Holocene Eurasia have been characterized genetically at
Received: 6 April 2023 broad regional scales1–4. However, insights into the population dynamics in the contact
zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal
Accepted: 13 November 2023
resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from
Published online: 10 January 2024 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and
Open access Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N
Check for updates content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that
Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures
form a distinct genetic cluster related to other Western European hunter-gatherers.
Despite shifts in material culture they displayed genetic homogeneity from around
10,500 to 5,900 calibrated years before present, when Neolithic farmers with
Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by
more than a millennium relative to Central Europe, it was very abrupt and resulted in a
population turnover with limited genetic contribution from local hunter-gatherers.
The succeeding Neolithic population, associated with the Funnel Beaker culture,
persisted for only about 1,000 years before immigrants with eastern Steppe-derived
ancestry arrived. This second and equally rapid population replacement gave rise to
the Single Grave culture with an ancestry profile more similar to present-day Danes.
In our multiproxy dataset, these major demographic events are manifested as parallel
shifts in genotype, phenotype, diet and land use.

The Mesolithic and Neolithic periods in southern Scandinavia are
marked by a number of pivotal and well-described cultural transitions8.
However, the genetic and demographic impacts of these events remain
largely uncharacterized. The early postglacial human colonization of
the Scandinavian peninsula (Sweden and Norway) is believed to com-
prise at least two distinct migration waves: a source related to western
European hunter-gatherers (WHG) from the south, and an eastern
European hunter-gatherer (EHG) source into the far north, before ven-
turing south along the Atlantic coast of Norway9,10. However, insight
into the fine-scale structure and mobility of Scandinavian Mesolithic
populations is limited, including an almost complete absence of genetic
data from southern Scandinavian populations associated with the con-
secutive Maglemose, Kongemose and Ertebølle cultures in Denmark.
The Neolithic transition represents a watershed event in European
prehistory, marked by the spread of domesticated crops and livestock
from Southwest Asia, starting around 11,000 bp. Although migrations
and population turnovers associated with this transition have been
demonstrated at broad geographical and chronological scales1–4, coarse
sampling and a one-sided focus on genetics have hindered insights on
social interaction and detailed demographic processes in the contact
zones between locals and newcomers5–7. Southern Scandinavia occu-
pies an enigmatic position in this discussion. The Neolithic transition
was delayed here by a millennium compared to Central Europe, during
which hunter-gatherer societies continued to flourish until around
5,900 calibrated years bp (cal. bp), only marginally affected by farmer
populations to the south11. The substantial delay could suggest that the
transition to farming in Denmark occurred by a different mechanism
involving a stronger element of cultural diffusion12 than the migration
of people (demic diffusion) observed in the rest of Europe13–15.
An extensive archaeological record has indicated that the Funnel
Beaker culture (FBC) thrived for the first millennium of the Neolithic
in Denmark, before an apparent decline16 was followed by the appear-
ance of the Single Grave culture (SGC). Owing to a lack of genetic data
and a robust absolute chronology, the relation between the FBC and
the SGC has been extensively debated17–19. Population dynamics asso-
ciated with this second cultural transition in Neolithic Denmark are
similarly unresolved, including its possible link to the ‘steppe migra-
tions’ that transformed the gene pools elsewhere in Europe around
the same time1,2.
To investigate these defining events at high temporal and spatial
resolution, we analyse a detailed and continuous dataset of 100 ancient
Danish shotgun-sequenced genomes (0.01× to 7.1× autosomal cover-
age3), spanning about 7,300 years from the Early Mesolithic Magle-
mose, the Kongemose and Late Mesolithic Ertebølle epochs, the Early
and Middle Neolithic FBC and the SGC, up until the Bronze Age (Fig. 1
and Supplementary Data 1). The archaeological record in Denmark
represents a very large assemblage of well-documented Mesolithic
and Neolithic human skeletal remains, from a wide range of chrono-
logical, topographical and socio-cultural contexts. This is a result of
an environment and climate that was amenable to both Mesolithic
fisher-hunter-gatherer lifeways20 and the later Neolithic farming
practices, combined with taphonomically favourable preservation
conditions for skeletal remains, and a long, prolific history of archaeo-
logical research. We used a multiproxy approach, combining autosomal

A list of authors and their affiliations appears at the end of the paper.

Nature | Vol 625 | 11 January 2024 | 329

Article
a b
Calibrated age (years) Phase 0.06
11,700-5,900 Mesolithic East
5,900-5,800 Transitional
N Caucasus and Iran
5,800-4,800 Early Neolithic
4,800-4,600 Transitional Steppe
4,600-3,000 Late Neolithic to
Early Bronze Age
0.03

cline
erer
r-gath
PC2 (0.65%)
0

hunte
Europe

pean
post-Neolithic
Levant

Euro
−0.03 Early

line
Late rc
me
West far
an
ro pe
Eu
−0.06
100 km
−0.06 −0.03 0 0.03

Anatolia PC1 (1.37%)

c Neolithic
Mesolithic Steppe BA Late Neolithic
Italy Sweden Russia Yamnaya Mesolithic Transitional Early Neolithic Transitional Early BA Iron Age Viking Age

Fig. 1 | Overview of dataset. a, Geographic locations and age ranges relating to
the 100 sequenced genomes from Denmark. Groupings are designated through
a combination of chronology, culture, and ancestry (see Supplementary Notes
1 and 3). b, PCA for 179 ancient Danish individuals (Supplementary Data 3)
ranging from the Mesolithic to the Viking Age, including previously published
ones1,47,57,76, in the context of broader West Eurasian genetic diversity (n = 983
modern individuals, open grey circles; n = 1,105 ancient individuals, filled grey
circles). Ancient individuals from Denmark are coloured according to the period
as defined in a and c. c, Unsupervised model-based clustering (ADMIXTURE)
for K = 8 ancestry components in Danish individuals, as well as contextual data
from selected groups (left) that represent relevant ancestry components. See
Extended Data Fig. 1 for individual labels. Black crosses indicate low-coverage
genomes represented by pseudo-haploid genotypes. BA, Bronze Age.

imputed genomes3,21 with Y chromosomal and mitochondrial haplo-
groups, 14C-dating, genetic phenotype predictions, as well as 87Sr/86Sr,
δ13C and δ15N isotope data as proxies for mobility and diet. Moreover,
to investigate a direct link between demographic and environmental
processes, we align the genetic changes observed in the Danish popula-
tion over time with changes in local vegetation, based on pollen analyses
and quantitative vegetation cover reconstruction.
The Mesolithic period
It is not known whether shifts in southern Scandinavian Mesolithic
material culture occurred in a population continuum or were facilitated
by incoming migrants. The Early Mesolithic settlement in Denmark is
associated with the Maglemose culture (around 11,000–8,400 cal. bp),
characterized archaeologically by small flint projectiles in geometric
shapes. Until the recent development of underwater archaeology,
this culture was known mainly from inland locations along lakes and
rivers22. During the succeeding Kongemose culture (around 8,400–
7,400 cal. bp), trapeze-shaped flint points dominate the assemblages
of arrowheads23 along with high quality long blades. Most of the larger
settlements cluster at good fishing locations along the coasts24, but
there are also specialized hunting camps in the interior25. The Late Mes-
olithic Ertebølle culture (about 7,400–5,900 cal. bp), is characterized by
flint points with transverse edges. Pottery was introduced from other
hunter-gatherer groups to the east and perhaps the southwest26 and
‘exotic’ shaft-hole axes suggest exchange with farming societies south
of the Baltic Sea27. The larger habitation sites, densely scattered along
the coasts, probably represent multi-family, year-round occupation24,28
and they have provided important insights into the physical anthropol-
ogy and spiritual culture of the period.
By analysing genomes from 38 Danish hunter-gatherers and infer-
ring their ancestry, we examine whether cultural transitions observed
in the Danish archaeological record are associated with any genetic
changes in the population. Model-based clustering (ADMIXTURE),
PCA and IBD-sharing analyses show that throughout the Maglemose
(n = 4), Kongemose (n = 8) and Ertebølle (n = 27) epochs the region dis-
played a remarkable genetic homogeneity across a 4,500-year transect
(Figs. 1–3 and Extended Data Figs. 1–3), supporting interpretations of
demographic continuity favoured by some archaeologists23–25. From the
earliest known skeleton in Denmark, ‘Koelbjerg Man’ (NEO254, 10,648–
10,282 cal. bp29), to the most recent Mesolithic skeleton included here,
‘Rødhals Man’ (NEO645, 5,916–5,795 cal. bp), the individuals derive
their ancestry almost exclusively from the same southern European
source (Italy_15000BP_9000BP) that predominated in WHG ancestry
in Mesolithic Western Europe3.
In the IBD-based principal components analysis (PCA), the Dan-
ish Mesolithic individuals cluster closely together (Extended Data
Fig. 4a), but beyond this tight local genetic connection they share most
recent ancestry with the geographically and temporally proximate
hunter-gatherer individuals from Western Europe (such as Cheddar
Man, Loschbour and Bichon, commonly referred to as WHG; genetic
cluster EuropeW_13500BP_8000BP; Fig. 2). A subtle shift of the earli-
est Danish individuals towards these western individuals probably
reflects their closer temporal proximity captured through IBD sharing
(Extended Data Fig. 4a). Although pressure-debitage of blades in the
Maglemosian culture and pottery in the Ertebølle culture are both

330 | Nature | Vol 625 | 11 January 2024

 Scandinavia_5600BP_4600BP

Scandinavia_4600BP_3800BP

Scandinavia_4200BP_3200BP

Scandinavia_4000BP_3000BP
Denmark_10500BP_6000BP

EuropeNE_4800BP_3000BP
Europe_4500BP_2000BP
IBD sharing rate

Sweden_5000BP
0.03

0.06

0.09

Ukraine_10000BP_4000BP
MiddleDon_7500BP
DonRiver_5800BP_5300BP
RussiaNW_7000BP_5000BP
HG_EuropeE
RussiaNW_11000BP_8000BP
Norway_9300BP_4300BP
Sweden_5000BP
Sweden_10000BP_7500BP
EuropeE_8600BP_6000BP
Romania_8800BP
Baltic_8300BP_6000BP
Denmark_10500BP_6000BP HG_EuropeW
EuropeW_13500BP_8000BP
Iberia_9000BP_7000BP
Italy_15000BP_9000BP
Caucasus_13000BP_10000BP HG_Caucasus
Turkmenistan_7000BP_5000BP
Farmer_Iran
Iran_10000BP_8500BP
Anatolia_8500BP_8000BP
Boncuklu_10000BP
EuropeEW_8500BP_6500BP Farmer_Europe_early
EuropeCE_7000BP_5500BP
EuropeS_8000BP_6000BP
Scotland_5200BP_4800BP
EuropeNW_6000BP_5000BP
Italy_5500BP_4000BP Farmer_EuropeW_late
Iberia_7300BP_3500BP
EuropeSW_6000BP_3500BP
Poland_5000BP_4700BP
Farmer_EuropeE_late
Scandinavia_5600BP_4600BP
Steppe_5000BP_4300BP Nomad_Steppe_early
EuropeNE_4800BP_3000BP
Scandinavia_4200BP_3200BP
PostNeol_EuropeW
Scandinavia_4600BP_3800BP
Europe_4500BP_2000BP
Scandinavia_4000BP_3000BP PostNeol_EuropeN
Yana_31000BP
HG_Eurasia_UP
Europe_37000BP_33000BP
syltholm

Gjerrild5
VK214
NEO898
NEO254

NEO759
NEO123
NEO122

NEO683
NEO932
NEO589
NEO791
NEO749
NEO745
NEO747
NEO586
NEO583
NEO733
NEO855
NEO570
NEO568
NEO856
NEO852
NEO751
NEO941
NEO598
NEO853
NEO960
NEO645

NEO891
NEO790

NEO595

NEO753
NEO942

NEO886
NEO866
NEO757
NEO945
NEO896
NEO933

NEO744
NEO935
NEO597
NEO599

NEO925
NEO943
NEO875
NEO737

NEO878
NEO870

NEO738
NEO739
NEO861
NEO860

NEO735
NEO752
NEO951
NEO792

NEO563
NEO590
NEO946
NEO91

NEO19

NEO29

NEO23

NEO28

NEO43

NEO25

NEO92

NEO93
RISE61

RISE71
Fig. 2 | Identity-by-descent sharing patterns in ancient Danish individuals
from circa 10,500–3000 cal. BP. Heat map showing relative IBD-sharing rate
of 72 imputed ancient individuals from Denmark (n = 67 individuals reported in
this Article, n = 5 previously published individuals1,47,57,76) from the Mesolithic to
the Bronze Age with selected genetic clusters. Individuals are grouped by their
genetic cluster membership. See Supplementary Data 3 for dataset and ancestry
category definition.

argued to have an eastern origin9,10,30,31, our data show no evidence for
admixture with more eastern hunter-gatherers during those times.
This points to cultural diffusion as the source of these introductions in
Denmark. When tested with D-statistics, all Danish Mesolithic individu-
als form a clade with the earliest individual (NEO254), to the exclusion
of Swedish Mesolithic hunter-gatherers (Sweden_10000BP_7500BP;
Extended Data Fig. 2a) despite the close proximity to Sweden. However,
a weak signal of gene flow with EHGs was shared across the whole Danish
Mesolithic transect (Extended Data Fig. 2b), suggesting contact with
communities further to the east prior to their expansion into Denmark
before or during the earliest Mesolithic.
Genetic phenotype predictions (Supplementary Note 2) indicate a
high probability of blue eye pigmentation throughout the Mesolithic,
consistent with previous findings1,15,32, showing that this feature was
present already in the early Mesolithic but was not fixed in the popula-
tion. The Mesolithic hunter-gatherers from Denmark all display high
probability of brown or black hair and height predictions generally
suggest slightly lower and/or less variable stature than in the succeeding
Neolithic period. We caution, however, that the relatively large genetic
distance to modern individuals included in the genome-wide associa-
tion studies (GWAS) panel produces scores that are less applicable to
Mesolithic individuals than to more recent groups33.
Stable isotope δ13C values in collagen can inform on the proportion of
marine versus terrestrially-derived protein, whereas δ15N values reflect
the trophic level of the protein sources34. The earliest skeleton (NEO254)
shows depleted dietary isotopic values (Fig. 3) representing a lifestyle of
inland hunter-gatherers of the Early Mesolithic. This result is mirrored
in the second earliest known skeleton from Denmark (Tømmerupgårds
Mose34). From later Maglemose (around 9,500 cal. BP) and throughout
the Kongemose and Ertebølle epochs, we observe gradually increased
δ13C and δ15N values (Extended Data Fig. 5 and Supplementary Figs. 4.1
and 4.2). This implies that marine foods progressed to constitute the
major supply of proteins, as suggested previously based on data from
more than 30 Mesolithic humans and dogs, from both coastal and
inland sites in Denmark34,35. During this period global sea-level rise
gradually transformed present-day Denmark into an archipelago, where
all human groups had ample access to coastal resources within their
annual territories24. The local Mesolithic population adapted their diet
and culture over time to the changing landscape and our data show
that this occurred in a continuous population, without any detectable
influx of migrants over a 4,500-year period. Low variability in 87Sr/86Sr
isotope ratios throughout the Mesolithic (Fig. 3 and Supplementary
Note 5) could indicate limited long-range mobility and/or deriving
dietary sources from more homogeneous environments (for example,
marine) than in the succeeding Neolithic periods.
Notably, some of the Danish Mesolithic individuals proved to be
closely related3. Close kinship is demonstrated in the case of two indi-
viduals (NEO568/NEO569), father and son, interred next to each other
in the locus classicus shell midden site of Ertebølle, and in the case of
two individuals (NEO732/NEO733), mother and daughter, that were
buried together at Dragsholm. The Ertebølle grave was the first dis-
covered human skeleton in Denmark (excavated in the 1890s) that
indisputably represented hunter-gatherers. After the excavation of
this site, academic reasoning rooted in Biblical narration about early
prehistory in Scandinavia lost momentum. The excavation data cannot
reveal whether they were buried simultaneously; it can be ascertained

