Advances in Anthropology
2012. Vol.2, No.1, 14-23
Published Online February 2012 in SciRes (
Copyright © 2012 SciRes.
A Time Series of Prehistoric Mitochondrial DNA Reveals
Western European Genetic Diversity Was Largely Established
by the Bronze Age
François-Xavier Ricaut1*, Murray P. Cox2*, Marie Lacan1,3, Christine Keyser3,
Francis Duranthon1, Bertrand Ludes3, Jean Guilaine4 , Eric Crubézy1
1Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche
Scientifique, Université de Toulouse (Paul Sabatier), Toulouse, France
2Institute of Molecular BioScienc es, Massey University, Palmerston North, New Zealand
3Laboratoire d’Anthropologie Moléculaire, Centre National de la Rech erche Scientifique, Institute of
Legal Medicine, University of Strasbourg, Strasbourg, France
4Centre de Recherche sur la Préh istoire et la Protohistoire de la Méditerra née, École des Hautes Etudes
en Sciences Sociales, To ulouse, France
Email: *, *
Received December 8th, 2011; revised J anu ary 1st, 2012; accepted February 1st, 2012
A major unanswered question concerns the roles of continuity versus change in prehistoric Europe. For
the first time, genetic samples of reasonable size taken at multiple time points are revealing piecemeal
snapshots of European prehistory at different dates and places across the continent. Here, we pull these
disparate datasets together to illustrate how human genetic variation has changed spatially and temporally
in Europe from the Mesolithic through to the present day. Mitochondrial DNA (mtDNA) haplogroups
were determined for 532 European individuals from four major eras: the Mesolithic, Neolithic, Chalco-
lithic (late Neolithic/early Bronze Age transition) and Modern periods. The Mesolithic was characterized
by low mtDNA diversity. These initial European settler haplogroups declined rapidly in the Neolithic, as
farmers from the east introduced a new suite of mtDNA lineages into Western Europe. For the first time,
we show that the Chalcolithic was also a time of substantial genetic change in Europe. However, rather
than the arrival of new mtDNA lineages, this period was characterized by major fluctuations in the fre-
quencies of existing haplogroups. Besides the expansion of haplogroup H, there were few major changes
in mtDNA diversity from the Chalcolithic to modern times, thus suggesting that the basic profile of mod-
ern western European mtDNA diversity was largely established by the Bronze Age.
Keywords: Europe; Prehistory; MtDNA; Haplogroup Diversity; Temporal Dynamics
Modern European genetic diversity is increasingly well char-
acterized. Researchers have detailed the geographic distribution
of maternal (mtDNA) and paternal (Y chromosome) lineages,
and are now delving into the spatial distribution of autosomal
variants. European individuals can be assigned to modern na-
tions, and even in particular cases, to areas as small as villages
(Novembre et al., 2008). Yet how this genetic diversity has
changed through time is much less well understood. Precise
real-time information is largely restricted by advances in an-
cient DNA research, a growing but challenging field. Never-
theless, samples of reasonable size taken at multiple time points
are now starting to provide snapshots of genetic variation dur-
ing European prehistory at different times and places across the
continent. It therefore seems timely to attempt a first pass at
describing how human genetic variation has changed spatially
and temporally in Europe from the Stone Age through to the
present day.
A major unanswered question concerns the roles of continu-
ity versus change in prehistoric Europe. For instance, the main
drivers of the agricultural expansion have long been a topic of
considerable debate. What originally was perceived as a simple
disti nctio n betwe en demi c vers us cultural diffusion is now gen-
erally recognized as a more complex set of processes. These
processes produced broad-scale demographic trends, while still
allowing mosaic regional patterns (e.g., Ammerman & Cavalli-
Sforza, 1984; Whittle, 1996; Whittle & Cummings, 2007). This
more nuanced view emphasizes cultural and population disper-
sals, as well as variable patterns of population admixture,
where the relative biological contributions of Near Eastern
Neolithic farmers and indigenous Mesolithic hunter-gatherers
are not distributed uniformly across Europe (Sampietro et al.,
2007; Bramanti et al., 2009; von Cramon-Taubadel & Pinhasi,
2011). Current understanding emphasizes two different migra-
tion routes; a relatively rapid diffusion via a southern route
along the Mediterranean coast (associated with the Impressed
Ware and Cardial Ware culture), together with a slower north-
ern route along the Danube valley into central Europe (associ-
ated with the Linearbandkeramik, or LBK, culture) (Guilaine,
1997, 2003; Gronenborn, 1999; Zvelebil, 2004; Guilaine &
Manen, 2007). Mosaic models such as these emphasize the
complex processes by which the transition to agriculture in
Europe probably took place, simultaneously explaining the
seemingly conflicting results obtained from archaeological
evidence (e.g., Guilaine, 2003; Bar-Yosef, 2004; Pinhasi et al.,
*Corresponding author.
