Paleogenomic Evidence For Multi-Generational Mixing Between Neolithic Farmers and Mesolithic HG in Lower Danube

Report
Paleogenomic Evidence for Multi-generational

Mixing between Neolithic Farmers and Mesolithic
Hunter-Gatherers in the Lower Danube Basin
Highlights Authors
d Demic and cultural diffusions underlie the Neolithic period in Gloria González-Fortes,
the Danube basin Eppie R. Jones, Emma Lightfoot, ...,
Ron Pinhasi, Andrea Manica,
d A large WHG genome component was present in Eneolithic Michael Hofreiter
communities in this region
d The further east in Europe, the weaker the genetic component

Correspondence
of Anatolian farmers [email protected] (G.G.-F.),
[email protected] (E.R.J.),
d Environmental factors may account for a demic diffusion [email protected] (R.P.),
[email protected] (A.M.),
breakdown in these regions
[email protected] (M.H.)
In Brief
A key question in archaeological research
is whether the transition from hunting and
gathering was more reliant on the
movement of people or ideas. González-
Fortes et al. show, based on genomes of
several ancient humans, that in parts of
Romania, it was actually a mix of both
processes that took place during this so-
called Neolithization process.
González-Fortes et al., 2017, Current Biology 27, 1801–1810

June 19, 2017 ª 2017 The Authors. Published by Elsevier Ltd.
http://dx.doi.org/10.1016/j.cub.2017.05.023
Current Biology
Report
Paleogenomic Evidence for Multi-generational

Mixing between Neolithic Farmers and Mesolithic
Hunter-Gatherers in the Lower Danube Basin
Gloria González-Fortes,1,2,14,* Eppie R. Jones,3,14,* Emma Lightfoot,4 Clive Bonsall,5 Catalin Lazar,6
Aurora Grandal-d’Anglade,7 Marı́a Dolores Garralda,8 Labib Drak,8 Veronika Siska,3 Angela Simalcsik,9
Adina Boroneant‚,10 Juan Ramón Vidal Romanı́,7 Marcos Vaqueiro Rodrı́guez,7 Pablo Arias,11 Ron Pinhasi,12,13,*
Andrea Manica,3,* and Michael Hofreiter2,15,*
1Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara 44100, Italy
2Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam OT Golm, Germany
3Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
4McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
5School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Teviot Place,
Edinburgh EH8 9AG, UK

6National History Museum of Romania, Bucharest 030026, Romania
7Instituto Universitario de Xeoloxı́a, Universidade da Coruña, A Coruña 15081, Spain
8Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid 28040, Spain
9‘‘Olga Necrasov’’ Centre for Anthropological Research of the Romanian Academy, Ias xi Branch, Theodor Codrescu Strada 2, 700481 Ias
xi,
Romania
10‘‘Vasile Pârvan’’ Institute of Archaeology, Romanian Academy, Henri Coanda Strada 11, Bucharest 010667, Romania
11International Institute of Prehistorical Research, University of Cantabria-Government of Cantabria-Bank of Santander,
Santander 39005, Spain

12School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
13Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
14These authors contributed equally
15Lead Contact
*Correspondence: [email protected] (G.G.-F.), [email protected] (E.R.J.), [email protected] (R.P.), [email protected] (A.M.),

[email protected] (M.H.)
http://dx.doi.org/10.1016/j.cub.2017.05.023
SUMMARY ancestry in a Romanian Eneolithic sample with a

minor, but sizeable, contribution from Anatolian
The transition from hunting and gathering to farmers, suggesting multiple admixture events be-
farming involved profound cultural and technological tween hunter-gatherers and farmers. Dietary stable-
changes. In Western and Central Europe, these isotope analysis of this sample suggests a mixed
changes occurred rapidly and synchronously after terrestrial/aquatic diet. Our results provide support
the arrival of early farmers of Anatolian origin [1–3], for complex interactions among hunter-gatherers
who largely replaced the local Mesolithic hunter- and farmers in the Danube basin, demonstrating
gatherers [1, 4–6]. Further east, in the Baltic region, that in some regions, demic and cultural diffusion
the transition was gradual, with little or no genetic were not mutually exclusive, but merely the ends of
input from incoming farmers [7]. Here we use ancient a continuum for the process of Neolithization.
DNA to investigate the relationship between hunter-
gatherers and farmers in the Lower Danube basin, a RESULTS
geographically intermediate area that is character-
ized by a rapid Neolithic transition but also by the We investigated the interactions between hunter-gatherers and
presence of archaeological evidence that points to Neolithic farmers in the Lower Danube basin in Romania by
cultural exchange, and thus possible admixture, be- recovering the genomes of four prehistoric individuals: a Meso-
tween hunter-gatherers and farmers. We recovered lithic hunter-gatherer from Ostrovul Corbului (OC1_Meso) dated
at 8.7 thousand years ago (kya), two Mesolithic hunter-gatherers
four human paleogenomes (1.13 to 4.13 coverage)
from Schela Cladovei (SC1_Meso and SC2_Meso) dated at
from Romania spanning a time transect between
around 8.8 kya, and an Eneolithic (the period between the
8.8 thousand years ago (kya) and 5.4 kya and supple- Neolithic and the Bronze Age) individual dated at 5.3 kya
mented them with two Mesolithic genomes (1.73 and from Gura Baciului (GB1_Eneo), located north-northeast of the
5.33) from Spain to provide further context on Iron Gates on a terrace of the Suceag creek (Figure 1A and
the genetic background of Mesolithic Europe. Our STAR Methods, Method Details). Contact between hunter-
results show major Western hunter-gatherer (WHG) gatherers and farmers has been hypothesized for a number of
Current Biology 27, 1801–1810, June 19, 2017 ª 2017 The Authors. Published by Elsevier Ltd. 1801
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
A
Pleistocene/Holocene A.D. 106

Boundary Roman conquest of Dacia
11.65 9.3 8.0 6.4 4.4 3.1 ka cal BP
B C SC1_Meso
SC2_Meso
OC1_Meso
GB1_Eneo
Chan_Meso
Canes1_Meso
La_Braña
WHG
SHG
Latvia_HG
EHG
Ukraine_N
Ukraine_N
Latvia_N
CHG
Anatolia_N
Europe_EN
Europe_MNChL
Europe_LNBA
Figure 1. Geographical, Archaeological, and Genetic Information for the Ancient Spanish and Romanian Samples
(A) Map showing the location of the archaeological sites: Chan do Lindeiro (Chan_Meso), Canes (Canes1_Meso), Schela Cladovei (SC1_Meso and SC2_Meso),
Ostrovul Corbului (OC1_Meso), and Gura Baciului (GB1_Eneo). Gura Baciului is some 250 km north-northeast of the Iron Gates (Schela Cladovei and Ostrovul
Corbului), on a small river that eventually connects with the Danube via the River Tisza. Along with the map we include a timeline with the radiocarbon dates of our
samples and the time frame of the different prehistoric periods in Romania.
(legend continued on next page)
1802 Current Biology 27, 1801–1810, June 19, 2017

archaeological sites across Europe. In 2012, Skoglund et al. [4] strong positive selection for skin depigmentation in the ances-
reported the first genomic data suggesting different origins tors of modern Europeans, the three Romanian Mesolithic indi-
for hunter-gatherers and early farmers in Scandinavia. Further viduals were predicted to have had dark skin pigmentation.
work [1, 5, 6] provided additional paleogenomic evidence that The Eneolithic individual most likely had a lighter skin tone, as
Neolithization was driven by immigration of farming populations, it was homozygous for the derived version of SLC45A2 and
supporting the demic diffusion model, at least for Scandinavia heterozygous for the derived version of SLC24A5. Although an
and Western and Central Europe. In Southeast Europe, the increase in the frequencies of these variants is generally associ-
Lower Danube Basin has provided some of the best evidence ated with the Neolithic, it should be noted that they were already
for cultural exchange, and thus possible mixing, between hunt- present at low frequency among Scandinavian hunter-gath-
er-gatherers and farmers [10–12]. Archaeological data put the erers [8], and a copy of the derived variant of SLC45A2
arrival of the typical Neolithic package, including farming, pot- was also present in our late Spanish Mesolithic sample,
tery, and new burial practices, at around 8 kya. Isotopic analysis Canes1_Meso. All individuals investigated were unlikely to be
of very late Mesolithic burials from Lepenski Vir around that time able to digest lactose as adults, as they all carried ancestral
revealed several individuals whose diets were relatively high in alleles at two key positions in the gene MCM6 (rs4988235 and
terrestrial proteins, a profile more typical of farming communities rs182549).
[11]; although the genetic origin of these individuals is unknown,
their presence points to contact of this Mesolithic community Mitochondrial and Y Chromosome Haplogroups
with farmers (either through cultural exchange or immigration). At the level of mitochondrial DNA sequences, SC1_Meso be-
The presence of personal ornaments of Neolithic type in some longs to U5b (Table 1), the same subhaplogroup to which a num-
Late Mesolithic (8.3–8.0 kya) graves at Lepenski Vir and Vlasac ber of Western hunter-gatherers (WHGs) belong [17–20].
[13] and the recovery of cereal starch granules from dental calcu- SC2_Meso was assigned to U5a, a subhaplogroup mainly found
lus on Mesolithic teeth from Vlasac [12] further support the hy- in Scandinavian [5, 21] and Latvian hunter-gatherers and also in
pothesized adoption of new practices by local hunter-gatherers some samples from later periods in Eastern and Central Europe
in the Lower Danube basin [11]. [6, 7, 22]. The two other samples from Romania, the Mesolithic
OC1_Meso and the Eneolithic GB1_Eneo, both belong to K1, a
Laboratory and Next-Generation Sequencing Data haplogroup commonly found among early European farmers
Processing [17, 18] (see Table S4 and Method Details in STAR Methods
We extracted DNA from petrous bone samples of each individ- for description of haplogroup assignment). At the Y chromosome
ual, constructed one double-stranded Illumina sequencing level, all of our three male samples, SC1_Meso, SC2_Meso, and
library from each extract, and sequenced the libraries on a OC1_Meso, were assigned to the R1 and R1b haplogroups, both
HiSeq2000 platform. After mapping and filtering, endogenous common in modern Europeans (Table 1 and STAR Methods,
content ranged from 23.7% to 55.2%, and genome coverage Quantification and Statistical Analysis).
ranged from 1.13 to 5.33 (Table 1). All samples displayed char-
acteristic ancient DNA (aDNA) damage patterns, with the Population Genomic Analysis
average read length between 62 and 109 base pairs and We investigated the genome-wide relationships of our samples
deamination rates of 14% to 25% at the ends of the molecules to modern and other ancient humans by performing principal-
(Figure S1). Contamination estimates, based on the number of component analysis (PCA) defined by a subset of Eurasian pop-
non-consensus bases in the mitochondria and the X chromo- ulations from the Human Origins dataset [8, 9] (Figure 1B). Our
some in males, were between 0.4% and 2.2% (Table S2). Romanian genomes were projected onto the first two PCA
axes, together with a broad panel of ancient individuals (see
Phenotypic Traits Data S1 for sample details), augmented by two newly sequenced
We investigated a number of phenotypic traits in our ancient Spanish Mesolithic hunter-gatherer genomes (Chan_Meso, an
samples. All three Romanian Mesolithic individuals were pre- Early Mesolithic dated at 9,131 ± 124 cal BP (calibrated age
dicted to have dark hair and brown eyes, whereas the Eneolithic before present), and Canes1_Meso, a Late Mesolithic dated at
individual was predicted to have dark hair and light eye pigmen- 7,115 ± 130 cal BP) to provide better coverage for this important
tation (Figure S2 and Table S3). Based on the presence of the period (Table 1 and STAR Methods, Method Details). The three
ancestral forms of both SLC45A2 (rs1426654) and SLC24A5 Romanian Mesolithic genomes clustered together with other
(rs16891982), two genes that were found to have gone through Mesolithic samples, including the two new Spanish ones, and
(B) Principal-component analysis (PCA). Ancient data (Data S1) were projected onto the first two principal components defined by selected Eurasians from the
Human Origins dataset [8, 9]. The Spanish (Chan_Meso and Canes1_Meso) and Romanian (SC1_Meso, SC2_Meso, and OC1_Meso) Mesolithic samples cluster
close to European hunter-gatherer samples. The Eneolithic Romanian sample (GB_Eneo) locates in a different region of the plot, between European hunter-
gatherer and farmer samples.
(C) ADMIXTURE analysis. ADMIXTURE results are shown at K = 17. The Spanish and Romanian hunter-gatherer samples are composed entirely of the ‘‘blue’’
component, which is also found in other European hunter-gatherer samples, with the exception of the oldest Spanish Mesolithic sample, Chan_Meso, which also
has a ‘‘lilac’’ component found in South Indians. The Eneolithic individual GB1_Eneo has the ‘‘blue’’ as well as the ‘‘orange’’ component that predominates in early
European and Anatolian farmer samples.
Error bars in (A) correspond to the radio carbon ages of samples SC1_Meso, OC1_Meso, and GB1_Eneo as reported in Table 1. See also Figures S1–S4 and
Table S3.
Current Biology 27, 1801–1810, June 19, 2017 1803