Nature | Vol 625 | 11 January 2024 | 331

Article
Maglemose Kongemose Pitted Ware
Ertebølle Funnel Beaker Single Grave
Dagger Bronze Age

10450 BP 9450 BP 8450 BP 7450 BP 6450 BP 5450 BP 4450 BP 3450 BP 2450 BP

8500 BC 7500 BC 6500 BC 5500 BC 4500 BC 3500 BC 2500 BC 1500 BC 500 BC
Timeline

NEO254

NEO759
NEO123
NEO122
NEO600
NEO683
NEO589
NEO587
NEO932
NEO748
NEO814
NEO749
NEO791
NEO586
NEO746
NEO583
NEO822
NEO930
NEO733
NEO732
NEO745
NEO856
NEO747
NEO941
NEO570
NEO751
NEO852
NEO855
NEO568
NEO569
NEO598
NEO853
NEO960
NEO645
NEO601
NEO962
NEO891
NEO790
NEO595
NEO564
NEO571
NEO753
NEO942
NEO886
NEO866
NEO757
NEO896
NEO945
NEO933
NEO888
NEO744
NEO795
NEO702
NEO935
NEO597
NEO865
NEO594
NEO961
NEO599
NEO602
NEO566
NEO898
NEO925
NEO943
NEO580
NEO792
NEO876
NEO870
NEO737
NEO738
NEO861
NEO878
NEO872
NEO735
NEO875
NEO739
NEO934
NEO857
NEO860
NEO752
NEO815
NEO563
NEO951
NEO590
NEO946
NEO13
NEO91

NEO19

NEO29
NEO23

NEO41
NEO28

NEO43

NEO33

NEO25

NEO92

NEO93
NEO1

NEO3

NEO7
Autosomal DNA
1.00
Italy_15000BP_9000BP
0.75 Anatolia_8500BP_8000BP

0.50 RussiaNW_11000BP_8000BP

Steppe_5000BP_4300BP
0.25
+Possibly contaminated
* Low coverage (<0.05)
0 * + + + * * * * * * * * +
* *
Sex
Ancestry

XY
XX
Y chromosome haplotypes
I2
R1b
I1
Q1
L1
I
R1a
Mitochondrial haplotypes
U
H
K
R
J
N
T
V
W
Eye colour
1.00
0.75
0.50 +Possibly contaminated
0.25 #Low GP
0 # ^Low coverage (<0.1)
## + ## + + #^ ## # # # # ## # # # # # # ^ # # +
^ ^^ ^^ # # ^ ^^ ^ ^ ^ ^ ^ ^ ^ ^ ^^ ^ ^ ^ ^
Hair colour ^ ^
1.00
Phenotypes

0.75
0.50
0.25
0 # ## + ## + + #^ +# # # # # # # +# ## # # # ^ # # +
^ ^^ # ^^ # # ^ #^ ^ ^ ^ ^ ^# ^ ^^ ^ ^ ^ ^ ^
Height ^ ^ ^ ^

2.5
0
−2.5
−5.0
87Sr/ 86Sr

0.714
0.712
0.710

δ13C
−10.0
−12.5
−15.0
Isotopes

−17.5
−20.0
−22.5
δ15N
15.0
12.5
10.0
7.5
NEO254

NEO759
NEO123
NEO122
NEO600
NEO683
NEO589
NEO587
NEO932
NEO748
NEO814
NEO749
NEO791
NEO586
NEO746
NEO583
NEO822
NEO930
NEO733
NEO732
NEO745
NEO856
NEO747
NEO941
NEO570
NEO751
NEO852
NEO855
NEO568
NEO569
NEO003
NEO598
NEO853
NEO960
NEO645
NEO601
NEO891
NEO790
NEO595
NEO564
NEO571
NEO753
NEO942
NEO886
NEO866
NEO757
NEO896
NEO945
NEO933
NEO888
NEO744
NEO795
NEO702
NEO935
NEO597
NEO865
NEO594
NEO961
NEO599
NEO602
NEO566
NEO898
NEO925
NEO943
NEO580
NEO792
NEO876
NEO870
NEO737
NEO738
NEO861
NEO878
NEO872
NEO735
NEO875
NEO739
NEO934
NEO857
NEO860
NEO752
NEO815
NEO563
NEO951
NEO590
NEO946
NEO962
NEO13
NEO91

NEO19

NEO29
NEO23

NEO41
NEO28

NEO43

NEO33

NEO25

NEO92

NEO93
NEO1

NEO7

Pollen-based vegetation cover

100 Crops
Grassland

75 Secondary forest
Vegetation

50
Primary forest

25

0
6500 BP 6000 BP 5500 BP 5000 BP 4500 BP

Fig. 3 | See next page for caption.

only that the boy (infant, less than two years of age) was positioned less goods suggesting an Early Neolithic date for the latter36. A close kin
than one metre from his father (the ‘Ertebølle Man’). Excavations at relationship was suggested for the two Dragsholm women on the basis
Dragsholm in 1973 uncovered a well-preserved double burial containing of physical anthropological observations37. It was suggested that they
a grave with two Mesolithic women as well as a male grave with grave were sisters, but this can now be corrected to a co-burial of a mother