2005; Bailey & Spikins, 2008; Bocquet-Appel et al, 2009;
Rowley-Conwy, 2011), osteological data (e.g., Crubézy et al.,
2002; Pinhasi & von Cramon-Taubadel, 2009; von Cramon-
Taubadel & Pinhasi, 2011), modern genetic analyses (e.g.,
Cavalli-Sforza et al., 1994; Chikhi et al., 1998; Renfrew &
Boyle, 2000; Bellwood & Renfrew, 2002; Richards, 2003;
Belle et al., 2006; Balaresque et al, 2010; Palanichamy et al.,
2010; Soares et al., 2010) and ancient DNA studies (e.g., Haak
et al., 2005, 2010; Sampietro et al., 2007; Bramanti et al., 2009;
Malmström et al., 2009; Lacan et al., 2011).
Although considerable research has been focused on the
spread of agriculture through Europe (as evidenced by the large
number of studies cited above), the periods immediately prior
to, and following, the agricultural revolution have been explored
in far less detail. In this context, three subject areas would seem
to warrant further examination:
1) Ancient southwestern/Mediterranean biological data are
typically underrepresented, mainly due to bone preservation
issues outside the colder/temperate climate regions of the north.
Extant research has typically focused on ancient northern or
central European populations (Haak et al., 2005, 2010; Bra-
manti et al., 2009; Pinhasi & von Cramon-Taubadel 2009; von
Cramon-Taubadel & Pinhasi 2011). Few studies have analyzed
and compared ancient biological data from multiple sites or
regions across Europe.
2) The effects of cultural differences on genetic diversity
between southern and northern Europe through the Neolithic
and Chalcolithic periods have not been addressed. This time
frame saw two contrasting Neolithic cultures in Europe (Lin-
earbandkeramik in central Europe and the Impressed/Cardial
Ware culture in southern Europe), each seemingly linked to a
different Chalcolithic subsistence strategy (a cattle-based, fresh
milk dairying economy in northern Europe, and agropastoral
cultures based on preserved milk sheep/goat farming in south-
ern Europe) (Itan et al., 2009). The role of genetic connections
between these two regions and cultures remains unclear.
3) Little is known about changes in genetic diversity during
the important post-Neolithic transitional period. In addition to
the Mesolithic/Neolithic transition, the Chalcolithic period also
witnessed substantial culture change, particularly in terms of
the adoption of metal tools, new agricultural techniques (yoke
and ard-plough), means of transport (wheeled vehicles) and
emerging long-distance exchange networks (Sherratt 1981).
These important cultural processes had the potential for major
demographic impacts on European populations.
While studies of nuclear DNA still involve extremely small
numbers of individuals (Burger et al., 2007; Haak et al., 2008,
2010; Malmström et al., 2009; Lacan et al., 2011) and are not
considered further here, the accumulation of mtDNA sequences
from ancient European individuals is increasing rapidly. We
now have mtDNA data for >100 individuals from the Meso-
lithic period (more than ~9000 years before present), the Neo-
lithic period (the samples in this study are from the early Neo-
lithic, ~9000 - 5500 years before present) and the Chalcolithic
period (the transition from the late Neolithic to the early Bronze
Age, ~5500 - 3700 years before present).
This dataset, while still modest, is an extraordinary achieve-
ment, and at last provides a test bed to explore simple demo-
graphic scenarios that begin to move our perspective of Euro-
pean genetic prehistory beyond intra-site/intra-region analyses.