Table 1. Origin, Age, Next-Generation Sequencing Data, Uniparental Haplogroups, and Stable Carbon and Nitrogen Isotope Values
Related to Diet for the Samples Analyzed in This Study
Cal BP Age Range Genome Isotope Values (&)b
Sample ID Site (2s) [OxCal 4.2]a Coverage Biol. Sex mtDNA hg. Y hg. d13C d15N C:N Ratioc
SC1_Meso Schela Cladovei (Romania) 8,814 ± 261 1.113 XY U5b2c R 18.5 15.0 3.2
SC2_Meso Schela Cladovei (Romania) 2.833 XY U5a1c R1 19.1 14.7 3.2
OC1_Meso Ostrovul Corbului (Romania) 8,704 ± 269 1.863 XY K1 + 16362 R1b 18.7 15.5 3.1
GB1_Eneo Gura Baciului (Romania) 5,377 ± 77 4.053 XX K1a4a NA 20.0 12.7 3.3
Chan_Meso Chan do Lindeiro (Spain) 9,131 ± 124 5.283 XX U5b NA 20.5 8.4 3.1
Canes1_Meso Canes (Spain) 7,115 ± 130 1.733 XX U5a2a NA 20.0 7.9
Cal BP, calibrated age before present; hg., haplogroup. See also Figure S4 and Tables S1, S2, and S4.
a
The radiocarbon dates of samples from the Iron Gates (Schela Cladovei and Ostrovul Corbului) were corrected for the Danube Freshwater Reservoir
Effect [14].
b
Isotope values for SC1_Meso, Canes1_Meso, and Chan_Meso were published by [14], [15], and [16], respectively. Isotope values for OC1_Meso,
SC2_Meso, and GB1_Eneo were obtained in this study.
c
The C:N atomic ratio serves as an indicator of collagen preservation suitable for radiocarbon dating and paleodiet reconstruction.
close to modern Northern European populations (Figure 1B). The eages. The Romanian Eneolithic individual, on the other hand,
Romanian Eneolithic genome GB1_Eneo, on the other hand, was once again showed a mix of affinities. Based on outgroup f3,
placed in a different region of the plot, located in a unique posi- the genomes that shared the most drift with this Eneolithic
tion between European Mesolithic hunter-gatherers and Early sample are WHGs, in line with the large amount of that ancestry
Neolithic farmers on PC2. We confirmed the intermediate nature detected in ADMIXTURE. However, its affinity to Neolithic
of this genome by estimating ancestral components using samples is also relatively high compared to the Romanian
the clustering algorithm ADMIXTURE. Whereas the Romanian Mesolithic samples (Data S2). This conclusion is supported
Mesolithic hunter-gatherers had a single major ancestral compo- by D statistics of the form D(GB1_Eneo, Romanian HG, Anato-
nent shared with other WHGs, the Romanian Eneolithic sample lian Neolithic, Mbuti), which indicate some Near Eastern
was characterized by a mixture between this WHG component ancestry (Table 2). Our three Romanian hunter-gatherer sam-
and a component maximized in Neolithic farmers (Figures 1C ples are not direct representatives of the hunter-gatherer
and S3B). Other admixed European Neolithic and Eneolithic/ component in GB1_Eneo (Table 2); however, this might be
Chalcolithic farmers had at most 20%–30% WHG ancestry in due simply to the geographic distance between the sites, espe-
ADMIXTURE analysis, and the Romanian Eneolithic is the only cially given the observed heterogeneity among Spanish Meso-
individual who is genetically predominantly Mesolithic (61.7%, lithic hunter-gatherers.
95% confidence interval [CI] 59.9%–63.4%) with a minority Analysis of runs of homozygosity (ROH) showed that the Eneo-
contribution from the Neolithic. We note that Gok2, a Swedish lithic sample had a profile intermediate between Early Neolithic
Neolithic sample, was originally estimated to have 77% hunter- farmers and hunter-gatherers, consistent with the sample’s
gatherer ancestry [5], but in our analysis it has a much lower per- mixed origins (Figure S4A). Finally, we also tested the proportion
centage (27.2%, 95% CI 25.1%–29.4%), in line with other recent of Neanderthal ancestry in each sample, which was consistent
analyses [23]. Although GB1_Eneo is chronologically close to the with the age of the sample (Figure S4B) [24].
beginning of the Bronze Age, we did not find the green compo-
nent (Figure 1C) characteristic of individuals from the Yamnaya Stable-Isotope Analysis
culture, showing that the large hunter-gatherer component in In order to further assess the cultural affinities of these sam-
this Eneolithic individual is unlikely to be due to admixture with ples, we performed stable-isotope analysis on samples OC1_
incoming steppe pastoralists (Table 2). Meso, SC2_Meso, and GB1_Eneo, whereas isotope data
We formalized these inferences by computing outgroup f3 from the other individuals involved in this study were collected
in the form f3(ancient1, ancient2, Mbuti), thus estimating the from the literature [14–16]. The three Romanian Mesolithic indi-
amount of shared drift between pairs of ancient samples with viduals, OC1_Meso, SC1_Meso, and SC2_Meso, have isotopic
respect to an African outgroup. Our three Romanian Mesolithic values (Table 1 and Figures S4C and S4D) that indicate a high
samples share the most drift with each other (Figure 2), fol- proportion of freshwater protein in an otherwise C3-based diet.
lowed by other WHGs, including our new Spanish samples. By contrast, the lower d13C and d15N values of the Eneolithic
The genetic affinity among the Romanian Mesolithic samples individual GB1_Eneo suggest a mixed terrestrial/aquatic diet
was such that they form a clade to the exclusion of other in which the aquatic component was lower than that consumed
ancient samples, as shown by D statistics of the form D(Roma- by the Iron Gates Mesolithic population. Although the GB1_
nian Mesolithic 1, Romanian Mesolithic 2, other_ancient, Mbuti) Eneo results cannot be directly compared to the data from
(Table 2). Interestingly, this was not the case for the Spanish the Iron Gates, its stable-isotope values are similar to those
Mesolithic samples, as Chan is somewhat divergent from found in some Neolithic individuals in the Iron Gates sites
Canes1 and La Braña (Figure S3A and Table 2), highlighting and at Vinc a-Belo Brdo in Serbia, also on the Danube
the genetic diversity of European Mesolithic hunter-gatherer lin- [11, 25–27].