332 | Nature | Vol 625 | 11 January 2024

Fig. 3 | Genetic, phenotypic, dietary and environmental shifts in Denmark
through time. Evidence of two population turnovers in chronologically sorted
multiproxy data from 100 Danish Mesolithic, Neolithic and Early Bronze Age
skeletons (Supplement Data 1). The figure shows concomitant changes in
(from the top) admixture proportions in non-imputed genome-wide data,
Y chromosomal and mitochondrial haplogroups, genetic phenotype predictions
(based on imputed data) and 87Sr/86Sr and δ13C and δ15N isotope data as proxies
for mobility and diet, respectively. Predicted height values represent differences
(in cm) from the average height of the present-day Danish population;
and daughter. Our data also show that the male in the adjacent burial
(‘Dragsholm Man’, NEO962) was not related to the two women. These
cases show that close biological kinship was socially relevant to Late
Mesolithic groups in Northern Europe and affected the mortuary treat-
ment of dead members of their society.
Early Neolithic transition
The emergence of the Neolithic FBC in Denmark has occupied a central
position in archaeological research and debate throughout the past
175 years8,38,39. The defining element of the Neolithic, a food-producing
economy based on domesticates of southwest Asian origin, was indis-
putably present in Denmark from around 5,900 cal. bp11,38. The neoli-
thization saw a boom of new shapes and types introduced in Danish
material culture, including funnel-shaped beakers and polished flint
axes. From about 5,800 cal. bp, monumental long barrows of wood and
earth were added to the repertoire, and about 200 years later, burials
built of soil, surrounded by raised stones and including stone-built
chambers, were erected as dominant landmarks in the farmland40.
After 5,300 cal. bp, larger and more complex stone-constructed pas-
sage graves in large earthen tumuli emerged41. Meanwhile, simple,
non-monumental burials continued along with the megalithic tombs
all through the FBC epoch42. Habitation deposits, dating to the earliest
centuries of the Neolithic, on top of many Mesolithic Ertebølle coastal
shell middens may be interpreted as a local continuation of marine
gathering and fishing. By contrast, other settlements with regular long
houses on easily farmed soils further inland are associated with remains
of domestic plants and animals suggesting a very clear distinction from
the previous Mesolithic Ertebølle period39,43.
Regardless of these nuances, at around 5,900 cal. bp, our multi-
proxy dataset documents a marked and abrupt concomitant shift
in genetic, phenotypic, dietary and vegetation parameters (Fig. 3).
This is robust evidence for demic diffusion, settling a long-standing
debate8,38. As observed elsewhere in Europe13–15, the introduction of
farming in Denmark was unequivocally associated with the arrival
of people with Anatolian farmer-related ancestry. This resulted in a
population replacement with limited genetic contribution from the
local hunter-gatherers. The earliest example of this typical Neolithic
ancestry in our Danish dataset is observed in a bog skeleton of a female
from Viksø Mose (NEO601) dated to 5,896–5,718 cal. bp (95%). In the
PCA, all Danish Early Neolithic individuals cluster at the ‘late’ end of
the European Neolithic farmer cline and consistently show some of
the largest amounts of hunter-gatherer ancestry (10–35%) among
all European Neolithic farmer genomes included (Figs. 1 and 3 and
Extended Data Figs. 1 and 5a and Supplementary Data 4). In IBD clus-
tering analyses, the Danish individuals form part of a genetic cluster
(Scandinavia_5600BP_4600BP) together with FBC-associated indi-
viduals from Sweden and Poland, and also show close affinity with
Polish individuals from the Globular Amphora culture (GAC) (Extended
Data Fig. 4b). This could suggest an eastern European proximate ori-
gin of the Early Neolithic farmers in Denmark. Using more proximate
ancestry modelling, we find that Neolithic FBC-associated individuals
across Denmark, Sweden and Poland derived their hunter-gatherer
ancestry component predominantly from a source related to WHG
probabilities for the hair colours (blond, brown, black and red) and eye colours
(blue and brown) are shown, with grey denoting probability of intermediate eye
colour (including grey, green and hazel). Lower panel shows the quantitative
changes in vegetation cover, based on pollen analyses at Lake Højby in Zealand.
Note that the vegetation panel covers a shorter time interval than the other
panels. Black vertical lines mark the first presence of Anatolian Neolithic farmer
ancestry and Steppe-related ancestry, respectively. Individuals with low genomic
coverage, signs of possible contamination and/or low genotype prediction score
(GP) are indicated (Methods).
(EuropeW_13500BP_8000BP). Ancestry related to Danish Mesolithic
hunter-gatherers (Denmark_10500BP_6000BP) is found in smaller
proportions (less than around 10%) and only in a subset of the FBC
individuals from Denmark (Extended Data Fig. 6). Moreover, this
tends to occur in more recent individuals (dated to around 5,400 cal.
BP onwards) who are also showing the overall largest amount of total
hunter-gatherer ancestry (for example, NEO945 and NEO886; Fig. 3
and Extended Data Figs. 3 and 6a,b). Using DATES44, we found that
admixture times for a large proportion of Danish Neolithic individuals
predates 5,900 cal. bp when FBC emerged in Denmark, particularly for
the earliest individuals (Extended Data Fig. 7). More recent admixture
times (post dating the arrival of FBC in Denmark) were mainly observed
in individuals dated to after about 5,400 cal. bp, and were associated
with overall higher hunter-gatherer proportions. These observations
were in marked contrast to FBC-associated individuals from Sweden,
where admixture times and hunter-gatherer ancestry did not change
over time, and no admixture with local Swedish hunter-gatherers was
detected.
Our results demonstrate a population turnover in Denmark at the
onset of the neolithisation by incomers who displayed a mix of Ana-
tolian Neolithic farmer ancestry and non-local hunter-gatherer ances-
try. Ancestry related to the local Danish hunter-gatherers could be
detected only late in the Danish Neolithic gene pool, suggesting gene
flow with groups of late surviving hunter-gatherers, as also documented
in other European regions (Iron Gates45, Central Europe13 and Spain46).
We do not know how the Mesolithic Ertebølle population disappeared.
Some may have been isolated in small ‘pockets’ of brief existence
and/or adapted to a Neolithic lifestyle. The most recent individual in our
Danish dataset with hunter-gatherer ancestry is the aforementioned
Dragsholm Man (NEO962), dated to 5,947–5,664 cal. bp (95% confidence
interval) and archaeologically assigned to the FBC based on his grave
goods37. Our data confirm a typical Neolithic diet matching the cul-
tural affinity but contrasting his hunter-gatherer ancestry. He clearly
represents a local person of Mesolithic ancestry who lived in the short
Mesolithic-Neolithic transition and adopted the culture and diet of the
immigrant farmers. A similar case of late hunter-gatherer ancestry in
Denmark was observed when analysing human DNA obtained from a
piece of chewed birch pitch from the site of Syltholm on Lolland47, dated
to 5,858–5,661 cal. bp (95%). Thus, individuals with hunter-gatherer
ancestry persisted for decades and perhaps centuries after the arrival
of farming groups in Denmark, although they have left only a minor
genomic imprint on the population of the subsequent centuries. Similar
‘relic’ hunter-gatherer ancestry is also found in the Evensås individual
(NEO260) from west-coast Sweden, dated to 5913–5731 cal. bp3.
From the onset of the Neolithic in Denmark, diet shifted abruptly to
a dominance of terrestrial sources as evidenced by δ13C values around
−20‰ and δ15N values around 10‰ (Fig. 3 and Extended Data Fig. 5).
In line with archaeological evidence, these isotopic data show that
domesticated crops and animals provided the main supply of pro-
teins from this point onwards. Isotope values remained stable at these
levels throughout the following periods, although with somewhat
greater variation after about 4,500 cal. bp (Fig. 3). Five Neolithic and
Early Bronze Age individuals have δ13C and δ15N values that indicate
a substantial intake of high trophic marine food. This is especially
Nature | Vol 625 | 11 January 2024 | 333
Article
Age (years)
0.05
10,000
7,500
5,000
2,500
0 0
PC2
PC2
−0.05
−0.10
−0.05 0 0.05
PC1
Fig. 4 | Genetic legacy of ancient Danish individuals. PCA of 2,000 modern
Danish genomes from the iPSYCH study62 in the context of ancient western
Eurasian individuals. Coloured symbols indicate sample age for ancient Danish
individuals, whereas grey symbols indicate 1,145 ancient imputed individuals
pronounced for the individual NEO898 (Svinninge Vejle), one of two
Danish Neolithic individuals displaying ancestry related to Swedish
late hunter-gatherers (see below). A considerably higher variability in
individual 87Sr/86Sr values can be seen with the start of the Neolithic. This
continues in the later periods (Supplementary Note 5) and is not easily
explained by biases in sampling as most of our samples, regardless of
ancestry and time period, are concentrated in the more easterly parts
of Denmark where bone preservation conditions are generally good
(Fig. 1 and Supplementary Fig. 5.3). This pattern could suggest that the
Neolithic farmers in Denmark occupied and/or consumed food from
more diverse landscapes, or were more mobile than the preceding
hunter-gatherers. The Neolithic transition also marks a considerable
rise in frequency of major effect alleles associated with light hair pig-
mentation48, whereas predictions throughout the first millennium of
the Neolithic (FBC epoch) mostly indicate a lower stature than present
day, echoing previous findings32,49.
Pitted Ware culture (PWC) originated on the Scandinavian peninsula
and the Baltic islands east of the Swedish mainland but emerged around
5,100–4,700 cal. bp in the northern and eastern part of Denmark, where
it coexisted with the FBC50,51. It is characterized by coarse pottery that
is often decorated with pits and subsistence based on a combination
of marine species and agricultural products. No burials associated
with the PWC have been discovered in Denmark. Of note, however,
the genomes of two approximately 5,200-year-old male individuals
(NEO33, NEO898) found in Danish wetland deposits proved to be
of hunter-gatherer ancestry related to that of PWC individuals from
Ajvide on the Baltic island of Gotland (Sweden)52 (Figs. 2, 3 and Exten­
ded Data Fig. 4a). Of the two individuals, NEO033 (Vittrup, Northern
Jutland) also displays an outlier Sr signature (Fig. 3), perhaps suggest-
ing a non-local origin that matches his unusual ancestry. Overall, our
results demonstrate direct contact across the sea between Denmark
and the Scandinavian peninsula during this period, which is in line with
archaeological findings50,51.
Later Neolithic and Bronze Age
Europe was transformed by large-scale migrations from the Pontic–
Caspian Steppe around 5,000–4,800 cal. bp. This introduced steppe-
related ancestry to most parts of the continent within a 1,000-year span
and gave rise to the Corded Ware culture (CWC) complex1,2. In Denmark,
this coincided with the transition from the FBC to the SGC, the regional
334 | Nature | Vol 625 | 11 January 2024
0.05
Age (years)
6,000
5,000
4,000
3,000
2,000
1,000
−0.05
−0.10
−0.05 0 0.05
PC1
from across Western Eurasia3. Modern Danish individuals are indicated by
black filled circles and are shown on the right. Inset, a magnified view of the
cluster with modern Danes. The colour scale in the inset represents the age
range of the ancient samples within the magnified region only.
manifestation of the CWC complex. The transition to single graves in
round tumuli has been characterized archaeologically by two expan-
sion phases: a primary and rapid occupation of central, western and
northern Jutland (west Denmark) starting around 4,800 cal. bp and a
later and slower expansion across the Eastern Danish Islands starting
around 4,600 cal. bp53,54. In the eastern parts of the country, SGC traits
are less visible, whereas FBC traditions such as burial in megalithic
grave chambers persisted55. This cultural shift represents another clas-
sical archaeological enigma, with explanations favouring immigration
versus cultural acculturation competing for generations19,56.
Insights from a few low-coverage genomes1,57 have indeed shown
a link to the Steppe expansions, but by mapping out ancestry com-
ponents in the 100 ancient genomes we now uncover the full impact
of this event and demonstrate a second near-complete population
turnover in Denmark within just 1,000 years. This genetic shift was
evident from PCA and ADMIXTURE analyses, in which Danish individu-
als dating to the SGC and Late Neolithic and Bronze Age (LNBA) cluster
with other European LNBA individuals and show large proportions of
ancestry components associated with Yamnaya groups from the Steppe
(Figs. 1 and 3 and Extended Data Fig. 1). We estimate around 60–85%
of ancestry related to Steppe groups (Steppe_5000BP_4300BP), with
the remainder contributed from individuals with farmer-related ances-
try associated with Eastern European GAC (Poland_5000BP_4700BP;
10–23%) and to a lesser extent from local Neolithic Scandinavian farm-
ers (Scandinavia_5600BP_4600BP; 3–18%) (Extended Data Fig. 6a,b).
Although the emergence of SGC introduced a major new ancestry com-
ponent in the Danish gene pool, it was not accompanied by apparent
shifts in dietary isotopic ratios, or Sr isotope ratios (Fig. 3). Our com-
plex trait predictions, however, indicate an increase in height (Fig. 3
and Supplementary Note 2), which is consistent with ancient Steppe
individuals being predicted taller than average European Neolithic
individuals before the steppe migrations32,49,58.
Because of poor preservation conditions in most of western Den-
mark, we do not have skeletons from the earliest phase of the SGC
(around 4,800 cal. bp) so we cannot unequivocally demonstrate that
these people carried steppe-related ancestry. SGC burial customs were
implemented in different ways in the southern and the GAC-related
northern parts of the peninsula, respectively18 and considering recent
genetic results in other regions59, it is plausible that differing demo-
graphic processes unfolded within Denmark. However, we know that
steppe ancestry was present 200 years later in SGC-associated skeletons
from the Gjerrild grave57. The age of the Gjerrild skeletons (from around
4,600 cal. bp) matches the earliest example of steppe-related ancestry
in our current study, identified in a skeleton from a megalithic tomb at
Næs (NEO792). We estimated around 85% of Steppe-related ancestry in
this individual, the highest amount among all Danish LNBA individuals
(Extended Data Fig. 6a). Notably, NEO792 is also contemporaneous
with the two most recent individuals in our dataset showing Anatolian
farmer-related ancestry without any steppe-related ancestry (NEO580,
Klokkehøj and NEO943, Stenderup Hage) testifying to a short period
of ancestry co-existence before the FBC disappeared—similar to the
disappearance of the Mesolithic Ertebølle people of hunter-gatherer
ancestry a thousand years earlier. Using Bayesian modelling we estimate
the duration between the first appearance of Anatolian farmer-related
ancestry to the first appearance of Steppe-related ancestry in Denmark
to be between 876 and 1,100 years (95% prob. interval, Supplementary
Note 3) implying that the former type of ancestry was dominant for
less than 50 generations.
The following Late Neolithic ‘Dagger’ epoch (around 4,300–
3,700 cal. bp) in Denmark has been described as a time of integration
of culturally and genetically distinct groups54. Bronze became domi-
nant in the local production of weapons while elegantly surface-flaked
daggers in flint were still the dominant male burial gift. Unlike the SGC
epoch, this period is richly represented by human skeletal material.
Although broad population genomic signatures suggest genetic sta-
bility in the LNBA (Figs. 1 and 3), patterns of pairwise IBD-sharing and
Y chromosome haplogroup distributions in a temporal transect of 38
LNBA Danish and southern Swedish individuals indicate at least three
distinct ancestry phases during this approximately 1,000-year time
span (Extended Data Figs. 4c and 8).
LNBA phase I: an early stage between around 4,600 and 4,300 cal.
bp, in which Scandinavians cluster with early CWC individuals from
Eastern Europe, rich in Steppe-related ancestry and males with an R1a
Y chromosomal haplotype (Extended Data Fig. 8a,b). Archaeologically,
these individuals are associated with the later stages of the Danish SGC
and the Swedish Battle Axe Culture.
LNBA phase II: an intermediate stage largely coinciding with the
Dagger epoch (around 4,300–3,700 cal. bp), in which Danish individu-
als cluster with central and western European LNBA individuals domi-
nated by males with distinct sub-lineages of R1b-L513 (Extended Data
Fig. 8c,d). Among them are individuals from Borreby (NEO735, 737)