Using these ancient mtDNA sequences, we interrogate hap-
logroup frequency distributions to resolve through-time bio-
logical relationships between two different regions in western
Europe (southern and northern), four different time points
(Mesolithic, Neolithic, Chalcolithic and the Modern era), and
two different cultural traditions (Linearbandkeramik versus the
Impressed/Cardial Ware culture). To our knowledge, this is the
first extended analysis of spatial and temporal genetic continu-
ity through European prehistory.
Mitochondrial DNA haplogroup classifications were deter-
mined for 532 European individuals from four major eras: the
Mesolithic, Neolithic, Chalcolithic and Modern periods (Table
1). This dataset includes 109 ancient samples, representing 15
individuals from the Mesolithic period (Bramanti et al., 2009),
56 individuals from the Neolithic (Haak et al., 2005, 2010;
Haak, 2006; Sampietro et al., 2007; Deguilloux et al., 2011),
and 38 individuals from the Chalcolithic (Itan et al., 2009;
Haak et al., 2008). The Mesolithic dataset analyzed here spe-
cifically excludes Mesolithic communities in close proximity to
Neolithic sites, because these samples are potentially affected
by gene flow from neighboring Neolithic peoples (Bramanti
Table 1.
Population samples use d in t hi s stu dy.
Period Geographic Ar ea Location Dates n Culture Reference
Mesolithic Central/North Germany, Russia,
Poland, Lith u ania 13,400 - 2250 BC15 Kunda, Na rva,
Zedmar, Beuronien Bramanti et al., 2009
Neolithic Central/North Austria, Hungary,
Germany, 5500 - 5000 BC 47 Linearbandkeramik (LBK) Haak et al., 2005; Haak, 2006
Southwestern Spain 3500 - 3000 BC 11 ND Sampietro et al., 2007
Southwestern France 4200 BC 3 Megalithic Deguilloux et al., 2011
Chalcolithic Central/North Germany 2700 - 2400 BC 9 Corded Ware Culture (CWC) Haak et al ., 2008
Southwestern France 3030 - 2890 BC 29 ND Lacan et al., 2011
Modern Central/North Germany 2000 AD 213 - Tetzlaff e t al., 2007
Southwestern France 2000 AD 210 - Dubut et al., 2004
Abbreviations: n, number of samples; NS, not determined.
Copyright © 2012 SciRes. 15
et al., 2009). For purposes of comparison, we also included 423
modern Europeans from locations near the ancient DNA sam-
pling sites (Dubut et al., 2004; Tetzlaff et al., 2007).
Despite the few ancient DNA datasets available, we pur-
posely excluded any data from studies where any doubts have
been raised about ancient DNA reliability, unclear sample pro-
venance, uncertain dating or cultural affiliation (particularly
during the Mesolithic), or sites that fall outside the geographic
range under study here (i.e., essentially central/western Europe)
(Izagirre & de la Rúa, 1999; Di Benedetto et al., 2000; Chan-
dler et al., 2005; Fernández Domínguez, 2005; Ermini et al.,
2008; Bramanti et al., 2009; Malmström et al., 2009).
Mitochondrial DNA Haplogroups
The ancient and modern samples were clustered into 24 hap-
logroups, 7 of which are found only in individuals living today
(Table 2). We used the same haplogroup affiliations as deter-
mined in the original studies wherever possible. These were
checked manually against the sequence data. Due to the small
number of individuals carrying some lineages, related sub-
haplogroups were sometimes clustered into their root-hap-
logroup to provide sufficient power for the following analyses.
Table 2.
Observed mtDNA haplogroup frequencies across the Mesolithic, Neo-
lithic, Chalcolithic and Mode rn periods.
Time Period
Hg Mesolithic Neolithic Chalcolithic Modern
U* 0.133 0 0.026 0.014
U2 0 0 0 0.014
U3 0 0.016 0 0.002
U4 0.133 0.033 0 0.033
U5 0 0 0.105 0.007
U5a 0.267 0.033 0 0.059
U5b 0.467 0.016 0.053 0.024
U6a1 0 0 0 0.005
U7 0 0 0 0.002
U8 0 0 0 0.007
HV 0 0.066 0.079 0.047
H 0 0.230 0.184 0.423
N 0 0.131 0 0.005
K 0 0.098 0.158 0.090
T 0 0.033 0 0.026
T1 0 0 0 0.028
T2 0 0.164 0.053 0.064
T3 0 0 0 0.002
J 0 0.033 0 0.014
J1 0 0.082 0.158 0.047
J2 0 0 0 0.012
I 0 0.016 0.026 0.021
W 0 0.033 0 0.024
X 0 0.016 0.158 0.012
ND 0 0 0 0.017
Abbreviations: Hg, haplogroup; ND, not determined.