Table 2. Key D Statistics of the Form D(A,B; X,Y)
A B X Y D Z Score Loci
The Romanian Samples Form a Clade with Each Other (jZj < 3; the Most Positive and Negative Statistics Are Shown for Each Comparison)
Mbuti Natufian SC1_Meso SC2_Meso 0.03 1.635 26,749
Mbuti ElMiron SC1_Meso SC2_Meso 0.0281 1.921 44,549
Mbuti GoyetQ116-1 SC1_Meso OC1_Meso 0.0272 1.896 41,197
Mbuti SC2_Meso SC1_Meso OC1_Meso 0.0283 2.036 57,452
Mbuti Kostenki14 OC1_Meso SC2_Meso 0.023 1.964 79,553
Mbuti Armenia_EBA OC1_Meso SC2_Meso 0.0188 2.192 77,923
There Is Anatolian-Farmer-Related Admixture in the Romanian Eneolithic Sample as Compared to the Romanian Mesolithic Samples
Mbuti Anatolia_NW SC1_Meso GB1_Eneo 0.0261 3.523 70,707
Mbuti Anatolia_NW SC2_Meso GB1_Eneo 0.0273 4.469 101,212
Mbuti Anatolia_NW OC1_Meso GB1_Eneo 0.0302 4.614 89,601
The Romanian Eneolithic Sample Is Equally Related to Neolithic Farmers from Central Anatolia and Northwest Anatolia
Mbuti GB1_Eneo Anatolia_NW Anatolia_C 0.0038 0.590 93,551
The Spanish Mesolithic Sample Canes_Meso Forms a Clade with the Spanish Mesolithic Sample La Braña (jZj < 3; the Most Positive and Negative
Statistics Are Shown)
Mbuti Belarusian La Braña Canes1_Meso 0.0206 2.81 73,417
Mbuti Armenia_EBA OC1_Meso SC2_Meso 0.0188 2.192 77,923
The Spanish Mesolithic Sample Chan Does Not Form a Clade with Other Spanish Mesolithic Samples; We Suggest that the Chan Lineage Did Not
Directly Contribute Much to Later Populations (the Five Most Positive Statistics Using Modern Populations Are Shown)
Mbuti Ukrainian Chan_Meso La Braña 0.0289 4.637 91,325
Mbuti Croatian Chan_Meso La Braña 0.0286 4.53 91,325
Mbuti Bulgarian Chan_Meso La Braña 0.0269 4.446 91,325
Mbuti Russian Chan_Meso La Braña 0.0259 4.361 91,325
Mbuti Greek Chan_Meso La Braña 0.0261 4.346 91,325
Mbuti Czech Chan_Meso Canes1_Meso 0.036 5.185 83,744
Mbuti Croatian Chan_Meso Canes1_Meso 0.0354 5.158 83,744
Mbuti Belarusian Chan_Meso Canes1_Meso 0.0354 5.138 83,744
Mbuti Lithuanian Chan_Meso Canes1_Meso 0.0363 5.064 83,744
Mbuti Russian Chan_Meso Canes1_Meso 0.0326 4.965 83,744
Our Romanian Mesolithic Samples Are Not Directly Representative of the HG Ancestry in the Eneolithic Sample GB1_Eneo
Mbuti GB1_Eneo WHG Romanian_HG 0.0179 3.016 107,575
The Romanian Hunter-Gatherer Samples Have Some Additional Eastern Hunter-Gatherer-Related Ancestry Relative to WHGs
Mbuti EHG WHG Romanian_HG 0.0177 3.329 103,285
We Do Not Detect Yamnaya Admixture in the Eneolithic Sample GB1_Eneo
Mbuti Yamnaya Romanian_HG GB1_Eneo 0.0118 2.135 107,443
Mbuti Yamnaya WHG GB1_Eneo 0.0036 0.728 108,273
Ancient samples are highlighted in bold. WHG includes the samples I0585, I1507, Loschbour, Bichon, Villabruna, Ranchot, Rochedane, and Canes1_-
Meso. EHG (Eastern hunter-gatherer) includes the samples I0124 and I0061. Other samples included in each ancient group can be found in Data S1.
DISCUSSION Neolithic has already been noted in other parts of Europe

[6, 24], even though the relative contribution of this ancestry
The genetic analysis of the Eneolithic individual from Gura Baciu- was limited compared to the levels we report for Romania. The
lui provides support for a scenario of complex interactions be- fact that our Romanian hunter-gatherers are not direct represen-
tween hunter-gatherers and farmers in the Lower Danube Basin. tatives of the hunter-gatherer ancestry in GB1_Eneo (Table 2)
At this stage, we cannot discern at what point during or after the provides some support for this latter scenario, but the
Neolithic transition the observed hunter-farmer admixture geographic distance between the Mesolithic and Neolithic/
occurred. Stable isotopic data from Lepenski Vir suggested early Eneolithic sites might also explain this lack of a direct link.
contacts between Neolithic immigrants and Mesolithic commu- Although our results provide evidence for admixture between
nities, whereby the first incomers changed the subsistence prac- these communities, we do not know whether it resulted from
tices of the local fisher-hunter-gatherers, but not necessarily the incoming farmers establishing their own communities into
other cultural traits such as funerary practices [11, 28]. On the which the hunter-gatherers mixed or from small numbers of
other hand, a resurgence of Mesolithic ancestry in the Late farmers joining existing hunter-gatherer communities.

Figure 2. Outgroup f3 Statistics
Outgroup f3 statistics of the form f3(ancient1, ancient2; Mbuti) for (A) SC1_Meso, (B) SC2_Meso, (C) OC1_Meso, and (D) GB1_Eneo. The highest 20 values of the
test are given for each sample. The Romanian Mesolithic samples, SC1_Meso, SC2_Meso, and OC1_Meso, share the most drift with each other, followed closely
by the WHG individuals. The Romanian Eneolithic sample, GB1_Eneo, also shares the most affinity with WHGs. See also Figure S3 and Data S2 for more values of
this test.
Our analysis of uniparental markers provides a caveat on their investigation of the demographic processes that led to the
use to infer the dynamics of interactions among different popu- observed patterns in D and f statistics. However, when our
lations. Although two of our Romanian Mesolithic samples findings are considered together with the observation of an
belong to mtDNA haplogroups (U5a and U5b), which are typical Early Neolithic individual from Hungary (KO1), whose ancestral
of that group, another Mesolithic individual of similar age and component was completely derived from WHG [32], as well as
geographical origin (OC1_Meso) shares the same haplogroup the most recent finding that the Neolithic transition in the Baltic
(K1) with the much later Eneolithic individual GB1_Eneo and and Ukraine occurred with little or no input from farmers of
four previously described Middle/Late Neolithic and Eneolithic Anatolian ancestry [7], a picture emerges in which the further
samples from Romania [29]. K1 has mostly been found in early north and east we go from the Carpathian Basin, the lesser the
farmers from Europe [6, 17, 18, 30–32] and has been hypothe- role of a demic diffusion in the spread of the Neolithic traits,
sized to have its origin in the Near East [1, 9, 18]. Although the thus implying an increase in importance of cultural exchange.
latter hypothesis is not invalidated by our data, the occurrence Interestingly, a similar gradient has been suggested for East
of this haplogroup in a Mesolithic sample from Romania sug- Asia, with high levels of genetic continuity with hunter-gatherer
gests that it entered the European gene pool clearly ahead of populations in the northern parts of the region and admixture be-
the Neolithic transition and should therefore not be used as a tween this lineage and incoming farmers further south [35]. We
marker for tracking farmers of Anatolian origin. Similarly, all three do not know what determined this cline. We could speculate,
Romanian Mesolithic individuals belonged to the Y chromosome though, that the Neolithic package, which was developed in
haplogroup R1. This haplogroup is thought to have originated the Near East, might have been somewhat unsuitable for the
shortly after the Late Glacial Maximum (LGM) [33], but its fre- new climates and environments encountered in the northeast
quency is found to increase greatly in Central Europe during of Europe, leading to a progressive mixing with local hunter-
the Late Neolithic and Bronze Age, leading to the hypothesis gatherers and acquisition of local knowledge, with the eventual
that these haplotypes expanded from the East only after 4.5 breakdown of demic diffusion and the spread of isolated
kya [6]. Its presence in all of our Romanian Mesolithic individuals Neolithic traits by cultural diffusion. Another scenario is that
and in older European human remains [7, 34] suggests that this hunter-gatherers were in higher densities in these eastern re-
haplotype was already found at high frequencies in certain regions and hence that interactions between hunter-gatherers
gions of Europe well before then, even though this observation and farmers were more frequent than in regions further west.
does not negate that the changes in frequency during the Bronze
Age might reflect migration by steppe pastoralists. STAR+METHODS
The genome-wide data that we obtained from the Romanian
Mesolithic and Eneolithic individuals suggest that the interaction Detailed methods are provided in the online version of this paper
between farmers and hunter-gatherers was much more complex and include the following:
than the simple picture of mostly demic replacement of hunter-
gatherers by farmers that has been suggested by previous d KEY RESOURCES TABLE
studies of ancient genomes from Western and Central Europe. d CONTACT FOR REAGENT AND RESOURCE SHARING
The limited number of samples in this study prevents a formal d METHOD DETAILS

B Description of the archaeological context: sites and 3. Hofmanová, Z., Kreutzer, S., Hellenthal, G., Sell, C., Diekmann, Y., Dı́ez-
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Neolithic Aegeans. Proc. Natl. Acad. Sci. USA 113, 6886–6891.
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B Stable isotope analysis 4. Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P.,
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d QUANTIFICATION AND STATISTICAL ANALYSIS
(2012). Origins and genetic legacy of Neolithic farmers and hunter-gath-
B Processing and alignment of NGS data erers in Europe. Science 336, 466–469.
B Test of DNA authenticity
5. Skoglund, P., Malmström, H., Omrak, A., Raghavan, M., Valdiosera, C.,
B Molecular sex determination Günther, T., Hall, P., Tambets, K., Parik, J., Sjögren, K.G., et al. (2014).
B Analysis of phenotypic traits Genomic diversity and admixture differs for Stone-Age Scandinavian
B Mitochondrial analysis and haplogroup assignment foragers and farmers. Science 344, 747–750.
B Y chromosome analysis 6. Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas,
B Population genetic analyses B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al.
d DATA AND SOFTWARE AVAILABILITY (2015). Massive migration from the steppe was a source for Indo-
European languages in Europe. Nature 522, 207–211.
7. Jones, E.R., Zarina, G., Moiseyev, V., Lightfoot, E., Nigst, P.R., Manica,
SUPPLEMENTAL INFORMATION
A., Pinhasi, R., and Bradley, D.G. (2017). The Neolithic transition in the
Baltic was not driven by admixture with early European farmers. Curr.
Supplemental Information includes four figures, four tables, and two data files
Biol. 27, 576–582.
and can be found with this article online at http://dx.doi.org/10.1016/j.cub.
2017.05.023. 8. Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S.,
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AUTHOR CONTRIBUTIONS ulations for present-day Europeans. Nature 513, 409–413.
9. Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D.C., Rohland, N.,
M.H., A.M., and R.P., supervised the study. G.G.-F. performed sampling and
Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al.
labwork. G.G.-F., E.R.J., V.S., and A.M. analyzed genetic data. E.L. and C.B.
(2016). Genomic insights into the origin of farming in the ancient Near
performed isotope analysis. E.L., A.G.-D., and C.B. analyzed and/or helped
East. Nature 536, 419–424.
to interpret isotope data. R.P., C.B., C.L., A.G.-D., M.D.G., L.D., A.S., A.B.,
J.R.V.R., M.V.R., and P.A. provided samples and/or input about archaeolog- 10. Bonsall, C. (2008). The Mesolithic of the Iron Gates. In Mesolithic
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input from all co-authors. pp. 238–279.
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ACKNOWLEDGMENTS
for thought: re-assessing Mesolithic diets in the Iron Gates. Radiocarbon
57, 689–699.
This research was supported by a European Research Council (ERC) Starting
Grant (ERC-2010-StG 263441) to R.P. G.G.-F. was also supported by MSC In- , D. (2016). Dental cal-
12. Cristiani, E., Radini, A., Edinborough, M., and Boric
dividual Fellowship (NeoGenHeritage, grant no. 655478). E.R.J. was supported culus reveals Mesolithic foragers in the Balkans consumed domesticated
by a Herchel Smith Research Fellowship. M.H. and A.M. were supported by plant foods. Proc. Natl. Acad. Sci. USA 113, 10298–10303.
ERC consolidator grants 310763 GeneFlow and 647797 LocalAdaptation, , D. (2016). Deathways at Lepenski Vir. Patterns in Mortuary
13. Boric
respectively. V.S. was supported by the Gates Cambridge Trust. The work of (Serbian Archaeological
Practice: Excavations of Dragoslav Srejovic
C.L. was undertaken through the Partnerships in Priority Areas Program Society).
PN II, developed with the support of MEN-UEFISCDI (project no. PN-II-PT- 14. Cook, G.T., Bonsall, C., Hedges, R.E.M., McSweeney, K., Boroneant‚, V.,
PCCA-2013-4-2302). A.G.-D. is supported by the research project BIOGEOS and Pettitt, P.B. (2001). A freshwater diet-derived 14C reservoir effect at
(CGL2014-57209-P) of the Spanish MINECO. The research of P.A., M.D.G., the Stone Age sites in the Iron Gates gorge. Radiocarbon 43, 453–460.
and L.D. on Los Canes is currently supported by the project CoChange
15. Arias, P. (2005). Determinaciones de isótopos estables en restos hu-
(HAR2014-51830-P) of the Spanish State Plan for R+D+i (MINECO). We would
manos de la región Cantábrica: aportación al estudio de la dieta de las
like to thank Ronny Friedrich for his advice on the radiocarbon date analysis of
poblaciones del Mesolı́tico y el Neolı́tico. Munibe 57, 359–374.
the samples. We would also like to thank Daniel G. Bradley, Lara Cassidy,
Valeria Mattiangeli, and Guido Barbujani for their assistance. 16. Grandal d’Anglade, A., and Vidal Gorosquieta, A. (2017). Caracterización
isotópica de Elba, la mujer mesolı́tica de Chan do Lindeiro (Pedrafita,
Received: February 28, 2017 Lugo, Penı́nsula Iberica). Cadernos do Laboratorio Xeolóxico de Laxe
Revised: April 21, 2017 39, 89–110.
Accepted: May 4, 2017 17. Bramanti, B., Thomas, M.G., Haak, W., Unterlaender, M., Jores, P.,
Published: May 25, 2017 Tambets, K., Antanaitis-Jacobs, I., Haidle, M.N., Jankauskas, R., Kind,
C.J., et al. (2009). Genetic discontinuity between local hunter-gatherers
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STAR+METHODS
KEY RESOURCES TABLE
REAGENT or RESOURCE SOURCE IDENTIFIER