and Madesø (NEO752).
LNBA phase III: a final stage from around 4,000 cal. bp onwards, in
which a distinct cluster of Scandinavian individuals dominated by males
with I1 Y-haplogroups appears (Extended Data Fig. 8e). Y chromosome
haplogroup I1 is one of the dominant haplogroups in present-day Scan-
dinavians, and we here document its earliest occurrence in an approxi-
mately 4,000-year-old individual from Falköping in southern Sweden
(NEO220). The rapid increase in frequency of this haplogroup and asso-
ciated genome-wide ancestry coincides with increase in human mobility
seen in Swedish Sr isotope data, suggesting an influx of people from
eastern or northeastern regions of Scandinavia, and the emergence of
stone cist burials in Southern Sweden60, which were also introduced in
eastern Denmark during that period54,61.
Using genomes from LNBA phase III (Scandinavia_4000BP_3000BP)
in supervised ancestry modelling, we find that they form the predomi-
nant ancestry source for later Iron and Viking Age Scandinavians
(Extended Data Fig. 6d) and other ancient European groups with a
documented Scandinavian or Germanic association (for example,
Anglo-Saxons and Goths; Extended Data Fig. 6e). When projecting
2,000 modern Danish genomes62 on a PCA of ancient Eurasians, the
modern individuals occupy an intermediate space on a cline between
the LNBA and Viking Age individuals (Fig. 4). This result shows that
the foundation for the present-day gene pool was already in place in
LNBA groups 3,000 years ago, but the genetic structure of the Danish
population was continually reshaped during succeeding millenia.
Environmental impact
The two documented major population turnovers were accompanied
by substantial changes in land use, as apparent from the high-resolution
pollen diagram from Lake Højby in Northwest Zealand (Fig. 3) recon-
structed using the landscape-reconstruction algorithm (LRA; Supple-
mentary Note 6). We uncovered a direct synchronic link between shifts
in a populations’ ancestry profile and land use. During the Mesolithic,
the landscape was dominated by primary forest trees (Tilia, Ulmus,
Quercus, Fraxinus, Alnus and so on). At the onset of the Neolithic, the
primary forest diminished, cleared by FBC farmers. A new type of for-
est with more secondary and early successional trees (Betula and then
Corylus) appeared, whereas the proportion between forest and open
land remained almost unaltered. From about 5,650 cal. bp deforesta-
tion intensified, resulting in an open grassland-dominated landscape.
This open phase was short-lived, and the secondary forest expanded
again from around 5,500 to 5,000 cal. bp, until another episode of
forest clearance occurred during the last part of the FBC epoch. We
conclude that the agricultural practice during the FBC was character-
ized by repeated clearing of the forest followed by regrowth. After
about 4,600 cal bp, this strategy changed with the emergence of the
SGC and the arrival of Steppe-related ancestry in Denmark. In Western
Denmark ( Jutland), the arrival of the SGC was characterized by perma-
nent large-scale opening of the landscape to create pastureland63,64 and
we observe here a similar increase in grassland and cropland at Højby
Sø in Eastern Denmark around 4,600 cal. bp (Fig. 3). Notably, this was
accompanied by an increase in primary forest cover, especially Tilia
and Ulmus, probably reflecting a development of a more permanent
division of the landscape into open grazing areas and primary forests.
Drivers of change
We have demonstrated examples of both cultural and demic diffusion
during the Mesolithic and Neolithic periods in Denmark. Shifts in the
Mesolithic material culture appeared without any detectable levels of
changes in ancestry, whereas the two cultural shifts in the Neolithic
period were clearly driven by new people coming in. Accordingly,
groupings of artefacts and monuments into archaeological cultures
do not always represent genetically distinct populations and the under-
lying mechanisms responsible for prehistoric cultural shifts must be
examined on a case-by-case basis.
It remains a mystery why the Neolithic farming expansion came to a
1,000-year standstill before entering Southern Scandinavia. It may be
that it was complicated by a high Mesolithic hunter-gatherer population
density owing to a very productive marine and coastal environment20,65.
Further, the Danish Ertebølle population may have been acquainted
with armed conflict11,66 enabling territorial defence against intruders.
Alternatively, it has been argued that changing climatic conditions
around 6,000 cal. bp became a driver since it enhanced the potential
for farming further north67, but other studies have not confirmed this68.
The second population turnover in the late Neolithic resulted in a short
period of three competing cultural complexes in Denmark, namely the
FBC, the PWC and the SGC. The latter introduced the steppe-related
ancestry which has prevailed to this day. There is archaeological evi-
dence that this was a violent time, both in Denmark69 and elsewhere70,71.
Additionally, ancient DNA evidence has demonstrated that plague was
widespread during this period72,73. In tandem with other indicators of
population declines74, and widespread reforestation after 5,000 cal.
bp75, it suggests that the local populations of Central and Northern
Europe may have been severely impacted prior to the arrival of new-
comers with Steppe-related ancestry. This could explain the rapid
population turnover and limited admixture with locals we observe.
While the two major shifts in Danish Mesolithic and Neolithic mate-
rial culture may have had different drivers and causes, the outcomes
were ultimately the same: new people arrived and rapidly took over
Nature | Vol 625 | 11 January 2024 | 335
Article
the territory. With this arrival, the local landscape was modified to
fit the lifestyle and culture of the immigrants. This is the hallmark of
the Anthropocene, observed here in high resolution in prehistoric
Denmark.
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edgements, peer review information; details of author contributions
and competing interests; and statements of data and code availability
are available at https://doi.org/10.1038/s41586-023-06862-3.
1. Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
2. Haak, W. et al. Massive migration from the steppe was a source for Indo-European
languages in Europe. Nature 522, 207–211 (2015).
3. Allentoft, M. E. et al. Population genomics of post-glacial western Eurasia. Nature https://
doi.org/10.1038/s41586-023-06865-0 (2024).
4. Posth, C. et al. Palaeogenomics of Upper Palaeolithic to Neolithic European
hunter-gatherers. Nature 615, 117–126 (2023).
5. Johannsen, N. N., Larson, G., Meltzer, D. J. & Vander Linden, M. A composite window into
human history. Science 356, 1118–1120 (2017).
6. Furholt, M. Mobility and social change: understanding the European Neolithic period
after the archaeogenetic revolution. J. Archaeol. Res. 29, 481–535 (2021).
7. Kristiansen, K. Archaeology and the Genetic Revolution in European Prehistory (Elements
in the Archaeology of Europe) (Cambridge Univ. Press, 2022).
8. Fischer, A. & Kristiansen, K. The Neolithisation of Denmark. 150 Years of Debate (J. R. Collis,
2002).
9. Günther, T. et al. Population genomics of Mesolithic Scandinavia: investigating early
postglacial migration routes and high-latitude adaptation. PLoS Biol. 16, e2003703 (2018).
10. Kashuba, N. et al. Ancient DNA from mastics solidifies connection between material culture
and genetics of mesolithic hunter–gatherers in Scandinavia. Commun. Biol. 2, 185 (2019).
11. Fischer, A. in The Neolithisation of Denmark—150 years of debate (eds Fischer, A. &
Kristiansen, K.) 343–393 (J. R. Collis, 2002).
12. Price, T. D. Europe’s First Farmers (Cambridge Univ. Press, 2000).
13. Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early
European farmers. Nature 551, 368–372 (2017).
14. Mathieson, I. et al. The genomic history of southeastern Europe. Nature 555, 197–203 (2018).
15. Brace, S. et al. Ancient genomes indicate population replacement in Early Neolithic
Britain. Nat. Ecol. Evol. 3, 765–771 (2019).
16. Midgley, M. TRB Culture: The First Farmers of the North European Plain (Edinburgh Univ.
Press, 1992).
17. Iversen, R. in Tracing the Indo-Europeans: New evidence from Archaeology and Historical
Linguistics (eds Olsen, B. A., Olander, T. & Kristiansen, K.) 73–95 (Oxbow, 2019).
18. Nielsen, S. K. & Johannsen, N. N. Mortuary palisades, single graves, and cultural admixture:
the establishment of Corded Ware culture on the Jutland Peninsula. Praehistorische
Zeitschrift https://doi.org/10.1515/pz-2023-2022 (2023).
19. Kristiansen, K. Prehistoric migrations—the case of the Single Grave and Corded Ware
Cultures. J. Dan. Archaeol. 8, 211–225 (1991).
20. Lewis, J. P. et al. Marine resource abundance drove pre-agricultural population increase in
Stone Age Scandinavia. Nat. Commun. 11, 2006 (2020).
21. Sousa da Mota, B. et al. Imputation of ancient human genomes. Nat. Commun. 14, 3660
(2023).
22. Schilling, H. in Mesolithic on the Move (eds Larsson, L. et al.) 351–358 (2003).
23. Petersen, P. V. Chronological and regional variation in the Late Mesolithic of Eastern
Denmark. J. Dan. Archaeol. 3, 7–18 (1984).
24. Fischer, A. in The Danish Storebælt Since the Ice Age (eds Pedersen, L., Fischer, A. & Aaby,
B.) 63–77 (Sea and Forest, 1997).
25. Sørensen, S. A. The Kongemose Culture (Univ. Press of Southern Denmark, 2017).
26. Dolbunova, E. et al. The transmission of pottery technology among prehistoric European
hunter-gatherers. Nat. Hum. Behav. 7, 171–183 (2023).
27. Klassen, L. Jade und Kupfer: Untersuchungen zum Neolithisierungsprozess im westlichen
Ostseeraum unter besonderer Berücksichtigung der Kulturentwicklung Europas 5500–3500
bc vol. 47 (Aarhus Universitetsforlag, 2004).
28. Price, T. D. Seeking the First Farmers in Western Sjælland, Denmark: The Archaeology of the
Transition to Agriculture in Northern Europe (Oxbow Books, 2022).
29. Hansen, J. et al. The Maglemosian skeleton from Koelbjerg revisited: Identifying sex and
provenance. Dan. J. Archaeol. 6, 55–66 (2017).
30. Sørensen, M. in Ecology of Early Settlement in Northern Europe: Conditions for Subsistence
and Survival. The Early Settlement of Northern Europe Vol. 1 (eds. Persson, P., Riede, F. &
Skar, B.) 277–301 (Equinox, 2018).
31. Piezonka, H. et al. Stone Age pottery chronology in the Northeast European Forest Zone:
new AMS and EA-IRMS results on foodcrusts. Radiocarbon 58, 267–289 (2016).
32. Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature
528, 499–503 (2015).
33. Irving-Pease, E. K. et al. The selection landscape and genetic legacy of ancient Eurasians.
Nature https://doi.org/10.1038/s41586-023-06705-1 (2024).
34. Fischer, A. et al. Coast-inland mobility and diet in the Danish Mesolithic and Neolithic:
evidence from stable isotope values of humans and dogs. J. Archaeol. Sci. 34, 2125–2150
(2007).
35. Fischer, A. et al. The composition of Mesolithic food—evidence from a submerged
settlement on the Argus Bank, Denmark. Acta Archaeol. 78, 163–178 (2007).
336 | Nature | Vol 625 | 11 January 2024
36. Brinch Petersen, E. Gravene ved Dragsholm. Fra jægere til bønder for 6000 år siden.
Nationalmuseets Arbejdsmark 1974, 112–120 (1974).
37. Price, T. D. et al. New information on the Stone Age graves at Dragsholm, Denmark. Acta
Archaeol. 78, 193–219 (2007).
38. Sørensen, L. From Hunter to Farmer in Northern Europe. Migration and adaptation during
the Neolithic and Bronze Age. Acta Archaeologica Vol. 85 (Wiley–Blackwell, 2014).
39. Nielsen, P. O. & Nielsen, F. O. S. First Farmers on the Island of Bornholm (The Royal Society
of Northern Antiquaries and Univ. Press of Southern Denmark, 2020).
40. Sjögren, K.-G. & Fischer, A. The chronology of Danish dolmens. Results from 14C dates on
human bones. J. Neolit. Archaeol. 25, https://doi.org/10.12766/jna.2023.1 (2023).
41. Dehn, T. & Hansen, S. I. Birch bark in Danish passage graves. J. Dan. Archaeol. 14, 23–44
(2006).
42. Ebbesen, K. Simple, tidligneolitiske grave. Aarbøger for nordisk Oldkyndighed og Historie
1992, 47–102 (1994).
43. Gron, K. J. & Sørensen, L. Cultural and economic negotiation: a new perspective on the
Neolithic Transition of Southern Scandinavia. Antiquity 92, 958–974 (2018).
44. Chintalapati, M., Patterson, N. & Moorjani, P. The spatiotemporal patterns of major human
admixture events during the European Holocene. eLife 11, e77625 (2022).
45. González-Fortes, G. et al. Paleogenomic evidence for multi-generational mixing between
Neolithic farmers and Mesolithic hunter-gatherers in the Lower Danube Basin. Curr. Biol.
27, 1801–1810.e10 (2017).
46. Villalba-Mouco, V. et al. Survival of Late Pleistocene hunter-gatherer ancestry in the
Iberian Peninsula. Curr. Biol. 29, 1169–1177.e7 (2019).
47. Jensen, T. Z. T. et al. A 5700 year-old human genome and oral microbiome from chewed
birch pitch. Nat. Commun. 10, 5520 (2019).
48. Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old
Mesolithic European. Nature 507, 225–228 (2014).
49. Cox, S. L., Ruff, C. B., Maier, R. M. & Mathieson, I. Genetic contributions to variation in
human stature in prehistoric Europe. Proc. Natl Acad. Sci. USA 116, 21484–21492
(2019).
50. Klassen, L. (ed.) The Pitted Ware Culture on Djursland: Supra-regional Significance and
Contacts in the Middle Neolithic of Southern Scandinavia (Aarhus Univ. Press, 2020).
51. Iversen, R., Philippsen, B. & Persson, P. Reconsidering the Pitted Ware chronology.
Praehistorische Zeitschrift 96, 44–88 (2021).
52. Coutinho, A. et al. The Neolithic Pitted Ware culture foragers were culturally but not
genetically influenced by the Battle Axe culture herders. Am. J. Phys. Anthropol. 172,
638–649 (2020).
53. Glob, P. V. Studier over den Jyske Enkeltgravskultur (Gyldendal, 1945).
54. Müller, J. & Vandkilde, H. in Contrasts of the Nordic Bronze Age. Essays in Honour of
Christopher Prescott (eds. Austvoll, K.I., Hem Eriksen, M., Fredriksen, P.D., Melheim, A.L.,
Prøsch-Danielsen, L., Skogstrand, L.) 29–48 (Brepols, 2020).
55. Iversen, R. The Transformation of Neolithic Societies. An Eastern Danish Perspective on the
3rd Millennium BC Vol. 88 (Jutland Archaeological Society, 2015).
56. Damm, C. The Danish Single Grave Culture—ethnic migration or social construction?
J. Dan. Archaeol. 10, 199–204 (1991).
57. Egfjord, A. F.-H. et al. Genomic steppe ancestry in skeletons from the Neolithic Single
Grave Culture in Denmark. PLoS ONE 16, e0244872 (2021).
58. Grasgruber, P., Sebera, M., Hrazdíra, E., Cacek, J. & Kalina, T. Major correlates of male
height: a study of 105 countries. Econ. Hum. Biol. 21, 172–195 (2016).
59. Papac, L. et al. Dynamic changes in genomic and social structures in third millennium bce
central Europe. Sci. Adv. 7, eabi6941 (2021).
60. Blank, M. Mobility, Subsistence and Mortuary practices. An Interdisciplinary Study of
Neolithic and Early Bronze Age Megalithic Populations of Southwestern Sweden. PhD
thesis, Univ. of Gothenburg (2021).
61. Winther Johannsen, J. Late Neolithic expansion. Dan. J. Archaeol. 12, https://doi.org/
10.7146/dja.v12i1.132093 (2023).
62. Pedersen, C. B. et al. The iPSYCH2012 case–cohort sample: new directions for unravelling
genetic and environmental architectures of severe mental disorders. Mol. Psychiatry 23,
6–14 (2017).
63. Odgaard, B. V. The Holocene vegetation history of northern West Jutland, Denmark. Nord.
J. Bot. 14, 546–546 (1994).
64. Haak, W. et al. in The Indo-European Puzzle Revisited: Integrating Archaeology, Genetics,
and Linguistics (eds Kristiansen, K., Kroonen, G. & Willerslev, E.) 63–80 (2023).
65. Fischer, A., Gotfredsen, A. B., Meadows, J., Pedersen, L. & Stafford, M. The Rødhals kitchen
midden—marine adaptations at the end of the Mesolithic world. J. Archaeol. Sci. 39,
103102 (2021).
66. Bennike, P. in The Danish Storebælt Since the Ice Age (eds Pedersen, L., Fischer, A. &
Aaby, B.) 99–105 (A/S Storebælt Fixed Link, 1997).
67. Warden, L. et al. Climate induced human demographic and cultural change in northern
Europe during the mid-Holocene. Sci Rep. 7, 15251 (2017).
68. Krossa, V. R. et al. Regional climate change and the onset of farming in northern Germany
and southern Scandinavia. Holocene 27, 1589–1599 (2017).
69. Iversen, R. Arrowheads as indicators of interpersonal violence and group identity among
the Neolithic Pitted Ware hunters of southwestern Scandinavia. J. Anthropol. Archaeol.
44, 69–86 (2016).
70. Lidke, G. Violence in the Single Grave Culture of northern Germany? in Sticks, Stones,
and Broken Bones: Neolithic Violence in a European Perspective (eds Schulting, R. J. &
Fibiger, L.) 139-150 https://doi.org/10.1093/acprof:osobl/9780199573066.003.0008
(Oxford, 2012).
71. Schroeder, H. et al. Unraveling ancestry, kinship, and violence in a Late Neolithic mass
grave. Proc. Natl Acad. Sci. USA 116, 10705–10710 (2019).
72. Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.
Cell 163, 571–582 (2015).
73. Rascovan, N. et al. Emergence and spread of basal lineages of Yersinia pestis during the
Neolithic decline. Cell 176, 295–305.e10 (2019).
74. Hinz, M. et al. in Neolithic Diversities: Perspectives from a Conference in Lund, Sweden
43–51 (Lund Univ., 2015).
75. Feeser, I., Dörfler, W., Kneisel, J., Hinz, M. & Dreibrodt, S. Human impact and population