Biological Samples
SC1_Meso ‘‘Vasile Pârvan’’ Institute of Archaeology, M95/2
Romanian Academy, 11 Henri Coanda St
SC2_Meso ‘‘Vasile Pârvan’’ Institute of Archaeology, M96/3
Romanian Academy, 11 Henri Coanda St
OC1_Meso ‘‘Olga Necrasov’’ Centre for Anthropological M24
Research of the Romanian Academy,
Iasxi Branch
GB1_Eneo ‘‘Olga Necrasov’’ Centre for Anthropological M1
Research of the Romanian Academy,
Iasxi Branch
Chan_Meso University of A Coruna, Instituto Universitario Elba
de Xeoloxia Isidro Parga Pondal (IUX)
Canes1_Meso Universidad Complutense de Madrid. I-A
Department of Zoology and Physical
Anthropology. Museo Arqueológico
de Asturias. Oviedo, Spain
Canes2_Meso Universidad Complutense de Madrid. II-A
Department of Zoology and Physical
Anthropology. Museo Arqueológico
de Asturias. Oviedo, Spain
Chemicals, Peptides, and Recombinant Proteins
Guanidinium hydrochloride 99%, M 95,53 g/mo Roth Cas#50-01-1
Guanidinium thiocyanate (GuSCN) 99%, Roth Cas#593-84-0
M 118,16 g/mol
Sodium acetate Sigma Aldrich Cas#127-09-3
Silicon dioxide 500 G SLS Cas#7631-86-9
Isopropanol Sigma-Aldrich Cas#67-63-0
Tween-20 Sigma-Aldrich Cas#9005-64-5
Critical Commercial Assays
High sensitivity DNA chip (Bioanalyzer 2100) Agilent Cat#5067-4626
Deposited Data
SC1 This paper ENA: PRJEB20616
SC2 This paper ENA: PRJEB20614
OC1 This paper ENA: PRJEB20614
GB1 This paper ENA: PRJEB20614
Chan This paper ENA: PRJEB20614
Oligonucleotides
IS1_adapter.P5: 50 -A*C*A*C*TCTTTCCCTACACG [36] Sigma Aldrich
ACGCTCTTCCG*A*T*C*T-30 (here and below,
* indicates a PTO bond)
IS2_adapter.P7: 50 -G*T*G*A*CTGGAGTTCAGAC [36] Sigma Aldrich
GTGTGCTCTTCCG*A*T*C*T-30
IS3_adapter.P5+P7: 50 -A*G*A*T*CGGAA*G*A*G*C-30 [36] Sigma Aldrich
IS4: 50 -AATGATACGGCGACCACCGAGATCTACA [36] Sigma Aldrich
CTCTTTCCCTACACGACGCTCTT-30
P7 indexing: 50 -CAAGCAGAAGACGGCATACGAG [36] Sigma Aldrich
ATxxxxxxxxGTGACTGGAGTTCAGACGTGT-30
(Continued on next page)
Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e1

Continued
REAGENT or RESOURCE SOURCE IDENTIFIER
Software and Algorithms
Illumina Pipeline v1.4 Illumina https://support.illumina.com/
downloads.html
SeqPrep John St. John https://github.com/jstjohn/SeqPrep
Burrows-Wheeler Aligner (BWA) 0.7.5a-r405 [37] http://bio-bwa.sourceforge.net/
Picards-tools-1.98 Broad Institute https://sourceforge.net/projects/picard/
files/picard-tools/1.98/
GATK-3.0-0 [38] https://software.broadinstitute.org/
gatk/download/archive
Samtools-0.1.19 [39] https://sourceforge.net/projects/
samtools/files/samtools/0.1.19/
mapDamage [40] https://ginolhac.github.io/mapDamage/
Haplogrep [41] http://haplogrep.uibk.ac.at/
ANGSD [42] http://popgen.dk/angsd/index.php/
Contamination
Yfitter [43] https://sourceforge.net/projects/yfitter/
EIGENSOFT 5.0.1 [44] https://github.com/DReichLab/EIG
ADMIXTOOLS [44] https://github.com/DReichLab/
AdmixTools
ADMIXTURE [45] https://www.genetics.ucla.edu/
software/admixture/
PLINK [46] https://www.cog-genomics.org/plink2
Other
Proteinase K Promega Cat#MC5005
MinElute PCR Purification Kit QIAGEN Cat#28004
Mobicol M1050 MoBiTec GmbH Cat#S10011
Filter (small) 10 mm pore size MoBiTec GmbH Cat#M2110
Zymo-spin V column extension reservoir Zymo Research Cat#C1016-25
T4 polymerase Fermentas/ThermoFisher Cat#EP0062
T4 Polynucleotide kinase Fermentas/ThermoFisher Cat#EK0031
Buffer Tango Fermentas/ThermoFisher Cat#BY5
ATP ThermoFisher Cat#R0441
PEG-4000 Sigma Aldrich Cat#1546569
T4-ligase Fermentas/ThermoFisher Cat#EL0011
Bst-polymerase, large fragment (supplied with New England BioLabs Cat#M0275 S
10X ThermoPol reaction buffer)
Accuprime SuperMix I ThermoFisher Scientific Cat#12342010
CONTACT FOR REAGENT AND RESOURCE SHARING
Further information and requests for reagents may be directed to, and will be fulfilled by the Lead Contact, Michael Hofreiter (michi@
palaeo.eu).
METHOD DETAILS
Description of the archaeological context: sites and samples

The sampling was agreed in order to minimize damage to the archaeological remains and all samples were collected and analyzed in
accordance with the research ethics policies and procedures of the academic institutions involved in the research.
1. Schela Cladovei
Schela Cladovei (Romania), is a large, open-air site on an Early Holocene terrace adjacent to the River Danube
(44.6258333, +22.6066666), c. 7 km downriver from the Iron Gates I dam. Discovered in 1964, the first excavations were undertaken
e2 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

by the Romanian archaeologist Vasile Boroneant‚. From 1992 onward, the excavation became a joint Romanian–British research proj-
ect, co-directed by V. Boroneant‚, A. Boroneant and C. Bonsall.
Archaeological remains in the areas investigated relate mainly to the Late Mesolithic and Early Neolithic, with sporadic evidence of
later (Iron Age and Medieval) occupation. A large series of single-entity AMS 14C dates on animal and human remains [10] places the
Late Mesolithic occupation between c. 9,150 and 8,250 cal yBP, and the Early Neolithic occupation between 7,950 and 7,550 cal
yBP.
At least 75 burials, containing the remains of over a hundred individuals, have been excavated from the Schela Cladovei site so far,
most of them dated to the Late Mesolithic. The two individuals from Schela Cladovei included in this study were from burials M95/2
(Laboratory ID: SC1_Meso) and M96/3 (Laboratory ID: SC2_Meso), both found among 21 burials uncovered in an area c. 25 m x 4 m
immediately adjacent to the Danube riverbank between 1991 and 1996. Of those 21 burials, which included adults and children,
11 (all adults) have single-entity AMS 14C dates from the Oxford Radiocarbon Accelerator Unit (ORAU). The dating was done prior
to the use of ultrafiltration by ORAU. The calibrated ages (after correction for the Danube Freshwater Reservoir Effect, FRE) range
between 8,950 and 8,550 cal yBP.
Burials M95/2 and M96/3 are both extended inhumation burials. Body position, stratigraphic relationship to Early Neolithic pit fea-
tures, and d15N values of > 14& all point to a Late Mesolithic age, which is confirmed by the 14C date (OxA-8583) for SC1_Meso.
1. SC1_Meso: Adult male, age-at-death 35-45 (dental attrition). The skeleton was lying on the right side, with the legs slightly
flexed. The burial was truncated by an Early Neolithic pit, which removed the mid-section of the skeleton. The distal ends
of both femurs and the lower legs were missing, possibly removed by another pit feature. The skeletal remains were dated
to 8,380 ± 80 yBP (OxA-8583) and corrected to 7,960 ± 96 yBP (9,075-8,553 cal yBP) after considering the FRE [47]
(Table S1). The FRE is related to fish consumption; since fish from the Danube are relatively depleted in 14C, radiocarbon dates
for fish bones and the bones of animals (including humans) that consumed fish are older than their archaeological context. This
age offset can be quantified and corrected for based on the d15N ratio, as described by [47].
2. SC2_Meso: Child, 5-7 years of age at death. There is no 14C date for SC2_Meso, but it belongs to the same (Late Mesolithic)
burial cluster as SC1_Meso and all dates for those burials are statistically indistinguishable at the 2-sigma level [10, 48]; thus
SC2_Meso can be expected to date to the same time period as SC1_Meso.
2. Ostrovul Corbului
The Ostrovul Corbului site is also situated in the Iron Gates region of southwestern Romania (44.5154854, +23.52087725) on a former
island in the Danube River, 28km downstream of Schela Cladovei. Settlement remains, individual graves and a cemetery belonging to
various prehistoric periods (Mesolithic, Neolithic, Eneolithic, Bronze Age, and Iron Age) were identified during several excavation
campaigns between 1973 and 1984 [49]. Seven inhumation burials (no. 2, 9, 18, 24, 25, 30 and 32) were found in an area with Meso-
lithic and Early Neolithic settlement remains at the SW (downstream) end of the island. These were previously interpreted as Early
Neolithic in date, but AMS 14C dating has shown that burials no. 2, 25 and 30 belong to the Middle Mesolithic between about
9.7–9.3 kya, while burial no. 32 dates to the Late Mesolithic around 8.6 kya [10].
The individual from Ostrovul Corbului included in this study (laboratory ID: OC1_Meso) comes from burial no. 24. Only the upper
part of the skeleton was preserved, with the bones in anatomical position. The lower part of the skeleton appears to have been de-
stroyed by a later pit feature. From the surviving portion of the skeleton, burial 24 was interpreted as an extended, supine inhumation
oriented with the head toward the east [49]. The skeleton is that of an adult male, with age at death estimated at 30-35 year and stat-
ure at 172 cm [50, 51]. The AMS 14C date obtained for this study was 8,277 ± 34 yBP (MAMS-28615). After applying a FRE correction
using Method 1 of [47], this converts to a 2-sigma calibrated age range of 8,972–8,435 cal BP (Table S1), which overlaps with the
calibrated age of SC1 from Schela Cladovei.
3. Gura Baciului
The Gura Baciului site (46.7877247, +23.5208770) is located on a terrace of the Suceag creek, in Transylvania, near Cluj Napoca city
(Cluj county). Excavations by N. Vlassa (in 1960, 1962, 1965, 1967-1971) and Gh. Lazarovici (in 1990–1993) uncovered the remains of
a Starc evo-Crisx settlement with huts or houses, pits and concentrations of domestic refuse [52]. Food remains recovered in the ex-
cavations indicate a typical Early Neolithic farming economy based on crop (cereals, etc.) and livestock (cattle, sheep/goat and pig)
husbandry. The material culture remains included pottery, lithic artifacts (e.g., flint, obsidian, ground stone axes, seed grinding equip-
ment), anthropomorphic and zoomorphic figurines, and various kinds of personal ornaments (clay bracelets and buttons, bone rings,
Spondylus shell bracelets and pendants). Based on analysis of the pottery, the site was considered to have been occupied more-or-
less continuously throughout the greater part (stages IB–IVB) of the Starc evo culture time range [51]. There are very few 14C dates on
finds from the Gura Baciului excavations, but 14C results from other Starc evo culture sites in Transylvania indicate a time range for
phases I–IV of c. 7950–7350 cal BP (6,000–5,400 cal BCE) [53].
Seven primary inhumation burials (no. 1, 2, 3, 4, 5, 6, and 9), a cremation grave (no. 7) and a secondary burial (no. 10) were found
within the area of the Starcevo culture settlement, while ‘loose’ human bones (a complete skull [M8] or skull fragments) were discov-
ered in domestic contexts (e.g., pits and houses) belonging to the ‘cultural layer’. Most of the primary inhumations were buried in
crouched positions, on the left or right sides, with varying orientations. These crouched inhumations were assumed to be contem-
poraneous with the Starc evo culture occupation, although few if any chronologically diagnostic items (‘burial offerings’) were recov-
ered from the graves. Moreover, across Southeast Europe, Neolithic and later prehistoric people tended to bury their dead in formal

disposal areas on the periphery of (or some distance away from) their living areas, and it was not unusual for graves to be dug into
abandoned living areas.
Skeletal remains from grave no. 6 were dated to 6,400 ± 90 yBP (7,495–7,159 cal yBP; Lv-2157; [52, 54]). Recently, two other
graves from Gura Baciului were dated: grave no. 2 – 6,350 ± 40 yBP (7,415–7,174 cal yBP) and grave no. 3 – 6,370 ± 40 yBP
(7,420–7,182 cal yBP; [29]). However, there are no associated carbon and nitrogen stable isotope values from which to assess
evo culture period
the individuals’ diet. Assuming no freshwater reservoir effect, this date places the burial around the end of the Starc
and it is distinctly possible that the burial was emplaced after the living area had been abandoned. The only 14C date from Gura Ba-
ciului from a non-burial context is an AMS measurement on animal bone from a pit feature (possibly a dwelling structure) of 7,140 ± 45
yBP (8,035–7,860 cal BP; GrA-24137), which predates burial no. 6 by c. 600 years.
The individual from Gura Baciului included in this study (laboratory ID: GB1_Eneo) comes from grave no. 1 (archaeological ID: M1).
This grave was a chance find when the section of an older trench collapsed. Discovered in 1962 near a pit-house, it is a primary inhu-
mation of a single individual (GB1_Eneo) in anatomical connection, deposited in the crouched position on the left side, with ESE–
WNW orientation (head to east). The reported grave goods comprise ten flint flakes in the feet area and a bone awl and two ochre
fragments in the cheek and hip areas. Eighty-three fragments of animal bones (of Bos taurus, Ovis aries/Capra hircus, Cervus elaphus,
Bos primigenius), mollusca, broken stones and numerous ceramic fragments supposedly formed a ‘‘bed’’ underneath the body
[55–58]. Among this material were three ‘‘loose’’ human bones of an 11–13 year old child [56]. The skeleton from grave no. 1 is
that of an adult female, around 155 cm tall [50, 56]. The AMS 14C date of 4,621 ± 28 yBP (5,456–5,299 cal BP, MAMS-28614, this
study) (Table S1) places this burial in the Eneolithic period, and is further evidence of the post-abandonment use of the Starc evo
culture settlement as a formal burial area. The d15N value of +12.7& implies the individual had a high trophic level diet that may
have included significant amounts of fish, which in turn would likely result in a 14C age that is older than the archaeological context
(i.e., that includes a reservoir offset). Thus, the 14C date should be regarded as a maximum age for this individual. The Eneolithic
period date for burial no. 1 is not entirely surprising, since in early survey work in the Gura Baciului locality (prior to 1942 — items
from a private collection donated to the museum in 1942), traces of Eneolithic and EBA activity were recorded [52].
4. Chan do Lindeiro
The Chan do Lindeiro karstic system (42.7343714,-7.0305368, Pedrafita, Lugo, Spain) is a large vertical fracture associated with a
small doline. The human remains from this site belong to a single individual (laboratory ID: Chan_Meso; archaeological ID: Elba) and
were found with no funerary context in a deep cave gallery associated with a collapsed sinkhole [58]. The skeletal fragments were
scattered among the collapse debris and completely disarticulated. Only a few bones were recovered: a partial neurocranium, a sin-
gle tooth, some vertebrae, both clavicles, fragments of ribs, a partial ulna, both femora, a partial tibia and one metatarsal.
No other human remains or goods or lithic tools were found. The only other findings at the site are the remains of three small-sized
aurochs. The sedimentological analysis suggests that the collapse occurred in a single episode, and the radiocarbon ages for the
human and the aurochs overlap [16], suggesting that all these remains might be somehow related.
Chan_Meso (archeological ID: Elba) is a female individual of small size (around 153 cm tall and 56 kg in weight, according to [16])
but shows marked muscle scars and several pathologies indicating hard physical work from youth [59]. The only tooth recovered
shows a large caries lesion. Independent 14C dates are available from the skull (7,995 ± 70 14C years yBP; Ua-13398; [60]) and
the tibia (8,236 ± 51 14C yBP, Ua-38115; [16]). The weighted mean of the two 14C ages is 8,155 ± 42 yBP (R-combine, Oxcal 4.2)
and the 2-sigma calibrated age range calculated using OxCal 4.2 and the IntCal13 dataset is 9,255–9,007 cal yBP (Table S1).
5. Los Canes
Los Canes cave is located on the southern slope of Sierra de Cuera, a mountain chain in the eastern part of the Asturias region in
northern Spain (43.3550277, 4.7166763). There is evidence of human occupation from the Solutrean until the Bronze Age, and
several human remains have been found associated with these periods [61–64].
Three well preserved burials belonging to the Mesolithic period were found at the entrance of the cave:
Burial I: This corresponds to a woman of advanced age (laboratory ID: Canes1_Meso; archaeological ID: I-A) that was AMS 14C
dated to 6,265 ± 75 yBP (AA-5294; [62]) and 6,160 ± 55 yBP (OxA-7148; [65]). The weighted mean of the two measurements is
6,197 ± 45 yBP (R-combine, Oxcal 4.2), giving a 2-sigma calibrated age calculated using OxCal 4.2 and the IntCal13 dataset
of 7,245–6,985 cal yBP. Some objects have been interpreted as grave goods: a red deer (Cervus elaphus) scapula, an ungulate
rib and three perforated red deer canines. Also, a large quantity of shells of Cepaea nemoralis was found all around the skeleton,
probably an intentional deposit [61, 62].
Burial II: Remains of two individuals interred at different times were found in this grave [61, 62]. Most of the skeleton of the earlier
one (individual II-B, an adult), dated to 6,860 ± 65 yBP (AA-5295 [62]; 7,826–7,583 cal yBP) was probably removed when the later
individual (II-A) was buried, and only the feet in anatomical connection and some scattered bones and teeth were preserved. The
skeleton of individual II-A, a subadult male (laboratory ID: Canes2; archaeological ID: II-A), was found in anatomical connection,
lying on his left side in flexed position. It was dated by AMS 14C to 6,770 ± 65 yBP (AA-5296; [62]), 7,025 ± 80 yBP (AA-11744; [62])
and 7,208 ± 38 yBP (OxA-23185; [63]). The weighted mean of these three measurements is 7,092 ± 31 yBP (R-combine, Oxcal 4.2)
and the 2-sigma calibrated age range is 7,974–7,850 cal yBP. Several grave goods were associated with the II-A skeleton: two
frontlets of female ibex (Capra pyrenaica), a long cobble with traces of red colorant, a long, pointed bone, a perforated antler,
and a pecked cobble, possibly representing a human head. Pendants (most of them made of Trivia sp. shells) were found around
the head and shoulders of this individual, suggesting that they were sewn to a dress [66].