dynamics in the Neolithic and Bronze Age: multi-proxy evidence from north-western
Central Europe. Holocene 29, 1596–1606 (2019).
76. Margaryan, A. et al. Population genomics of the Viking world. Nature 585, 390–396
(2020).
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© The Author(s) 2024
Morten E. Allentoft1,2,42 ✉, Martin Sikora1,42 ✉, Anders Fischer3,4,42, Karl-Göran Sjögren5,
Andrés Ingason1,6, Ruairidh Macleod1,7,8, Anders Rosengren1,6, Bettina Schulz Paulsson3,
Marie Louise Schjellerup Jørkov9, Maria Novosolov1, Jesper Stenderup1, T. Douglas Price10,
Morten Fischer Mortensen11, Anne Birgitte Nielsen12, Mikkel Ulfeldt Hede13,
Lasse Sørensen11, Poul Otto Nielsen11, Peter Rasmussen11, Theis Zetner Trolle Jensen14,
Alba Refoyo-Martínez1, Evan K. Irving-Pease1, William Barrie7,15, Alice Pearson7,15,
Bárbara Sousa da Mota16,17, Fabrice Demeter1,18, Rasmus A. Henriksen1, Tharsika Vimala1,
Hugh McColl1, Andrew Vaughn19, Lasse Vinner1, Gabriel Renaud20, Aaron Stern19,
Niels Nørkjær Johannsen21, Abigail Daisy Ramsøe1, Andrew Joseph Schork9,22,
Anthony Ruter1, Anne Birgitte Gotfredsen14, Bjarne Henning Nielsen23, Erik Brinch Petersen24,
Esben Kannegaard25,44, Jesper Hansen26, Kristoffer Buck Pedersen27, Lisbeth Pedersen28,
Lutz Klassen25, Morten Meldgaard1,29, Morten Johansen30, Otto Christian Uldum30,
Per Lotz31,32, Per Lysdahl33, Pernille Bangsgaard14, Peter Vang Petersen11, Rikke Maring21,25,
Rune Iversen24, Sidsel Wåhlin33, Søren Anker Sørensen31, Søren H. Andersen34,
Thomas Jørgensen31, Niels Lynnerup35, Daniel J. Lawson36, Simon Rasmussen37,
Thorfinn Sand Korneliussen1, Kurt H. Kjær1, Richard Durbin15,38, Rasmus Nielsen1,39,
Olivier Delaneau16,17, Thomas Werge1,6,40,43, Kristian Kristiansen1,5,43 & Eske Willerslev1,7,41,43 ✉
1
Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen,
Copenhagen, Denmark. 2Trace and Environmental DNA (TrEnD) Laboratory, School of
Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia. 3Cluster of
Excellence ROOTS, Kiel University, Kiel, Germany. 4Sealand Archaeology, Kalundborg,
Denmark. 5Department of Historical Studies, Gothenburg University, Göteborg, Sweden.
6
Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University
Hospital, Copenhagen, Denmark. 7GeoGenetics Group, Department of Zoology, University of
Cambridge, Cambridge, UK. 8Research Department of Genetics, Evolution and Environment,
University College London, London, UK. 9Laboratory of Biological Anthropology, University of
Copenhagen, Copenhagen, Denmark. 10Laboratory for Archaeological Chemistry,
Department of Anthropology, University of Wisconsin–Madison, Madison, WI, USA. 11The
National Museum of Denmark, Copenhagen, Denmark. 12Department of Geology, Lund
University, Lund, Sweden. 13Tårnby Gymnasium og HF, Kastrup, Denmark. 14Globe Institute,
Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
15
Department of Genetics, University of Cambridge, Cambridge, UK. 16Department of
Computational Biology, University of Lausanne, Lausanne, Switzerland. 17Swiss Institute of
Bioinformatics, University of Lausanne, Lausanne, Switzerland. 18Eco-anthropologie (EA), Dpt
ABBA, Muséum National d’Histoire Naturelle, CNRS, Université Paris Cité, Musée de l’Homme,
Paris, France. 19Center for Computational Biology, University of California, Berkeley, USA.
20
Department of Health Technology, Section of Bioinformatics, Technical University of
Denmark, Kongens Lyngby, Denmark. 21Department of Archaeology and Heritage Studies,
Aarhus University, Aarhus, Denmark. 22Neurogenomics Division, The Translational Genomics
Research Institute (TGEN), Phoenix, AZ, USA. 23Vesthimmerlands Museum, Aars, Denmark.
24
The Saxo Institute, University of Copenhagen, Copenhagen, Denmark. 25Museum Østjylland,
Randers, Denmark. 26Svendborg Museum, Svendborg, Denmark. 27Museum Sydøstdanmark,
Vordingborg, Denmark. 28HistorieUdvikler, Kalundborg, Denmark. 29Department of Health and
Nature, University of Greenland, Nuuk, Greenland. 30The Viking Ship Museum, Roskilde,
Denmark. 31Museum Nordsjælland, Hillerød, Denmark. 32Museum Vestsjælland, Holbæk,
Denmark. 33Vendsyssel Historiske Museum, Hjørring, Denmark. 34Moesgaard Museum,
Højbjerg, Denmark. 35Laboratory of Biological Anthropology, Department of Forensic
Medicine, University of Copenhagen, Copenhagen, Denmark. 36Institute of Statistical
Sciences, School of Mathematics, University of Bristol, Bristol, UK. 37Novo Nordisk Foundation
Centre for Protein Research, Faculty of Health and Medical Sciences, University of
Copenhagen, Copenhagen N, Denmark. 38Wellcome Sanger Institute, Wellcome Trust
Genome Campus, Cambridge, UK. 39Department of Integrative Biology and Statistics, UC
Berkeley, Berkeley, CA, USA. 40Department of Clinical Medicine, University of Copenhagen,
Copenhagen, Denmark. 41MARUM Center for Marine Environmental Sciences and Faculty of
Geosciences, University of Bremen, Bremen, Germany. 42These authors contributed equally:
Morten E. Allentoft, Martin Sikora, Anders Fischer. 43These authors jointly supervised this
work: Thomas Werge, Kristian Kristiansen, Eske Willerslev. 44Deceased: Esben Kannegaard.
✉e-mail: morten.allentoft@curtin.edu.au; martin.sikora@sund.ku.dk; ew482@cam.ac.uk
Nature | Vol 625 | 11 January 2024 | 337
Article
Methods
Ancient genomic analyses
The 100 ancient Danish genomes analysed here contribute to the 317
shotgun-sequenced genomes in Allentoft et al.3. All details concerning
sampling, DNA extraction, library preparation, sequencing, basic bio-
informatics, authentication and dataset construction are found in ref. 3
together with all site descriptions and sample metadata. A condensed list
of metainformation on the 100 Danish individuals is released here (Sup-
plementary Data 1) together with a text summarizing the study sites and
skeletons (Supplementary Note 1). In brief, laboratory work was carried
out in dedicated ancient DNA cleanlab facilities (University of Copen-
hagen) using optimized ancient DNA methods1,77. Double-stranded
blunt-end libraries were sequenced (80 bp and 100 bp single-end reads)
on Illumina HiSeq 2500 and 4000 platforms. Initial shallow shotgun
screening was used to identify samples with sufficient DNA preservation
for deeper genomic sequencing. Of the 100 Danish samples that qualified
for this, 65 were from tooth cementum, 29 were petrous bones, and 6
were obtained from other bones (Supplementary Data 1). Sequence reads
were bioinformatically mapped to the human reference genome (build
37), filtered and merged to sample level followed by estimates of genomic
overage, post-mortem DNA damage, contamination, and genetic sex ID
(see3). For these 100 samples we observed C-to-T deamination fractions
ranging from 12.2% to 66.7%, with an average of 34.9% across all samples
(Supplementary Data 1), consistent with highly degraded ancient DNA.
We genetically identified 67 males, 32 females and one undetermined
in our dataset (Supplementary Data 1).
We utilized a new computational method optimized for low-coverage
data21, to impute genotypes based on genotype likelihoods of ancient
individuals with the samtools/bcftools pipeline, and using the 1000
Genomes phased data78 as a reference panel. To generate the main
dataset in3 this was jointly applied to 1,664 shotgun-sequenced ancient
genomes, including our 100 ancient Danish genomes, and resulted in
a dataset of 8.5 million common SNPs (>1% minor allele frequency and
imputation info score > 0.5) for imputed diploid ancient genomes.
After removing genomes with low coverage (<0.1X), low imputation
quality (average genotype probability <0.98), contamination estimates
>5%, or close relatives (first or second degree, lowest coverage relative
removed), 67 of the 100 Danish genomes were retained as imputed in
downstream analyses. The remaining 33 genomes were analysed as
pseudo-haploid genotypes.
For population genetic analyses, we combined ancient samples with
two different modern reference panels:
• ‘1000 G’ dataset: whole-genome sequencing data of 2,504 individuals
from 26 world-wide populations from the 1000 Genomes project,
with genotypes at 7,321,965 autosomal SNPs.
• ‘HO’ dataset: SNP array data of 2,180 modern individuals from 213
world-wide populations, with genotypes at 535,880 autosomal SNPs.
Analyses were based on the 1000 G dataset unless otherwise
noted. Individuals not passing imputation quality control cutoffs
mentioned above were included in PCA and ADMIXTURE analyses as
pseudo-haploid genotypes. Four Danish individuals showed possible
signs of DNA contamination (Fig. 3 and Supplementary Data 1) and were
excluded from most analyses. To take full advantage of the extensive
multiproxy data they were, however, included in Fig. 3. Individual meta-
data for all genetic analyses related to the ancient Danish individuals
as well as selected subset of relevant West Eurasian individuals, are
reported in Supplementary Data 3.
For PCA combining ancient and modern Western Eurasians (Fig. 1b),
we used the data and framework from3 to capture West Eurasian
genetic diversity based on n = 983 modern genomes and n = 1,105
ancient genomes (HO dataset). Data from a total of 179 ancient Danish
genomes are shown in Fig. 1b of which 83 are previously published1,47,57,76
(Supplementary Data 3)—the latter being primarily from the Bronze
Age and Viking periods. To perform PCA projection for low-coverage
individuals, we used smartpca with options ‘lsqproject: YES’ and
‘autoshrink: YES’.
The ADMIXTURE results presented in this study represent subsets
of individuals from the full ADMIXTURE runs in3 where 1,593 ancient
individuals were analysed (n = 1,492 imputed, n = 101 pseudo-haploid,
n = 71 excluded as close relatives or with a contamination estimate >5%;
HO dataset). Figure 1c represents 176 ancient Danish genomes after
excluding three close relatives (Supplementary Data 1 and 4).
D-statistics were obtained using pseudo-haploid genotypes at trans-
version SNPs in the 1000 G dataset, grouping the non-Danish individu-
als into populations using their membership in the genetic clusters
inferred from IBD sharing (Supplementary Data IV). We computed
D-statistics from genotypes in PLINK format using the qpdstat function
implemented in the ADMIXTOOLS 2 R package79.
Analysis of IBD sharing and mixture models were carried out as
described3, using the same set of inferred genetic clusters (see Sup-
plementary Data 4). In brief, we used IBDseq80 to detect IBD segments,
a carried out genetic clustering of the individuals using hierarchical
community detection on a network of pairwise IBD-sharing similarities.
IBD-based PCA was carried out in R using the eigen function on a covari-
ance matrix of pairwise IBD sharing between the respective ancient indi-
viduals. We estimated ancestry proportion in supervised modelling of
target individuals as mixtures of different sets of putative source groups
via non-negative least squares on relative IBD-sharing rate vectors.
Admixture time inference for FBC-associated individuals was car-
ried out using the linkage-disequilibrium-based method DATES44 (HO
dataset). We estimated admixture time separately for each target indi-
vidual from Denmark and Sweden, using hunter-gatherer individuals
(n = 58) and early farmer individuals (n = 49) as the two source groups.
For the PCAs presented in Fig. 4 including modern Danish samples we
projected 2,000 imputed samples81 of individuals born in 1981–2005
from the iPSYCH2012 case-cohort study62 onto the PCA space spanned
by the 1,145 non-low coverage or related european and western Asian
ancient imputed samples3. Otherwise, the analysis is identical to the
one described above. The modern individuals were selected from a
subset of the random population subcohort component of iPSYCH2012
having all four grandparents born in Denmark, and being of Danish or
European ancestry as determined in a separate already existing PCA
of main modern-day ancestry groups81. This was done using Eigensoft
7.2.1 on the intersect of imputed SNPs from the ancient and modern
samples, filtered by minor allele frequency 0.05, pruned using PLINK
v1.90b6.2182 based on source samples (parameters: –indep-pairwise
1000 50 0.25) leaving 146,895 variants.
The genetic predictions of eye and hair colour were done based on
the HIrisPlex system83. We used imputed effect allele dosages of 18 out
of 24 main effect HIrisPlex variants, available for the ancient samples,
to derive probabilities for brown, blue and grey/intermediate eye col-
our and blond, brown, black and red hair colour, following HIrisPlex
formulas (see further details in Supplementary Note 2). We predicted
relative ‘genetic height’ using allelic effect estimates from 310 common
autosomal SNPs with robustly genome-wide significant allelic effects
(P < 10−15) in a recent GWAS of height in the UK Biobank84. Per-sample
height polygenic score (PGS) was calculated for ancient individuals as
well as 3,467 Danish ancestry male conscripts from the random popu-
lation subcohort of the iPSYCH2012 case-cohort study62 by summing
allelic effect multiplied with the effect allele imputed dosage81 across
the 310 loci. For further details see Supplementary Note 2. Only a frac-
tion of the 100 Danish skeletons were suitable for stature estimation by
actual measurement, which is why these values are not reported here.
Radiocarbon dates and Bayesian modelling of ancestry
chronology
For the 100 sample ages in this study we use midpoint estimates of
the calibrated and reservoir corrected probability distribution of the
radiocarbon age (Supplementary Data 1; further 14C dates, associated
isotopic measurements, calibrations and reservoir corrections are
accessible in ref. 3). Focusing on estimating the interval between the
two major population turnovers, we established a precise chronology
using 81 radiocarbon dates from 64 Danish sites relevant to this par-
ticular interval (Supplementary Note 3). A Bayesian approach applied
to the radiocarbon dates unifies radiocarbon results, ancestry infor-
mation, and the high precision curve into one calibration process,
thereby gaining greater precision. All models and data calibrations
were performed using OxCal v4.485–88 and the calibration dataset from
Reimer et al.89. We used a trapezoidal phase prior90,91 for the calcula-
tion of the transitional time interval to determine duration between
the first appearance of Anatolian farmer-related ancestry to the first
appearance of Steppe-related ancestry in Denmark. We corrected the
reservoir effect on bones with significantly increased isotope values
(δ13C, −18.00 and δ15N, +12.00) directly in the models using previously
defined reservoir ages as input and calculated the diet reconstruction
estimates for the individual in 14C years based on the collagen isotope
values (Supplementary Note 3 and Supplementary Figs. 3.1 and 3.2);
for a similar method see refs. 92,93. For combining radiocarbon dates
related to the same individual we used the R_Combine() function.
Stable isotope proxies for diet and mobility
Bulk collagen isotope values of carbon (δ13C) and nitrogen (δ15N) rep-
resent protein sources consumed over several years before death,
depending on the skeletal part and the age at death of the individual94,95.
Generally, δ13C values inform on the proportion of marine versus ter-
restrial protein, whereas δ15N values reflect the trophic level from
which the proteins were acquired96,97. See Supplementary Note 4 for
further discussion. Stable isotope values were measured in collagen
from all 100 skeletons and the full assemblage of isotopic measure-
ments is available in Supplementary Data 2, and further discussed
in Supplementary Note 4. Most of the δ13C and δ15N measurements
were conducted at the 14C Centre, University of Belfast according to
standard protocols98, based on a modified Longin method includ-
ing ultra-filtration98,99. Measured uncertainty was within the gener-
ally accepted range of ±0.2‰ (1 s.d.) and all samples were within the
acceptable atomic C:N range of 2.9–3.6, showing low likelihood of
diagenesis100,101.
Strontium isotope analyses can provide a proxy for individual mobil-
ity102–104. The 87Sr/86Sr ratio in specific skeletal elements may reflect
the local geological signature obtained through diet by the individual
during early childhood and it will usually remain unchanged during life
and after death105. Ongoing controversies exist over the exact use of
geographically-defined baseline values106,107, which is why we restrict
our observations and interpretations of Sr variation to patterns that
are only relative to our own data. Measurements of 87Sr/86Sr ratios in
teeth and petrous bones were conducted at the Geochronology and
Isotope Geochemistry Laboratory (Department of Geological Sciences,
University of North Carolina- Chapel Hill) and data are found in Sup-
plementary Data 2. For further details see Supplementary Note 5.
Vegetation modelling
Using a high-resolution pollen diagram from Lake Højby, Northwest
Zealand108, we reconstruct the changes in vegetation cover during
the period 5,000–2,400 cal. bc using the landscape-reconstruction
algorithm (LRA109,110). Although the LRA has previously been applied
at low temporal resolution regional scale (fer example, in refs. 111,112.),
and to Iron Age (and later) pollen diagrams113,114, to our knowledge, this