Burial III: This grave contained the remains of a complete adult male (III-A), dated to 6,930 ± 95 yBP (AA-6071 [62]; 7,944–7,609 cal
yBP). Earlier skeletal remains from an infant (III-B) associated with coeval bones of the Iberian chamois (Rupicapra pyrenaica), red
deer (Cervus elaphus) and wild boar (Sus scrofa) were found over III-A’s knees, indicating the removal of a previous burial [63, 67].
The paleoanthropological characteristics of the Los Canes fossils place them within the variability described for the last hunter-
gatherers of the Late Upper Paleolithic/Early Mesolithic of Western Europe [67]. All adult individuals from Los Canes showed marked
muscle insertions, and especially I-A and III-A individuals had oral pathologies including caries, ante-mortem tooth loss and dental
calculus; marked wear of the crown surfaces was also observed [64]. Because of the availability of petrous bones, individuals I-A and
II-A were selected for genetic analysis. After estimating the percentage of endogenous DNA, only I-A was selected for genome
sequencing.
Sample preparation, DNA extraction and library building

All pre-amplification DNA procedures were carried out in dedicated aDNA laboratories at the University of York (UK). All laboratory
tools used to process the samples were either sterile and disposable or decontaminated with bleach (concentration 1:5) and exposed
to UV light for 24h before being used. DNA was extracted from the walls forming the channels of the inner ear within the petrous bone,
which tend to preserve comparatively high percentages of endogenous DNA [32, 68]. In total, 7 petrous bones were processed at this
step: 6 from human remains associated with Mesolithic sites in Romania (SC1_Meso, SC2_Meso and OC1_Meso) and Spain (Chan_
Meso, Canes1_Meso and Canes2_Meso); and 1 from a Neolithic/Eneolithic site in Romania (GB1_Eneo). Before extraction, the frag-
ments of petrous bones were treated for decontamination: they were first exposed to UV light for 10 min on each side, followed by
physical removal of the surface with a Dremel drill, and finally, once the surfaces were clean, they were exposed again to UV light for
another 10 min.
The bone fragments were ground to powder using a mortar and pestle and one DNA extract was obtained from each sample.
Because the samples from Romania and Spain were sampled and extracted at different times, we followed two different protocols
([69] and [70], respectively). From the Romanian samples, DNA was extracted following [69], starting from approximately 250 mg of
bone powder. Each sample was incubated in rotation with 5 ml of extraction buffer, consisting of 0.45 M EDTA (pH 8.0) and
0.25 mg/ml of proteinase K. After overnight incubation, the samples were centrifuged and the supernatant was transferred to a
new tube with 2.5 ml of binding buffer (5 M guanidinium thiocyanate (GuSCN) and 300 mM sodium acetate) and 100 ml of silica
suspension. The mix was incubated for 3 hr in gentle rotation at room temperature. After incubation, the tubes were centrifuged,
the supernatant discarded and the silica pellet was resuspended in 400 ml of binding buffer and transferred into a clean Mobicol col-
umn with an extra 10 mm filter (MoBiTec GmbH). The columns were centrifuged and then washed twice with 450 ml of washing buffer
(50% ethanol, 125 mM NaCl, 1 3 TE) in order to remove salts and PCR-inhibitors. Finally, the silica pellet was dried and the DNA
eluted into a clean tube using 50 ml of TE.
The Spanish samples were extracted following a more recent protocol from [70], which optimizes the recovery of short DNA frag-
ments from small quantities of bone powder. From each sample, 50 mg of bone powder were digested in 1 ml of an extraction buffer
consisting of 0.45 M EDTA (pH 8.0) and 0.25 mg/ml of proteinase K. After overnight incubation, 1 ml of supernatant was added to
13 ml of binding buffer (5M Guanidine hydrochloride (MW 95.53), 40% Isopropanol, 0.05% Tween-20, 9 mM Sodium Acetate)
and poured into a binding apparatus consisting of an extension reservoir (Zymo Research) fitted to a MinElute silica spin column
(QIAGEN). The binding apparatus was placed into a 50-ml falcon tube and centrifuged. During the centrifugation, the silica based
membrane in the MinElute column will retain the DNA molecules. This filter is washed by adding 650 ml of PE buffer (QIAGEN). Finally,
the filters are dried by centrifugation and the DNA molecules are eluted by adding a total of 25 ml of TET buffer (1 M Tris-HCL, pH 8.0,
0.5 M EDTA, 10% Tween-20).
Both extraction experiments were performed including two blank controls each.
Illumina libraries were built following the protocol described by [36], with the modifications suggested by [71], which minimize the
number of purification steps by introducing heat inactivation of the enzymes between consecutive reactions. We used 20 ml of DNA
extract as template to build one sequencing library per sample. As first step, we performed the blunt end repair of overhang strands
with enzymes T4 Polynucleotide kinase and T4 polymerase in the following reaction mix: 1x Buffer Tango, dNTP (100 mM each), 1 mM
ATP, 0.1 U/ml T4 PNK, 0.1 U/ml T4 Polymerase. After 20 min of incubation at 25 C, the mix was heat up to 72 C for 20 min, in order
to inactivate the enzymes. Following, the adaptor mix (1x T4 ligation buffer, 5% PEG-4000 and a mix 0.5 mM of the paired end
adapters P5 and P7) was added to the former reaction, without any purification step through columns. Just before starting the
incubation, 1.25 ml of T4 ligase (final concentration 5 U/ml) were added to each tube to complete the adaptor mix reaction. The tubes
were incubated for 30 min at 22 C and then the volume was filtered through silica-based MinElute columns (QIAGEN). In the next
step, the Bst polymerase was used to fill the nicks and to complete the double strand sequence of the adapters (reaction mix: 1x
Thermopol buffer, dNTP (250 mM) and 0.3 U/ml Bst polymerase). The mix was incubated at 37 C for 20 min and then heated up to
80 C for 20 min.
After the incubation, each library was indexed and amplified in three parallel reactions, without any filtration step between the
adaptor fill-in and the amplification. We used 5 ml of library as template for each reaction and the primers IS4 (50 -AATGATACGGC
GACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTT-3 0 ) and P7 indexing (50 -CAAGCAGAAGACGGCATACGAGATxxx
xxxxxGTGACTGGAGTTCAGACGTGT-30 ). The P7 indexing primer includes a barcode sequence of 8 nucleotides (denoted by the

eight x). We used a different barcode for each sample, so the libraries could be pooled and sequenced together. Library amplifica-
tions were carried out using Accuprime Supermix I (ThermoFisher Scientific), which includes a polymerase that is able to read over
uracils. The PCR mix was prepared for a total volume of 25 ml following the instructions from the manufacturer. Amplification condi-
tions were as follows: 95 C for 5 min; 12 cycles of: 95 C for 15 s, 60 C for 30 s, 68 C for 30 s and, finally, an extension of 68 C for
5 min. The three PCR reactions from each sample were pooled and purified on a MinElute column (QIAGEN), with a final elution in
15 ml of EB buffer. The amplified libraries were visualized on agarose gels and quantified on a Bioanalyzer 2100 with the High Senti-
tivity DNA chip (Agilent).
The endogenous DNA content of the libraries was tested by sequencing on an Illumina MiSeq platform at TrinSeq (Trinity Genome
Sequencing Laboratory, Trinity College Dublin, Ireland), using 50 bp single-end sequencing. Only samples with percentages
of endogenous DNA higher than 20% were selected for further sequencing (Table S1): SC1_Meso, SC2_Meso, OC1_Meso,
Chan_Meso, Canes1_Meso and GB1_Eneo.
Stable isotope analysis

Stable isotope data were available from the literature for Chan_Meso, Canes1_Meso and SC21_Meso. For individuals OC1_Meso,
SC2_Meso and GB1_Eneo, we sampled approximately 0.5 g of bone and extracted collagen following [72]. The ‘collagen’ was
then lyophilized before weighing for isotopic analysis. Each sample was analyzed in triplicate using a Costech elemental analyzer
coupled in continuous-flow mode to a Finnigan isotope ratio mass spectrometer (Delta V). Carbon and nitrogen isotopic ratios
were measured on the delta scale in comparison to international standards, VPDB and AIR respectively, in units of ‘permil’
[73, 74]. Repeated-measurements on international and in-house standards showed that the analytical error was < 0.2& for both
carbon and nitrogen.
All samples contained collagen deemed to be of good quality as it fulfilled the following criteria: an atomic C:N ratio of 2.9 to 3.6 [75];
a ‘collagen’ yield of >1% by mass; final carbon yields of >13%; and final nitrogen yields of >4.8% [76]. The results from these isotope
analyses are described in the main text and illustrated in Figures S4C and S4D. Figure S4C shows a bivariate plot of d13C and d15N
values for the studied Romanian humans compared against the overall ranges for Late Mesolithic and Early Neolithic humans and
fauna (terrestrial ungulates and fish) from the Iron Gates. The Romanian Mesolithic individuals have high d13C and d15N values indi-
cating a high proportion of freshwater protein in an otherwise C3-based diet. By contrast, the Eneolithic individual GB1_Eneo had
values similar to those found in Neolithic individuals from the Iron Gates sites, reflecting a more terrestrial C3-based diet but still
with an important aquatic component [11, 25, 26, 77].
Isotopic values from the individual Chan_Meso have been published [16]: d13C = 20.5& and d15N = 8.4&. These values are
relatively low for a hunter-gatherer, lower than those of the La Braña individuals (d13C = 19.3 and 18.9&, d15N = 10.6 and
10.4&; [78]), and more similar to Canes1_Meso (d13C = 20.0& and d15N = 7.9&; [15]) and later Neolithic farmers from Portugal
[79]. Moreover, the stable isotope signatures of the Chan_Meso and Canes1_Meso individuals differ considerably from other Meso-
lithic hunter-gatherers from the Cantabrian area [15], with the La Braña individuals situated in an intermediate position (Figure S4D).
However, the Cantabrian Mesolithic individuals came from coastal sites associated with shell middens, like the Portuguese Meso-
lithic sites studied in [79], while Canes1_Meso, Chan_Meso and La Braña are relatively far from the coast, in inland mountainous
areas. Judging by the isotopic signatures, their economic strategies did not include marine diet inputs, at least for Canes1_Meso
and Chan_Meso.
Isotopic values cannot be compared directly, as they depend largely on local values in soils, which in turn depend on altitude,
insulation, rainfall and other environmental parameters [80]. For a better interpretation, it is necessary to establish a local isotopic
baseline, ideally using contemporaneous faunal values [81]. When comparing the human values with those of contemporaneous
red deer from El Mirón, a nearby site in the Cantabrian area [77] and the three aurochs in Chan do Lindeiro cave, the isotopic offset
between ungulates and both humans is equivalent to a complete trophic level, confirming a diet based largely on terrestrial ungulates
but with an appreciable contribution from C3 vegetables (Figure S4D).
QUANTIFICATION AND STATISTICAL ANALYSIS
Processing and alignment of NGS data