is the first time that this quantitative method is applied at local scale
to a pollen record spanning the Mesolithic and Neolithic periods in
Denmark. In total 60 pollen samples between 6,900 and 4,400 cal. bp
were included and the temporal resolution between samples is approxi-
mately 40 years. Regional vegetation was estimated with the model
REVEALS109 based on pollen data from six other lakes on Zealand (see
Supplementary Fig. 6.1). From this, regional pollen rain is calculated
and local scale vegetation around Højby Sø calculated using the LOVE
model110. Average pollen productivity estimates for Europe115 for 25
wind pollinated species were applied. The reconstructed cover for
plant species were then combined into four land cover categories, crops
(only cereals), grassland (all other herbs), secondary forest (Betula and
Corylus) and primary forest (all other trees). The vegetation reconstruc-
tion from Højby Sø is used to illustrate the vegetation development
at the Mesolithic/Neolithic transition in eastern Denmark. For more
details see Supplementary Note 6.
Reporting summary
Further information on research design is available in the Nature Port-
folio Reporting Summary linked to this article.
Data availability
Sequencing data analysed in this study is released in the accompanying
study ‘Population genomics of post-glacial western Eurasia’3. These are
publicly available on the European Nucleotide Archive under accession
PRJEB64656, together with sequence alignment map files, aligned
using human build GRCh37. The full analysis dataset including both
imputed and pseudo-haploid genotypes for all ancient individuals used
in this study is available at https://doi.org/10.17894/ucph.d71a6a5a-
8107-4fd9-9440-bdafdfe81455. Aggregated IBD-sharing data as well
as hi-resolution versions of supplementary figures are available at
Zenodo under accession https://doi.org/10.5281/zenodo.8196989.
Maps were created in R using public domain Natural Earth map data.
77. Damgaard, P. B. et al. Improving access to endogenous DNA in ancient bones and teeth.
Sci. Rep. 5, 11184 (2015).
78. 1000 Genomes Project Consortium. A global reference for human genetic variation.
Nature 526, 68–74 (2015).
79. Maier, R., Flegontov, P., Flegontova, O., Işıldak, U., Changmai, P. & Reich, D. On the limits
of fitting complex models of population history to f-statistics. Elife 12, e85492 (2023).
80. Browning, B. L. & Browning, S. R. Detecting identity by descent and estimating genotype
error rates in sequence data. Am. J. Hum. Genet. 93, 840–851 (2013).
81. Appadurai, V. et al. Accuracy of haplotype estimation and whole genome imputation
affects complex trait analyses in complex biobanks. Commun. Biol. 6, 101 (2023).
82. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based
linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
83. Walsh, S. et al. The HIrisPlex system for simultaneous prediction of hair and eye colour
from DNA. Forensic Sci. Int. Genet. 7, 98–115 (2013).
84. Bycroft, C. et al. The UK Biobank resource with deep phenotyping and genomic data.
Nature 562, 203–209 (2018).
85. Bronk Ramsey, C. Development of the radiocarbon calibration program OxCal.
Radiocarbon 43, 355–363 (2001).
86. Bronk Ramsey, C. Deposition models for chronological records. Q. Sci. Rev. 27, 42–60
(2008).
87. Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).
88. Bronk Ramsey, C. Dealing with outliers and offsets. Radiocarbon 51, 1023–1045 (2009).
89. Reimer, P., Austin, W. & Bard, E. The IntCal20 Northern Hemisphere radiocarbon age
calibration curve (0–55 cal kbp). Radiocarbon 62, 725–757 (2020).
90. Karlsberg, A. J. Flexible Bayesian Methods for Archaeological Dating. PhD thesis, Univ.
Sheffield (2006).
91. Lee, S. & Ramsey, C. Development and application of the trapezoidal model for
archaeological chronologies. Radiocarbon 54, 107–122 (2012).
92. Meadows, J. et al. Dietary freshwater reservoir effects and the radiocarbon ages of
prehistoric human bones from Zvejnieki, Latvia. J. Archaeol. Sci. 6, 678–689 (2016).
93. Rose, H. A., Meadows, J. & Bjerregaard, M. High-resolution dating of a medieval multiple
grave. Radiocarbon 60, 1547–1559 (2018).
94. Hedges, R. E. M., Clement, J. G., David, C., Thomas, L. & O’Connell, T. C. Collagen turnover
in the adult femoral mid-shaft: modeled from anthropogenic radiocarbon tracer
measurements. Am. J. Phys. Anthropol. 133, 808–816 (2007).
95. Jørkov, M. L. S., Heinemeier, J. & Lynnerup, N. The petrous bone-a new sampling site for
identifying early dietary patterns in stable isotopic studies. Am. J. Phys. Anthropol. 138,
199–209 (2009).
96. Schoeninger, M. J. & Moore, K. Bone stable isotope studies in archaeology. J. World Prehist.
6, 247–296 (1992).
97. Hedges, R. E. M. & Reynard, L. M. Nitrogen isotopes and the trophic level of humans in
archaeology. J. Archaeol. Sci. 34, 1240–1251 (2007).
98. Reimer, P. et al. Laboratory protocols used for AMS radiocarbon dating at the 14Chrono
Centre. English Heritage Research Report Series 5-2015 https://historicengland.org.uk/
research/results/reports/6272/TheQueen%E2%80%99sUniversityBelfast_
LaboratoryprotocolsusedforAMSradiocarbondatingatthe14CHRONOCentre (2015).
99. Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241–242
(1971).
Article
100. Ambrose, S. H. & DeNiro, M. J. The isotopic ecology of East African mammals. Oecologia
69, 395–406 (1986).
101. van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon
measurements. J. Archaeol. Sci. 26, 687–695 (1999).
102. Alexander Bentley, R. Strontium isotopes from the earth to the archaeological skeleton:
A review. J. Archaeol. Method Theory 13, 135–187 (2006).
103. Frei, K. M. & Price, T. D. Strontium isotopes and human mobility in prehistoric Denmark.
Archaeol. Anthropol. Sci. 4, 103–114 (2012).
104. Holt, E., Evans, J. A. & Madgwick, R. Strontium (87Sr/86Sr) mapping: a critical review of
methods and approaches. Earth Sci. Rev. 216, 103593 (2021).
105. Price, T. D., Burton, J. H. & Bentley, R. A. Characterization of biologically available strontium
isotope ratios for the study of prehistoric migration. Archaeometry 44, 117–135 (2002).
106. Thomsen, E., Andreasen, R. & Rasmussen, T. L. Homogeneous glacial landscapes can
have high local variability of strontium isotope signatures: implications for prehistoric
migration studies. Front. Ecol. Evol. 8, 588318 (2021).
107. Price, T. D., Klassen, L. & Sjögren, K. G. Pitted ware culture: isotopic evidence for contact
between Sweden and Denmark across the Kattegat in the Middle Neolithic, ca. 3000 bc.
J. Anthropol. Archaeol. 61, 101254 (2021).
108. Hede, M. U. Holocene Climate and Environmental Changes Recorded in High-resolution
Lake Sediments from Højby Sø, Denmark. PhD thesis, Univ. Copenhagen (2008).
109. Sugita, S. Theory of quantitative reconstruction of vegetation I: pollen from large sites
REVEALS regional vegetation composition. Holocene 17, 229–241 (2007).
110. Sugita, S. Theory of quantitative reconstruction of vegetation II: all you need is LOVE.
Holocene 17, 243–257 (2007).
111. Nielsen, A. B. et al. Quantitative reconstructions of changes in regional openness in
north-central Europe reveal new insights into old questions. Q. Sci. Rev. 47, 131–147 (2012).
112. Githumbi, E. et al. Pollen-based maps of past regional vegetation cover in Europe over
twelve millennia—evaluation and potential. Front. Ecol. Evol. https://doi.org/10.3389/
fevo.2022.795794 (2022).
113. Nielsen, A. B. & Odgaard, B. V. Quantitative landscape dynamics in Denmark through the
last three millennia based on the landscape reconstruction algorithm approach. Veg.
Hist. Archaeobot. 19, 375–387 (2010).
114. Søe, N. E., Odgaard, B. V., Nielsen, A. B., Olsen, J. & Kristiansen, S. M. Late Holocene
landscape development around a Roman Iron Age mass grave, Alken Enge, Denmark.
Veg. Hist. Archaeobot. 26, 277–292 (2017).
115. Mazier, F. et al. Testing the effect of site selection and parameter setting on
REVEALS-model estimates of plant abundance using the Czech Quaternary Palynological
Database. Rev. Palaeobot. Palynol. 187, 38–49 (2012).
Acknowledgements The Lundbeck Foundation GeoGenetics Centre is supported by grants
from the Lundbeck Foundation (R302-2018-2155, R155-2013-16338), the Novo Nordisk
Foundation (NNF18SA0035006), the Wellcome Trust (WT214300), Carlsberg Foundation
(CF18-0024), the Danish National Research Foundation (DNRF94, DNRF174), the University of
Copenhagen (KU2016 programme) and Ferring Pharmaceuticals A/S, to E.W. This research has
been conducted using the UK Biobank Resource and the iPSYCH Initiative, funded by the
Lundbeck Foundation (R102-A9118 and R155-2014-1724). This work was further supported by
the Swedish Foundation for Humanities and Social Sciences grant (Riksbankens Jubileumsfond
M16-0455:1) to K.K. M.E.A. was supported by Marie Skłodowska-Curie Actions of the EU (grant
no. 300554), The Villum Foundation (grant no. 10120) and Independent Research Fund
Denmark (grant no. 7027-00147B). A.F. was funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC 2150–
390870439. R. Macleod was supported by an SSHRC doctoral studentship grant (G101449:
‘Individual Life Histories in Long-Term Cultural Change’). B.S.P. has received funding from the
European Union’s Horizon 2020 research and innovation programme under the ERC-StG grant
agreement No 94924. M.N. is funded by the Human Frontier Science Program Postdoctoral
Fellowship LT000143/2019-L4. A.R.-M. was supported by the Lundbeck Foundation (grant
R302-2018-2155) and the Novo Nordisk Foundation (grant NNF18SA0035006); E.K.I.-P. was
supported by the Lundbeck Foundation (grant R302-2018-2155) and the Novo Nordisk
Foundation (grant NNF18SA0035006). W.B. is supported by the Hanne and Torkel Weis-Fogh
Fund (Department of Zoology, University of Cambridge). A.P. is funded by Wellcome grant
WT214300. B.S.d.M. and O.D. are supported by the Swiss National Science Foundation (SFNS
PP00P3_176977) and European Research Council (ERC 679330). G.R. is supported by a Novo
Nordisk Foundation Fellowship (gNNF20OC0062491). N.N.J. is supported by Aarhus University
Research Foundation. A.J.S. is supported by a Lundbeckfonden Fellowship (R335-2019-2318)
and the National Institute on Aging (NIH award numbers U19AG023122, U24AG051129 and
UH2AG064706). R. Maring was funded by the Aarhus University Research Foundation through
a grant awarded to M. A. Mannino for the project titled Danish and European Diets in Time
(AUFF-E-2015-FLS-8-2). S.R. was funded by the Novo Nordisk Foundation (NNF14CC0001).
T.S.K. is funded by Carlsberg grant CF19-0712. R.D. is funded by the Wellcome Trust (WT214300).
R.N. is funded by the National Institute of General Medical Sciences (NIH grant R01GM138634).
T.W. is supported by the Lundbeck Foundation iPSYCH initiative (R248-2017-2003). We are
indebted to P. Bennike for her contribution during the formative years of the project until shortly
before her death in 2017. We acknowledge staff at the National Museum, the Anthropological
Laboratory, and the regional museums in Denmark, responsible for collecting, recording and
curating prehistoric skeletal remains studied herein. The process of identifying and sampling
suitable archaeological remains for the current study was dependent on numerous specialists
in Danish archaeology including researchers, museum employees and citizen scientists. We
thank the following in this regard (alphabetically ordered): A. H. Andersen, S. Bergerbrant,
K. Christensen, K. M. Gregersen, V. Grimes, E. Johansen, O. T. Kastholm, T. Lotz, E. Lundberg,
M. Mannino, J. Olsen, K. Rosenlund and H. H. Sørensen. We also acknowledge those who have
assisted in the sampling process or the gathering of provenance data on prehistoric human
remains which were not analysed here owing to insufficient DNA preservation. These include
H. Dahl (Tybrind Vig), I. B. Enghoff (Østenkær), A. B. Gurlev (Vedbæk Havn), L. Holten (Aldersro),
O. Lass (Hesselbjerg/Ferle Enge and Nivå), L. Matthes (Knudsgrund/Knudshoved) and
K. Randsborg (deceased) (Nivå). We are grateful for contributions from F. Racimo, and express
our gratitude to the many researchers who have supported laboratory work, analytical
procedures and evaluation of results that are presented here, including M. Mannino, P. Reimer
and M. Thompson. E.W. thanks St. John’s College, Cambridge, for providing a stimulating
environment of discussion and learning.
Author contributions M.E.A., M.S. and A.F. contributed equally to this work. E.W. initiated the
study. M.E.A., M.S., A.F., T.W., K.K. and E.W. led the study. M.E.A., M.S., A.F., M.M, R.N., T.W., K.K.
and E.W. conceptualized the study. M.E.A., M.S., T.S.K., R.D., R.N., O.D., T.W., K.K. and E.W.
supervised the research. M.E.A., R.D., R.N., T.W., K.K. and E.W. acquired funding for research.
A.F., M.E.A., J.S., K.-G.S., M.L.S.J., T.Z.T.J., M.U.H., B.H.N, E.K., J.H., K.B.P., L.P., L.K., P. Lotz.,
P. Lysdahl, P.B., P.V.P., R. Maring, S.W., S.A.S, S.H.A, T.J. and N.L. were involved in sample
collection. M.E.A., M.S., A.I., J.S., A.P., B.S.d.M., L.V., A.S., D.J.L., T.S.K., R.D., R.N., O.D., K.K. and
E.W. were involved in developing and applying methodology. M.E.A., J.S. and L.V. led the DNA
laboratory work research component. K.-G.S. led bioarchaeological data curation. M.E.A.,
M.S., A.R.-M., E.K.I.-P., W.B., A.I., A.P., B.S.d.M., B.S.P., R.A.H., T.V., H.M., A.V., A.B.N., P.R., G.R.,
A.D.R., A.J.S., A. Rosengren, R. Maring, S.R., T.S.K. and O.D. undertook formal analyses of data.
M.E.A., M.S., A.F., K.-G.S., A.I., R. Macleod, A. Rosengren, B.S.P., M.F.M., A.B.N., M.U.H., N.N.J.,
L.P., N.L., T.W., K.K. and E.W. drafted the main text (M.E.A., M.S. and A.F. led this). M.E.A., M.S.,
A.F., K.-G.S., A.I., R. Macleod., A. Rosengren, B.S.P., M.L.S.J., M.N., J.S., T.D.P., M.F.M., A.B.N.,
M.U.H., L.S., P.O.N., P.R., A.R.-M, E.K.I.-P., W.B., A.P., B.S.d.M., F.D., R.A.H., T.V., H.M., A.V., L.V., A.S.,
A.J.S., A. Ruter, A.B.G., B.H.N., E.B.P., E.K., J.H., K.B.P., L.P., L.K., M.J., O.C.U., P.L., P.B., P.V.P., R.
Maring, R.I., S.W., S.A.S., T.J., N.L., D.J.L., S.R., T.S.K., K.H.K., R.D., R.N., O.D., T.W. and K.K. drafted
supplementary notes and materials. All authors read, commented on, and agreed upon the
submitted manuscript.
Competing interests The authors declare no competing interests.
Additional information
Supplementary information The online version contains supplementary material available at
https://doi.org/10.1038/s41586-023-06862-3.
Correspondence and requests for materials should be addressed to Morten E. Allentoft,
Martin Sikora or Eske Willerslev.
Peer review information Nature thanks Patricia Fall, Birgitte Skar and the other, anonymous,
reviewer(s) for their contribution to the peer review of this work.
Reprints and permissions information is available at http://www.nature.com/reprints.
 NEO254 / Koelbjerg / 10465
NEO13 / Hedegaard (Bislev) / 9511
NEO91 / Strøby Grøftemark / 9134
NEO759 / Køge Sønakke / 9040
NEO123 / Orehoved Sejlrende / 8178
NEO122 / Orehoved Sejlrende / 8156
NEO19 / Rønsten / 8172
NEO600 / Vedbaek boldbaner / 7815
NEO683 / Tybrind Vig / 7521
NEO932 / Tudse Hage / 7398
NEO589 / Korsør Nor / 7475
NEO791 / Korsør Nor / 7033
NEO814 / Bodal K / 7115
NEO748 / Henriksholm−Bøgebakken (Vedbæk) / 7129
NEO749 / Henriksholm−Bøgebakken (Vedbæk) / 7072
NEO745 / Henriksholm−Bøgebakken (Vedbæk) / 6801
NEO747 / Henriksholm−Bøgebakken (Vedbæk) / 6728 Mesolithic
NEO586 / Koed / 7030
NEO583 / Koed / 6980
NEO822 / Dragsholm / 6973
NEO733 / Dragsholm / 6819
NEO930 / Fannerup F / 6892
NEO855 / Fannerup D / 6299
NEO570 / Fannerup E / 6372
NEO568 / Ertebølle / 6297
NEO856 / Nederst / 6778
NEO852 / Norsminde / 6306
NEO751 / Bjørnsholm / 6315
NEO941 / Havnø / 6374
NEO598 / Sølager / 6068
NEO853 / Langø Skaldynge / 6045
NEO960 / Ravnsbjerggård II / 5963
NEO645 / Rødhals / 5836
NEO962 / Dragsholm / 5785.5
syltholm / Syltholm / 5759.5 Transitional Mesolithic
NEO601 / Viksø Mose / 5807
NEO891 / Roskilde Fjord (syd for Jyllinge) / 5714
NEO790 / Tysmose / 5668
NEO29 / Lohals / 5559
NEO595 / Pandebjerg / 5545
NEO23 / Jorløse mose / 5536
NEO571 / Grøfte / 5535
NEO564 / Bygholm Nørremark / 5535
NEO753 / Sigersdal Mose 2 / 5533
NEO7 / Sigersdal Mose / 5240
NEO41 / Rude / 5531
NEO942 / Tissøe / 5495
NEO28 / Salpetermosen syd 8 / 5461
NEO886 / Dalmosegaard / 5458
NEO866 / Lundby−Falster / 5457
NEO865 / Lundby−Falster / 5184
NEO757 / Sejerby (Sejerø) / 5452
NEO945 / Læsten Mose / 5444
NEO896 / Mandemarke / 5444 Early Neolithic
NEO933 / Sludegård Sømose / 5438
NEO43 / Rude / 5392
NEO888 / Elkenøre / 5389
NEO795 / Porsmose / 5330
NEO744 / Vig Femhøve / 5363
NEO702 / Jørlundegård / 5271
NEO935 / Vibygårds Mose / 5248
NEO597 / Storelyng (Øgårde boat III) / 5214
NEO594 / Neverkær mose / 5181
NEO961 / Avlebjerg (Strøby) / 5149
NEO599 / Vanløse mose / 5141
NEO602 / Storelyng (Østrup Homo II) / 5139
NEO566 / Døjringe / 5135
NEO898 / Svinninge Vejle / 5081
NEO25 / Kainsbakke II / 5066
NEO925 / Myrebjerg mose / 4947
NEO33 / Vittrup / 5139
NEO943 / Stenderup Hage / 4617 Transitional Neolithic
NEO580 / Klokkehøj / 4612
NEO792 / Næs / 4496
NEO876 / Toftum mose / 4385
NEO870 / Toftum mose / 4255
NEO872 / Toftum mose / 4016
NEO875 / Toftum mose / 3986
RISE61 / Kyndeløse / 4621.5
NEO878 / Kyndeløse / 4038
NEO92 / Barhøj (Strøby Egede) / 4218
NEO737 / Borreby / 4111

published shotgun-sequenced ancient individuals from Denmark - including

NEO738 / Kolind / 4111

Extended Data Fig. 1 | Model-based clustering. Unsupervised model-based

NEO739 / Kolind / 3971

clustering results (ADMIXTURE) for K = 2 to K = 15 assumed components for all

NEO861 / Mosede Mose / 4111
NEO860 / Mosede Mose / 3667
Gjerrild5 / Gjerrild / 4110 Late Neolithic / Early Bronze Age
RISE71 / Falshøj / 4059.5
NEO735 / Borreby / 3995
NEO934 / Gammellung / 3834
VK214 / Gerdrup / 3782
NEO93 / Strøby Ladeplads / 3738
NEO857 / Lollikehuse / 3668
NEO752 / Madesø / 3649
NEO563 / Bybjerg / 3355
RISE47 / Sebber skole / 3361.5
NEO951 / Klæsterupholm Mose / 3306
NEO590 / Magleø / 3297
NEO946 / Hove Å / 3145
VK582 / Alken_Enge / 1900
VK521 / Brondsager Torsiinre / 1650
VK213 / Gerdrup / 1491 Iron Age
VK532 / Kragehave Odetofter / 1850
VK65 / Tollemosegard / 1200
VK69 / Tollemosegard / 1200
VK70 / Tollemosegard / 1200
VK71 / Tollemosegard / 1200
VK312 / Rantzausminde / 1075
VK313 / Rantzausminde / 1075
VK314 / Rantzausminde / 1075
VK329 / Ribe / 1163
VK325 / Ribe / 1091
VK328 / Ribe / 1079
VK326 / Ribe / 958
VK327 / Ribe / 945
VK324 / Ribe / 938
VK323 / Ribe / 900
VK322 / Ribe / 866
VK330 / Ribe / 861
VK301 / Ladby / 1185
VK319 / Ladby / 1150
VK294 / Bakkendrup / 1075
VK315 / Bakkendrup / 1075
VK369 / Bakkendrup / 1075
VK300 / Hesselbjerg / 1075
VK340 / Hesselbjerg / 1075
VK384 / Hesselbjerg / 1075
VK84 / Hesselbjerg / 1075
VK87 / Hesselbjerg / 1075
VK385 / Lejre / 1075
VK90 / Lejre / 1075
VK92 / Lejre / 1075
VK445 / Lejre / 900
VK94 / Lejre / 900
VK371 / Galgedil / 1065
VK134 / Galgedil / 900
VK138 / Galgedil / 900
VK139 / Galgedil / 900
VK278 / Galgedil / 900
VK280 / Galgedil / 900 Viking Age
VK370 / Galgedil / 900
VK372 / Galgedil / 900
VK373 / Galgedil / 900
VK446 / Galgedil / 900
VK141 / Galgedil / 900
VK279 / Galgedil / 900
VK289 / Bodkergarden / 1000
VK291 / Bodkergarden / 1000
VK281 / Barse / 900
VK298 / Besser / 900
VK286 / Bogovej / 900
VK288 / Bogovej / 900
VK292 / Bogovej / 900
VK320 / Bogovej / 900
VK338 / Bogovej / 900
VK361 / Bogovej / 900
VK362 / Bogovej / 900
VK363 / Bogovej / 900
VK364 / Bogovej / 900
VK365 / Bogovej / 900
VK366 / Bogovej / 900
VK367 / Bogovej / 900
VK368 / Bogovej / 900
VK284 / Grydehoj / 900
VK295 / Hessum / 900
VK316 / Hessum / 900
VK296 / Hundstrup / 1230
VK297 / Hundstrup / 1200
VK274 / Kaargarden / 900
VK275 / Kaargarden / 900
VK276 / Kaargarden / 900
VK285 / Kaargarden / 900
VK287 / Kaargarden / 900
VK317 / Kaargarden / 900
VK290 / Kumle / 900
VK282 / Stengade / 900

15 14 13 12 11 10 9 8 7 6 5 4 3 2

excluded). Imputed genomes were used where available3. For low-coverage

the herein presented 93 genomes (contamination <5% and close relative pairs

individuals (indicated with black cross) pseudo-haploid genotypes were used.

Article
Extended Data Fig. 2 | Allele sharing of Danish Mesolithic individuals.
a, D-statistic testing whether Danish Mesolithic individuals form a clade with
the earliest Danish Mesolithic individual in the dataset (NEO254, Koelbjerg
Man) to the exclusion of a genetic cluster of Mesolithic hunter-gatherer
individuals from Sweden (Sweden_10000BP_7500BP). b, D-statistic testing
whether Danish Mesolithic individuals form a clade with a genetic cluster of
Western European HG individuals (EuropeW_13500BP_8000BP) to the
exclusion of a genetic cluster of Eastern European HG individuals
(RussiaNW_11000BP_8000BP). Error bars indicate three standard errors.
Extended Data Fig. 3 | IBD sharing among ancient individuals from Denmark. and text indicate genetic cluster membership, and dendrograms show
Heatmap showing pairwise amount of total length of IBD shared between 72 clustering hierarchy.
ancient Danish individuals dated to older than 3,000 cal. BP. Colours in border
Article
Extended Data Fig. 4 | Genetic affinities of ancient individuals from
Denmark. Panels show principal component analyses based on pairwise
IBD-sharing of a, 30 imputed Danish Mesolithic individuals in context of 105
European HGs (right panel shows Danish individuals coloured by age); b, 22
imputed Danish early Neolithic individuals within the context of 170 Anatolian
and European Neolithic farmers c, 21 imputed Danish LNBA individuals within
the context of 127 European LNBA individuals. Symbol colour and shape indicate
the genetic cluster of an individual (Supplementary Data III). The extent of PCA
positions of individuals from Denmark are indicated with a dotted line hull.
Ancestry cluster categories defined in3.
Extended Data Fig. 5 | Dietary isotopic signatures. δ13C and δ15N values in observed at the transition from the Mesolithic to the Neolithic c. 5,900 cal. BP
bone/dentine samples from 100 ancient Danish individuals, coloured according (dashed line). Four anomalous individuals are highlighted. Data from3 and
to their main genetic ancestry group. A fundamental dietary and genetic shift is Supplementary Data II.
 VK582 / 1900 / I2a
VK532 / 1850 / I1a
VK521 / 1650 / I1a

e
d
VK213 / 1491

b
Source

Iron Age
VK296 / 1230 / I1

Denmark
VK297 / 1200 / I1a
VK65 / 1200
VK69 / 1200
Alh1 / 1500 / R1b VK70 / 1200 / I1a

a
NW54 / 1490.5 VK71 / 1200 / I1
Alh10 / 1489 VK301 / 1185 / I1a
STR486 / 1455 / I1a VK329 / 1163 / R1b
STR220c / 1445 VK319 / 1150
STR300b / 1430 VK325 / 1091
STR310 / 1430 VK328 / 1079
VK294 / 1075
Article

VK315 / 1075 / I1a

VK369 / 1075 / R1b

0.00
0.05
0.10
0.15
0.20
VK300 / 1075
VK340 / 1075

Germany Medieval
VK384 / 1075 / R1b
VK84 / 1075
VK87 / 1075 / R1b
VK385 / 1075
VK90 / 1075
VK92 / 1075
VK312 / 1075
VK313 / 1075 / R1b
VK314 / 1075
VK371 / 1065
VK289 / 1000 / R1b
VK291 / 1000 / I1a
VK326 / 958 / R1b
SZ11 / 1442 / R1b VK327 / 945 / I1a

MiddleDon_7500BP
Ukraine_10000BP_4000BP
Italy_15000BP_9000BP
LevantEuropeS_4700BP_1700BP
EuropeCE_7000BP_5500BP
EuropeEW_8500BP_6500BP
EuropeSW_6000BP_3500BP
EuropeNW_6000BP_5000BP
Scandinavia_5600BP_4600BP
Poland_5000BP_4700BP
Steppe_5000BP_4300BP
Norway_9300BP_4300BP
RussiaNW_7000BP_5000BP
MiddleDon_7500BP
EuropeW_13500BP_8000BP
Denmark_10500BP_6000BP
Romania_8800BP
EuropeE_8600BP_6000BP
EuropeCE_7000BP_5500BP
EuropeEW_8500BP_6500BP
MiddleDon_7500BP
Ukraine_10000BP_4000BP
Italy_15000BP_9000BP
Caucasus_13000BP_10000BP
Boncuklu_10000BP

Sweden_10000BP_7500BP
SZ15 / 1442 / R1a VK324 / 938 / R1b
SZ2 / 1442 / R1b VK281 / 900 / I1a
SZ3 / 1442 / I2a VK298 / 900
SZ36 / 1442 / T1a VK286 / 900 / R1b

0.02
SZ4 / 1442 / R1b VK288 / 900 NEO254 / 10465 / I2a
SZ45 / 1442 / I1a VK292 / 900 / R1a
SZ5 / 1442 / R1b VK320 / 900 / I1a
SZ43 / 1430.5 / I2a VK338 / 900 / R1b NEO91 / 9134 / I2a
VK361 / 900
VK362 / 900 / E1b
0.01

Viking Age
VK363 / 900 / I1a NEO759 / 9040 / I2

EuropeW_13500BP_8000BP
VK364 / 900
VK365 / 900 / R1b NEO123 / 8178
VK366 / 900
VK367 / 900 / I1a
VK368 / 900 NEO19 / 8172 / I2a
VK134 / 900 / R1b
VK138 / 900 / R1b

Hungary Medieval (Langobard)

VK139 / 900 / R1a NEO122 / 8156
VK141 / 900
VK278 / 900 NEO683 / 7521
VK279 / 900 / I1a
VK280 / 900 / I2a
VK370 / 900 NEO589 / 7475 / I2a
VK372 / 900
VK373 / 900 / R1b
M1489 / 2035 VK446 / 900 / I1a NEO932 / 7398
12880A / 2017 / R1b VK284 / 900
12884A / 1995 / R1b VK295 / 900 / I1 NEO749 / 7072 / I2a
VK316 / 900 / I1a

England
15579A / 1745
VK274 / 900 / R1a
VK275 / 900 / I1 NEO791 / 7033 / I2
VK276 / 900
15569A / 1490 VK285 / 900
15570A / 1482.5 VK287 / 900 / R1b NEO586 / 7030 / I2
15577A / 1477.5 VK317 / 900 / J2a
15558A / 1455 VK290 / 900 / R1b
12883A / 1246.5 VK445 / 900 / I1a
NEO583 / 6980
12881A / 1232 VK94 / 900
NO3423 / 1170 / I1a VK323 / 900 / R1b NEO733 / 6819
12885A / 1164.5 VK282 / 900 / R1a
VK322 / 866 NEO745 / 6801 / I2
Denmark_10500BP_6000BP
VK330 / 861

NEO856 / 6778
VK523 / 1800

Iron Age Medieval (Saxon)

NEO747 / 6728 / I2a
VK418 / 1500 / R1b
VK390 / 1350 / R1a
0.02

VK391 / 1350 NEO941 / 6374

Denmark_10500BP_6000BP

Norway
Iron Age
VK419 / 1100 / N1a NEO570 / 6372
VK514 / 1100 / R1a
VK519 / 1100 / I1
VK529 / 1050 / I1a NEO751 / 6315 / I2
VK528 / 1050 / R1b
VK548 / 1000 NEO852 / 6306
VK518 / 1000
VK525 / 1000
VK526 / 1000 NEO855 / 6299 / I2a
VK417 / 1000
VK392 / 1000
VK420 / 950 / I1a NEO568 / 6297 / I2
MJ−37 / 1635.5 VK448 / 950
MJ−19 / 1554 VK547 / 950 / I1a
VK415 / 950
NEO598 / 6068
VK393 / 900
VK394 / 900 / R1a NEO853 / 6045
VK422 / 900 / R1a
VK515 / 900 / I1a

Viking Age
VK524 / 900 / I1a NEO960 / 5963 / I2a
VK530 / 900
VK386 / 900 / R1b NEO645 / 5836 / I2
VK516 / 900 / R1a
VK389 / 900 / R1b
0.98 1.00 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 1.00 1.00