Six libraries were selected for HiSeq sequencing after the first screening: SC1_Meso, SC2_Meso, OC1_Meso and GB1_Eneo from
Romania and Chan_Meso and Canes1_Meso from Spain. Each library was sequenced on one lane of an Illumina HiSeq2000 platform
at Beijing Genomics Institute (BGI), except Chan_Meso, which was sequenced on two lanes. Sequencing was performed with 100 cy-
cles in paired end mode.
BCL files were converted to fastq format using the Illumina base-calling pipeline (Illumina Pipeline v1.4). Raw reads were assigned
to the corresponding samples based on the index sequence included in the adaptor P7, allowing no mismatches in the first base of
the sequence and a single mismatch at any other position [82, 83]. The software SeqPrep (https://github.com/jstjohn/SeqPrep) was
used to trim the adapters and merge the forward (R1) and reverse (R2) reads. Default parameters were used for minimum base pair
overlap to merge the reads (-o 15) and the quality score cutoff for mismatches to be counted in an overlap (-q 13), while a minimum
length of 30 was set as threshold to output a merged read.
The merged reads that passed all quality filters were mapped to the human reference genome using the software Burrows-Wheeler
Aligner (BWA) version 0.7.5a-r405 [37], with default parameters and seed option disabled (-l 1000). We used hg19 (GRCh37 build) as

reference genome, but the mitochondrial reference was replaced with the revised Cambridge Reference Sequence (rCRS,
NC_012920; [84]).
Clonal sequences were removed using MarkDuplicates.jar from picards-tools-1.98 (http://broadinstitute.github.io/picard/) and
indels were realigned using the tools RealignerTargetCreator and IndelRealigner from GATK-3.0-0 [38]. The resulting bam files
were filtered for a minimum mapping quality of 30 using Samtools 0.1.19 [39]. Finally, the tool GenomeAnalysisTK.jar from
GATK-3.0-0 was used to calculate the depth of coverage of the bam files. Table S2 summarizes the NGS output for each of the
samples.
Test of DNA authenticity

Negative controls were included during the wet lab stages and sequenced together with the samples in the MiSeq test run (Table S1).
A total of four blanks were sequenced for each protocol: eBL is the pool of the blanks 1 and 2 of the DNA extraction, and liBL is the
pool of the blanks 1 and 2 from the process of building these extracts into libraries. The suffix r indicates blanks from samples
extracted following [69], while d denotes [70]. The percentage of reads in the blanks aligning to the human reference sequence
ranged from 0.25 to 0.9% (Table S1). Furthermore, for each sample, we analyzed patterns of molecular damage and presence of
contaminants in monoparental chromosomes as explained below.
Read length and molecular damage
Because of molecular damage, ancient DNA molecules have short read length distributions and specific nucleotide misincorpora-
tions [85–87]; these two criteria can be used to verify the antiquity of DNA molecules. Patterns of molecular damage were estimated
using mapDamage [40, 88]. Figure S1A illustrates the mapDamage output with the percentages of C to T and G to A nucleotide
misincorporation rates at 50 and 30 ends, respectively, for each of the six samples, which ranged between 14% and 28%. We
estimated the distribution of read lengths before (using a custom awk script on the fastq files) and after mapping (using the
ReadLengthDistribution tool from GATK), Figure S1B. The average read length was between 79 and 102 for unmapped reads and
between 62 and 109 for mapped reads. Reads from Chan_Meso and Canes1_Meso are shorter than those from the Romanian
samples, probably because the latter were obtained with the [70] protocol, which is specifically designed for the recovery of short
fragments.
Mitochondrial DNA authentication
Possible contamination from modern human DNA was assessed by investigating the frequency of non-consensus calls in the mito-
chondrial DNA (mtDNA); specifically, we focused on haplogroup defining positions recovered from Haplogrep (http://haplogrep.uibk.
ac.at/), as these are known to be polymorphic in humans (monomorphic positions are less informative, as a non-consensus call would
be more likely to be due to damage or miscalling). For each sample, samtools 0.1.19 [39] view option was used to extract the reads
mapped to the rCRS to a single bam file, from which we called polymorphic positions using samtools mpileup tool. We computed
two estimates for each sample: the percentage of non-consensus calls, which includes both contamination and potential molecular
damage, %(C+MD), and the percentage excluding potentially damaged bases, %C, excluding transitions C to T and G to A
(Table S2).
X chromosome based authentication
The X chromosome is a uniparental chromosome in males, providing the opportunity to quantify contamination following the same
logic used for mtDNA. We used ANGSD [42], which implements the method described in [89], to assess the level of X chromosome
contamination in our three male samples (SC1_Meso, SC2_Meso and OC1_Meso). Parameters recommended on the ANGSD web-
site (http://popgen.dk/angsd/index.php/Contamination) were used with the minimum base quality threshold set to 30. Table S2
reports contamination estimates based on two tests: test 1, which uses all high quality reads per sample and then evaluates the
rate of contamination based on a maximum likelihood approach; and test 2, which samples a single read per site to calculate the
contamination rate. Low contamination ratios were found with both methods, with percentages around 1% for SC1_Meso and
SC2_Meso and 2% for OC1_Meso (Table S2).
Molecular sex determination

Sex was determined by evaluating the ratio (Ry) of reads aligning to the Y chromosome (nY) compared to the total number of reads
aligning to the sex chromosomes (nX + nY), i.e., Ry = (nY/nY+nX), as described in [90]. We observed that the highest fraction of reads
aligning to the Y chromosome were Ry = 0.0046 in females and Ry = 0.098 in males (Table S2). All samples could be assigned to one
of the two sexes with confidence higher than 95%, and all the genetic assignments were consistent with morphological
identifications.
Analysis of phenotypic traits

We used mapDamage to rescale the base quality score of T and A according to their probability of resulting from molecular damage
(C to U deaminations). We used these rescaled bam files and Samtools mpileup to call variants at specific positions that have been
identified as having a role in determining phenotypic traits. For SNP calling, we only used bases with quality R30 and positions
covered by at least 3 reads. Owing to the low coverage of some of the genomes, the identification of the genotype as homozygous

or heterozygous was inconclusive at some positions. The Hirisplex [91] and 8-plex [92] prediction systems were used to predict eye,
hair and skin color in the ancient samples. Furthermore, we also investigated loci related to lactase persistence.
We used imputation to maximize the genetic information for the phenotypic predictive systems. Imputation allows the inference of
missing alleles by comparison of the surrounding haplotypes in the test samples with a phased reference panel [93]. This method has
previously been used to infer genotypes from low coverage genomes (1x depth of coverage) in ancient specimens, showing a high
percentage of concordant predictions when compared to high-coverage observed data [20, 31]. In our analysis, we only considered
imputed genotypes if their likelihood score was equal to or higher than 85%.
Hair and eye color prediction
The HirisPlex prediction system is an assay based on 24 SNPs used in forensics to predict hair and skin color [91]. Table S3 reports
the HirisPlex imputed genotypes in our six ancient samples and Figure S2A reports the probability score of the predicted phenotypes.
In cases where incongruences occurred between an imputed and an observed variant, when the observed variant was covered by
less than 3 reads and the imputed probability was higher than 0.85, the imputed variant was used for HirisPlex predictions. When the
observed variant was covered by less than 3 reads and an imputed probability of less than 0.85, the genotype was left as missing (as,
for example, in SC1_Meso rs12913832 and OC1_Meso rs12203592 and rs12913832).
We also investigated pigmentation traits based on the 8-plex system [92], which predicts eye and skin color from the combination
of genotypes in eight SNPs, three of which are not included in the HirisPlex system (rs1426654 in gene SLC24A5, rs6119471 in gene
ASIP and rs1545397 in gene OCA2, Figure S2B and Table S3). The 8-plex system confirmed the HirisPlex predictions for eye color.
GB1_Eneo is homozygous GG at rs12913832, which excludes brown eyes; however, it does not carry any of the combinations of
alleles that would determine green or blue eyes based on this test. The most similar combination is GG at rs12913832 and CC at
rs16891982, which suggests green eyes, while GB1_Eneo carries GG at rs12913832 and CG at rs16891982. Thus, eye color assign-
ment for GB1_Eneo is inconclusive using 8-plex.
Skin color
Based on the 8-plex system, a combination of any two of the following genotypes will result in non-dark skin color: GG at rs12913832,
TT at rs1545397, GG at rs16891982, AA at rs1426654, AA at rs885479 and/or TT at rs12203592. Nevertheless, non-white skin color is
predicted when GG at rs6119471 occurs together with any of the six alleles for ‘‘non-dark skin color.’’
The imputed genotypes for these SNPs are included in Table S3. The test was inconclusive for most of our samples as none of
them, with the exception of GB1_Eneo, carry any of the possible combinations of alleles proposed by the 8-plex system to determine
skin color. However, GB1_Eneo was genotyped as GG at rs12913832 and AA at 1426654, which would predict light skin color in this
individual. Moreover, Canes1_Meso was genotype GG at rs12913832, but was heterozygous AG at rs1426654, which is not consid-
ered by the 8-plex system.
Despite the inconclusive results, we can still get an indication of skin color if we consider the SNPs included in the 8-plex system,
which are located in genes SLC45A2 and SLC24A5: rs16891982 and rs1426654, respectively (Figure S2A). Both genes are related to
pigmentation and their distribution in Europe is far from random, as the derived alleles contributing to light skin are almost fixed in
modern Europeans. Four of our samples (Chan_Meso, SC1_Meso, SC2_Meso and OC1_Meso) are homozygous for the ancestral
allele at these SNP positions: CC at rs16891982 and GG at rs1426654, suggesting that these individuals would not have had light
skin. Canes1_Meso is also homozygous CC at rs16891982, but is heterozygous (AG) at rs1426654. GB1_Eneo is heterozygous
GC at rs16891982 and homozygous AA at rs1426654. The presence of the derived alleles in these samples could be indicative
of lighter skin color in these individuals than in the older samples. Moreover, it shows that by the time of Canes’ population
(5.3 kya), the alleles determining light skin were already present in the most western part of Europe.
Lactase persistence
All ancient samples were homozygous for the ancestral allele (C) at rs182549 (Table S3 and Figure S2A), a genotype that is associated
with lactose intolerance in adulthood [94]. Furthermore, except for SC1_Meso, all of them were also homozygous for the ancestral
allele (G) at rs4988235, also associated with inability to digest lactose (Table S3 and Figure S2A). SC1_Meso carries an A at this
position; however, the genotype could not be determined because the position is covered by only 1 read. Imputation assigned
GG as the most likely genotype at this position for SC1_Meso, so it is likely that SC1_Meso was also unable to digest lactose.
Mitochondrial analysis and haplogroup assignment