VK520 / 900 syltholm / 5759.5

VK387 / 850
VK414 / 850 / R1a

target individuals is indicated by column facets. b, Spatial distribution of

VK388 / 700 / I1a
0.56
0.10
0.04
0.03
0.17
0.06
0.05
0.61
0.39

Ukraine Iron Age (Chernyakhiv)

VK113 / 650 NEO898 / 5081 / I2a Sweden_5000BP
VK114 / 650

estimated ancestry proportions of three different HG sources for Neolithic

VK117 / 650 / R1b
VK118 / 650 NEO891 / 5714
VK124 / 650

different sets of ancestry source groups (deep, fEur, postNeol, Supplementary

Extended Data Fig. 6 | Ancestry modelling of ancient individuals. a, Heatmap
of ancestry proportions for 72 ancient individuals from Denmark dated to older
than 3,000 cal. BP estimated from supervised mixture models. Results for three

Data IV) are distinguished in facet rows. Genetic cluster membership for Danish
NEO790 / 5668 / I2a

EuropeE_8600BP_6000BP
VK579 / 1650 / N1a
NEO29 / 5559
VK522 / 1564
RISE174 / 1431 NEO595 / 5545 / I2a

Sweden
VK350 / 1151

Iron Age
VK349 / 1121 / R1b
NEO23 / 5536 / I2a
VK355 / 1102 / L
VK442 / 1102 NEO753 / 5533
VK444 / 1102 / R1b
VK336 / 1097 / R1b
0.09

Target
VK358 / 1097 NEO942 / 5495

c
VK332 / 1092 / I2a
VK337 / 1092 / I1a NEO28 / 5461 / I2a
VK333 / 1065 / R1b
stg026 / 1053.5
0.10

grt035 / 995.5 / G2a NEO886 / 5458 / I2a

84001 / 988.5 / N1a
VK428 / 975
VK429 / 975 NEO866 / 5457 / R1b
VK430 / 975 / N1a
VK431 / 975 / R1b
0.07

VK432 / 975
NEO757 / 5452

0.0
0.1
0.2
0.3
VK433 / 975 Scandinavia_5600BP_4600BP
VK434 / 975 NEO945 / 5444
VK438 / 975 / R1a
VK439 / 975
0.03 0.11 0.06

VK455 / 975 NEO896 / 5444

VK456 / 975
VK457 / 975
0.10 0.13 0.17 0.13 0.06 0.09 0.16 0.13 0.14 0.19 0.11 0.18 0.06 0.16

VK458 / 975
NEO933 / 5438 / I2
VK459 / 975
0.01
0.21
0.04

VK460 / 975 NEO43 / 5392 / I

VK461 / 975 / N1a
VK463 / 975 / R1a
VK56 / 975 NEO744 / 5363 / Q1b
VK57 / 975 / R1b
VK58 / 975 NEO935 / 5248 / I2a
VK60 / 975 / R1a
VK63 / 975
0.06

VK64 / 975 / R1a NEO597 / 5214 / I2a

VK232 / 975 / R1b

Estonia_3000BP_2500BP
VK450 / 975

EuropeE_4000BP_2500BP
VK452 / 975 / R1a NEO599 / 5141 / Q1b

EuropeNW_4000BP_500BP
VK453 / 975 / R1a
VK454 / 975
0.15
0.03

Scandinavia_4000BP_3000BP
VK468 / 975 / R1b
NEO25 / 5066
VK469 / 975 / R1b
0.05 0.02

VK471 / 975 / R1a NEO925 / 4947

VK473 / 975 / I1a
VK474 / 975 / E1b
0.09 0.12 0.13 0.16 0.10 0.16 0.11
0.10
0.90 0.87 0.83 0.86 0.94 0.91 0.75 0.87 0.75 0.80 0.79 0.72 0.88 0.84 0.78 0.91 0.88 0.81 0.84 0.70 0.83 0.79
0.14 0.17 0.22 0.18 0.11 0.13 0.30 0.18 0.29 0.24 0.24 0.33 0.17 0.21 0.20 0.13 0.16 0.24 0.20 0.29 0.22 0.23
0.86 0.83 0.78 0.82 0.89 0.87 0.70 0.82 0.71 0.76 0.76 0.67 0.83 0.79 0.76 0.87 0.84 0.76 0.80 0.68 0.78 0.77

VK475 / 975 / R1a NEO943 / 4617 / I2a

VK476 / 975
Poland_5000BP_4700BP

VK477 / 975
VK478 / 975
0.02

Sources
VK479 / 975 / G2a
NEO792 / 4496 / I2a
VK48 / 975 / R1a EuropeNE_4800BP_3000BP
0.04
0.01
0.03 0.09
0.10 0.13
0.85 0.72
0.61 0.55
0.21 0.15
0.18 0.30

VK50 / 975 / I1a Gjerrild5 / 4110 / R1b

VK51 / 975 / N1a
VK53 / 975 / I2a
VK354 / 964 / R1a
0.03
0.03
0.01
0.06
0.23
0.63
0.53
0.13
0.33

stg021 / 924 RISE61 / 4621.5 / R1a Scandinavia_4600BP_3800BP

VK334 / 901
VK353 / 901
VK265 / 900 NEO870 / 4255 / R1b
VK266 / 900
VK268 / 900 / R1b

Viking Age
0.06 0.02

VK335 / 900 / R1b NEO92 / 4218 / R1b

VK342 / 900 / I2a
VK343 / 900 / I1a
VK344 / 900 / R1a NEO738 / 4111 / I2a
VK345 / 900 / R1b
VK346 / 900 / J2b
0.02
0.03

VK348 / 900 / I2a

NEO861 / 4111
VK352 / 900 / I1a
0.02 0.03
0.03

VK380 / 900 / I1 RISE71 / 4059.5

VK443 / 900 / I1a
VK533 / 900 / N1a
0.02 0.01 0.02

84005 / 900 / I1a NEO878 / 4038 Scandinavia_4200BP_3200BP

nuf002 / 900 / R1a

postBA reference set, Supplementary Data IV).

kls001 / 900 / R1a NEO735 / 3995 / R1b
kal006 / 900
kal009 / 900
stg020 / 900 NEO739 / 3971 / I2a

Europe_4000BP_2000BP
gtm021 / 900
97002 / 900 / R1b
0.03

EurasiaN_2000BP_1000BP
VK357 / 897 / I1a NEO860 / 3667 / R1b
grt036 / 877.5 / I2a

EuropeSW_6000BP_3500BP
urm035 / 874 / I1a
0.01 0.02 0.01 0.03
0.03 0.01

VK108 / 850
NEO752 / 3649 / R1b
VK217 / 850 / R1b
0.02
0.03
0.01
0.16 0.19 0.17 0.18 0.14 0.19 0.13 0.12 0.13 0.15 0.10
0.09 0.14 0.14 0.13 0.11 0.16 0.17 0.19 0.12 0.16 0.15
0.68 0.65 0.68 0.61 0.68 0.63 0.69 0.67 0.68 0.65 0.68
0.55 0.54 0.56 0.55 0.59 0.56 0.57 0.56 0.56 0.56 0.53
0.10 0.08 0.09 0.07 0.09 0.06 0.09 0.10 0.09 0.07 0.13
0.35 0.38 0.35 0.38 0.32 0.37 0.33 0.34 0.35 0.37 0.34

urm160 / 820.5 / R1b

LevantEuropeS_4700BP_1700BP
VK527 / 800
NEO951 / 3306
VK29 / 800 / I1a
VK30 / 800 / R1a
0.01

VK303 / 800 NEO737 / 4111 / R1b

VK306 / 800 / I1a Europe_4500BP_2000BP
VK308 / 800 / R1b
0.02 0.02
0.03 0.03
0.05 0.02
0.03
0.14 0.11
0.15 0.13
0.61 0.64
0.55 0.57
0.08 0.08
0.36 0.35

VK309 / 800 / R1a

NEO875 / 3986 / I1
VK31 / 800 / R1b
VK34 / 800 / R1b
0.03

VK35 / 800 / R1a VK214 / 3782

VK39 / 800 / G2a
VK395 / 800 / N1a
VK396 / 800 / R1b NEO93 / 3738 / I1a
VK397 / 800 / R1a
Scandinavia_5600BP_4600BP

VK398 / 800 / T1a

0.02
0.01 0.01

VK399 / 800 / N1a

NEO563 / 3355 / I1a Scandinavia_4000BP_3000BP
VK40 / 800 / R1b
VK400 / 800 / I1a NEO590 / 3297 / I1a
VK401 / 800 / R1a
VK402 / 800
0.02
0.12 0.12 0.10 0.16 0.15
0.20 0.18 0.21 0.18 0.15
0.65 0.69 0.66 0.65 0.67
0.62 0.60 0.62 0.56 0.61
0.03 0.07 0.04 0.04 0.04
0.35 0.33 0.34 0.39 0.35

VK403 / 800 / R1b NEO946 / 3145 / R1b

VK404 / 800 / I1a
VK405 / 800 / R1b
VK406 / 800 / N1a
VK407 / 800 / I1
postNeol fEur deep
VK42 / 800 / J2a
VK424 / 800 / R1b
VK425 / 800 / R1b

individuals from Scandinavia and Poland. d, Ancestry proportions for

VK426 / 800 / R1b
VK427 / 800 / I2a

Scandinavian Iron Age and Viking Age individuals (postBA reference set).
estimated ancestry proportions of two different farmer sources for LNBA
farmer individuals from Scandinavia and Poland. c, Spatial distribution of

e, Ancestry proportions for selected ancient European individuals with ancestry

related to Scandinavian LNBA individuals (source Scandinavia_4000BP_3000BP,
Extended Data Fig. 7 | Contrasting hunter-gatherer admixture dynamics in
Neolithic farmer individuals from Denmark and Sweden. a, Admixture time
estimated using DATES 44 as a function of age for Neolithic farmer individuals
from Denmark (left) and Sweden (right). Pie charts indicate ancestry composition
(light grey - farmer ancestry; dark grey - non-local hunter-gatherer ancestry;
colour - local hunter-gatherer ancestry). b, Total amount of hunter-gatherer
ancestry proportion as a function of admixture time for Neolithic farmer
individuals from Denmark (left) and Sweden (right). Error bars indicate ± 1
standard error of admixture time estimate.
Article
EuropeNE_4800BP_3000BP
a

0.3
I2a R1b
R1b

R1a R1a R1a 0.2

I2a
R1b R1a
R1a

PC2
I2a 0.1
R1a
Levant

0.0
R1b 1

NEO792 / 4496
Gjerrild5 / 4110
R1a 6
Steppe
I2 1 -0.1
I1
-0.15 -0.10 -0.05 0.00
PC1

Scandinavia_4600BP_3800BP
b
R1a
0.3
R1a R1a R1a
R1a

R1a
0.2
R1a

R1a
R1a

PC2
0.1

0.0
R1b

oll007 / 4630
RISE61 / 4621.5
ber2F / 4510
RISE94 / 4496.5
ber1M / 4495
NEO51 / 4341
R1a 3

I2 -0.1
I1

-0.15 -0.10 -0.05 0.00

PC1

Scandinavia_4200BP_3200BP
c

0.3 R1b R1b I2a R1b R1b I2a R1b R1b

I2a
R1b I2aR1b
R1b
R1bR1bR1b 0.2
I2a
R1b I2a R1b R1b
R1b R1b
PC2

0.1
R1b

0.0
R1b 6

NEO870 / 4255
NEO92 / 4218
NEO738 / 4111
NEO861 / 4111
RISE98 / 4103.5
RISE71 / 4059.5
NEO878 / 4038
NEO735 / 3995
NEO739 / 3971
RISE97 / 3905
NEO860 / 3667
NEO752 / 3649
NEO951 / 3306
R1a

I2 2 -0.1
I1

-0.15 -0.10 -0.05 0.00

PC1
Source
I2a R1b Scandinavia_5600BP_4600BP
R1a R1a R1a Poland_5000BP_4700BP
R1b R1b I2a R1b R1b I2a R1b R1b
Europe_4500BP_2000BP EuropeNE_4800BP_3000BP
R1b I1 R1b

I1 I1 I1a I1 I1a I1a I1a I1a R1b

Europe_4500BP_2000BP
EuropeNW_4000BP_500BP
−4500 −4000 −3500

Europe_4500BP_2000BP
d
0.3
R1b I1 R1b

I1 R1b
R1b 0.2

I1

R1b R1b
PC2

0.1
R1b R1a
R1b R1b
R1b R1b R1b 8 0.0
R1b R1a 1

I2
NEO44 / 4386
NEO737 / 4111
NEO875 / 3986
NEO52 / 3766

I1 1 -0.1

-0.15 -0.10 -0.05 0.00

PC1

Scandinavia_4000BP_3000BP
e
I1
I1 I1
0.3
I1a I1 I1 I1a I1 I1a I1a I1a I1a R1b

I1a
I1a R1b

I1a I1a 0.2

I1 I1 I1
I1a R1b
I1a
I1a
I1a
0.1
PC2

I1a

0.0
R1b 1
NEO220 / 3986
NEO227 / 3924
NEO224 / 3919
NEO261 / 3895
NEO228 / 3841
oll009 / 3790
VK214 / 3782
NEO225 / 3748
NEO93 / 3738
oll010 / 3720
NEO563 / 3355
NEO590 / 3297
NEO946 / 3145

R1a

I2 -0.1
I1 8

-0.15 -0.10 -0.05 0.00

PC1

Extended Data Fig. 8 | Fine-scale structure in late Neolithic and Early Individual assignments and frequency distribution of major Y chromosome
Bronze Age (LNBA) Scandinavians c. 4,500-3,000 cal. BP. a–e, Geographic haplogroups are indicated in maps and timeline. Plot symbols with black circles
locations and PCA based on pairwise IBD sharing (middle) of 148 European indicate the 38 Scandinavian individuals in the PCA panels. Ancestry proportions
LNBA individuals predating 3,000 cal. BP (Supplementary Data IV). Geographic for the 38 Scandinavian individuals estimated using proximal source groups
locations are shown for 65 individuals belonging to the five genetic clusters from outside Scandinavia (postNeolScand source set) are shown on the right of
observed in 38 ancient Scandinavians (a,b, LNBA phase I; c,d, LNBA phase II; the respective cluster results.
e, LNBA phase III; temporal sequence shown in timeline in centre of plot).
 nature portfolio | reporting summary
Morten Allentoft, Martin Sikora, Eske
Corresponding author(s): Willerslev
Last updated by author(s): Oct 18, 2023

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Study description The study undertook population genomics analysis of ancient individuals from Denmark, on data from the accompanying publication
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Research sample 100 human (Homo_sapiens) individuals from archaeological sites across Denmark, all >1000 years old.

Sampling strategy We sampled primarily individuals from the Mesolithic and Neolithic periods from Danish archaeological sites; sampling was restricted
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 Dating methods 272 novel radiocarbon dates were generated at the 14CHRONO laboratory, Queen’s University Belfast (242 samples), at the Oxford

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