Following whole genome alignment (see S3 for details), we used samtools view to extract the reads mapped to the rCRS to a single
bam file. From those bam files, we called positions at which the base differed from that in the reference mitogenome (NC_012920); for
this step, we used samtools mpileup and the option -s to specify the ploidy (1). Only bases with quality scores R 30 were considered
for analysis. Furthermore, we used Tablet [95] to visualize the alignments and checked by eye all the polymorphic positions reported
in the vcf file. Variants called at positions with less than 3 reads of depth, as well as variants called at the last 4 bases of any of the two
read ends were excluded from further analysis, as they could have resulted from molecular damage. Haplogroup assignment was
based on Haplogrep (http://haplogrep.uibk.ac.at/) (Table S4).
Y chromosome analysis
All our three male samples, SC1_Meso, SC2_Meso and OC1_Meso, were assigned to the R1 and R1b haplogroups (Table 1 in main
text) using Yfitter, a maximum likelihood method to assign Y haplogroups from low coverage sequence data [43]. Furthermore, we
inspected the alignments by eye at defining positions for haplogroup R, following [96] and the updated positions on the ISOGG

database. Based on the observed variants, we could confirm the assignment of all samples to haplogroup R1. The individuals
SC2_Meso and OC1_Meso were assigned to subhaplogroup R1b1c based on the presence of the following variants:
SC2_Meso: M306(1A), P224(4T), P229(1C), P285(3A), M173(1C), M306(1A), P225(1T), P231(3G), P233(2G), P234(1C), P236(2G),
P238(1A), P242(2A), P286(3T), P294(1C), M343(3A), M269(1T
OC1_Meso: M207(1G), M306(1A), P224(2T), P229(1C), P285(2A), M173(1C), M306(1A), P225(2T), P233(1G), P234(1C), P236(2G),
P238(1A), P242(1A), P286(1T), M343(2A), M269(1T)
The low coverage of SC1_Meso prevented a more detailed assignment of this individual.
R1b is the major West European linage in present day populations [96]. Ancient DNA studies have reported a notable increase of
subhaplogroups R1b and R1a in central Europe during the Late Neolithic and Bronze Age, leading to the hypothesis that they
expanded from the East only after 4,500 yBP [6], although genetic analysis based on modern populations suggests an older Eastern
origin, shortly after the LGM [33]. Recent studies have found haplogroup R1b in a 14,000 year old human from Italy [24, 34]) and in a
Latvian sample dated to 7,000 years [7]. Our Mesolithic samples document the presence of haplogroup R1 in Romania as early as
8,814 ± 261 cal yBP and R1b at 8,703.5 ± 268.5 yBP, which corroborates a wide distribution of the haplogroup in Europe before the
Bronze Age.
Population genetic analyses

A reference dataset of modern [8, 9] and ancient samples (Data S1) described in [7] was used for population genetic analyses. We
also realigned BAM files from [2], as described in the ‘‘Processing and alignment of NGS data’’ section above, and added these
samples to our dataset. We also realigned BAM files from [5]. Genotypes in our ancient Romanian and Spanish samples, which
overlapped with this dataset, were called using GATK Pileup [38]. Triallelic SNPs were discarded and bases were required to
have quality R 30. Alleles were not called within the first and last 2 bp of reads. For positions with more than one base call, one allele
was randomly chosen with a probability equal to the frequency of the base at that position. This allele was duplicated to form a
homozygous diploid genotype. Only transversion sites were used for PCA, f3-statistics, D-statistics and ADMIXTURE to reduce
the effects of post-mortem molecular damage on analyses. Furthermore, ancient samples were required to have R15,000 called
SNPs in order to meet the inclusion criteria.
Principal components were defined using a Eurasian subset of the modern data and ancient individuals were projected onto the
resulting eigenvectors. This analysis was carried out using EIGENSOFT 5.0.1 smartpca [44], removing one SNP from each pair in
linkage disequilibrium with r2 > 0.2 [4] and without removing outlying data.
We used outgroup f3-statistics [97, 98] to evaluate the amount of shared drift between our ancient samples since their divergence
from an African (Mbuti) outgroup. Figure S3A reports the results of these tests for the Spanish samples Chan_Meso and Canes1_
Meso, both of which share the most drift with other Western European Hunter-Gatherers. Outgroup f3 statistics for the Romanian
genomes in our dataset are reported in Figure 2 (highest 20 values). f3-statistics were computed using the qp3Pop program in the
ADMIXTOOLS package [44].
D-statistics were used to test for admixture [82]. These statistics were computed using the qpDstat programs in the ADMIXTOOLS
package [44]. The results of these tests are reported in Table 2.
We used ADMIXTURE [45] to perform a clustering analysis. The minimal cross validation error for the reference dataset has pre-
viously been found at 17 clusters (K) [7]. Based on our PCA and D-statistics results, we did not expect our Romanian and Spanish
samples to define new components, so we added the Romanian and Spanish samples to this dataset and ran 10 runs at K = 17 with
fivefold cross-validation and different random seeds. We repeated this analysis at K = 10, K = 15 and K = 20. The results of the
ADMIXTURE analysis of all individuals at K = 17 are reported in Figure S3C and for ancient samples at K = 10, K = 15 and K = 20
in Figure S3B.
We used the ADMIXTURE results to estimate hunter-gatherer-, and farmer-related ancestries in our Eneolithic sample GB1_Eneo.
We performed bootstrapping by resampling SNPs with replacement 1000 times and estimated errors and confidence intervals on this
empirical distribution. For each bootstrap replicate, we inferred the ancestry proportions by numerically maximizing the following
likelihood function on the bootstrapped SNPs, following the logic of [22, 99]:
( " # " #)
XX X X
LðQ; FÞ = gij ln qik fkj + 2 gij ln qik ð1 fkj Þ ;
i j k k
where gij is the count of allele 1 (0, 1 or 2) of individual i at SNP j, qik is the fraction the inferred ancestral population k contributes to
individual i’s genome and fkj is the frequency of allele 1 at SNP j in the inferred ancestral population k. The likelihood was maximized
using the minimize function from scipy, with the ‘‘L-BFGS-B’’ method and proportions bounded between [1e-5,1-1e-5] and con-
strained to sum to unity. We used inferred allele frequencies of the ancestral populations, fkj, from the run at K = 17 with the lowest
cross-validation error.
We used a custom python script to perform bootstrapping on a single individual. The code is available on GitHub: https://github.
com/siskavera/genetics_scripts/tree/master/admixture-projection.
We examined runs of homozygosity in our two samples with the highest coverage: GB1_Eneo and Chan_Meso. We also included
published high coverage hunter-gatherer and Neolithic farmer samples for comparison (namely NE1 [32], Bichon [20], Stuttgart and

Loschbour [8] and Bon002 [2]). We trimmed 10 bp from read termini to mitigate the effects of postmortem damage which tends to be
concentrated at the ends of reads. We called genotypes in our samples at positions which had a minor allele frequency of R 10% in
Yoruban individuals from Phase 3 of the 1000 Genomes Project [2, 100] using GATK [51]. Genotypes in our ancient samples were
required to have a minimum depth of 4, a maximum depth of twice the average genome coverage and heterozygous sites were
required to have each allele called at least twice. ROH analysis which was carried out using PLINK [46] following the parameters
described in [32].
We estimated the proportion of Neanderthal ancestry ðQÞ in each of our samples using the f4 ratio described in [24]:
f4 ðWest and Central Africans; Chimp; test; Altai NeanderthalÞ
Q=1 :
f4 ðWest and Central Africans; Chimp; Dinka; Altai NeanderthalÞ
We extracted genotypes from Dinka, West and Central African (i.e., Mbuti, Yoruba and Mende), Chimp and Altai Neanderthal sam-
ples which were included in the Simons Diversity Project [101]. We kept sites which were biallelic in Phase 3 of the 1000 Genomes
Project [100] and which overlapped the 2.2 million SNP capture panel described in [24]. For each of our ancient samples we clipped
10bp from the starts and ends of reads for the reasons described above. We called pseudo-haploid genotypes in our samples as
described at the beginning of this section. We merged these data with the Simons Panel data using PLINK [46] and calculated f4
ratios using the qpF4ratio package in ADMIXTOOLS [44]. For context in Figure S4B we also include estimates of Neanderthal
ancestry for a selection of Late Pleistocene and Holocene samples (those included in [24] Figure 2 but with Oase1 omitted as it
has recent Neanderthal introgression).
DATA AND SOFTWARE AVAILABILITY
All newly generated genome data have been deposited in ENA: PRJEB20614 and PRJEB20616.

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Paleogenomic Evidence for Multi-generational

d The further east in Europe, the weaker the genetic component

González-Fortes et al., 2017, Current Biology 27, 1801–1810

Paleogenomic Evidence for Multi-generational

Edinburgh EH8 9AG, UK

Santander 39005, Spain

*Correspondence: [email protected] (G.G.-F.), [email protected] (E.R.J.), [email protected] (R.P.), [email protected] (A.M.),

SUMMARY ancestry in a Romanian Eneolithic sample with a

Pleistocene/Holocene A.D. 106

11.65 9.3 8.0 6.4 4.4 3.1 ka cal BP

(legend continued on next page)

1802 Current Biology 27, 1801–1810, June 19, 2017

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1804 Current Biology 27, 1801–1810, June 19, 2017

DISCUSSION Neolithic has already been noted in other parts of Europe

Current Biology 27, 1801–1810, June 19, 2017 1805

1806 Current Biology 27, 1801–1810, June 19, 2017

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1808 Current Biology 27, 1801–1810, June 19, 2017

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1810 Current Biology 27, 1801–1810, June 19, 2017

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER

Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e1

CONTACT FOR REAGENT AND RESOURCE SHARING

Description of the archaeological context: sites and samples

e2 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e3

e4 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

Sample preparation, DNA extraction and library building

Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e5

Stable isotope analysis

QUANTIFICATION AND STATISTICAL ANALYSIS

Processing and alignment of NGS data

e6 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

Test of DNA authenticity

Molecular sex determination

Analysis of phenotypic traits

Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e7

Mitochondrial analysis and haplogroup assignment

e8 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

Population genetic analyses

Current Biology 27, 1801–1810.e1–e10, June 19, 2017 e9

DATA AND SOFTWARE AVAILABILITY

e10 Current Biology 27, 1801–1810.e1–e10, June 19, 2017

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