Differences in haplogroup frequencies between temporally
separated European populations were determined using an in-
house resampling algorithm implemented in R (http://www. (code available on request). The frequency pro-
bability density was inferred for each haplogroup via Monte
Carlo simulation. Because sample sizes are small, ancient hap-
logroup frequencies typically have large uncertainty. The fre-
quency probability density explicitly accounts for this uncer-
tainty. For each haplogroup, the observed frequency in the
younger sample was compared with the frequency probability
density of the older sample. This process yields the probability
of the younger sample frequency being observed given uncer-
tainty around the ancestral sample frequency. In effect, we
asked whether time-adjacent haplogroup frequencies differ sig-
nificantly, and therefore, whether haplogroup frequencies have
changed between older and younger samples; or whether hap-
logroup frequencies are statistically indistinguishable, and there-
fore, show no evidence of change between adjacent time points.
We emphasize that this statistical approach explicitly accounts
for small sample sizes, even when these are extremely limited
(e.g., Eulau). Smaller sample sizes are merely reflected by lar-
ger confidence intervals. All population comparisons were
performed in natural time order: Modern deriving from Chalco-
lithic, Chalcolithic deriving from Neolithic, and Neolithic de-
riving from Mesolithic.
We explored mtDNA haplogroup frequencies in 532 western
European individuals from four different time points: the Me-
solithic, Neolithic, Chalcolithic and Modern periods. Indivi-
duals carrying 24 different haplogroups were identified (Table
2). Notably, however, the distribution of these haplogroups
(supplemental Tables 1-4) changed markedly across the four
sampled time points (Figure 1).
Figure 1.
Pie charts showing mtDNA haplogroup frequencies through time.
For visual clarity, haplogroups with frequencies <5% across all
four samples have been collapsed into a “not determined” cate-
gory. (Also see supplemental Movie 1, which illustrates dynami-
cally how mtDNA haplogroup frequencies have changed through
the four sampled time points).
Copyright © 2012 SciRes.
The Mesolithic/Neolithic Transition
This time period is characterized by substantial change, with
significant reductions in many of the U haplogroups (U*, U4,
U5a and U5b), together with the sudden appearance of several
new haplogroups, including H, HV, I, J, J1, K, N1, T, T2, W
and X. The small size of the Mesolithic sample (n = 15) greatly
reduces the statistical power of this analysis. Therefore, with
the exception of haplogroup H, the sudden appearance of non-
U haplogroups is not statistically significant in our analysis.
However, we anticipate that the sudden arrival of these hap-
logroups will be recognized as significant as additional typing
increases the Mesolithic sample size and overcomes the low
power of the current dataset. Indeed, while several U hap-
logroups (i.e., U*, U4, U5 and U8) are traditionally associated
with the Upper Paleolithic settlement of Europe, many non-U
haplogroups are thought to reflect later phases of population
migration and colonization (Richards et al., 2000; Bramanti
et al., 2009; Malyarchuk et al., 2010; Soares et al., 2010). We
anticipate that future sampling will increase the resolution of
this important phase in European prehistory.
The Neolithic/Bronze Age or Chalcolithic Transition
This time period is much less well studied than the agricul-
tural revolution. Surprisingly, we also observe considerable
change in haplogroup frequencies in the lead up to the Chalco-
lithic period, with significant increases in U5 and X, and statis-
tically significant decreases in U3, U4, U5a, J, N1, T, T2 and
W. While the Neolithic has long been recognized as a period of
substantial immigration and population change, the transition to
the Bronze Age is usually considered more of an indigenous
affair. However, our analysis illustrates that the Chalcolithic
transition was, from the perspective of haplogroup frequencies,
at least as demographically disruptive as the earlier agricultural
The Chalcolithic/Modern Transition
Conversely, there is little evidence of change in haplogroup
frequencies between the Chalcolithic and Modern periods. The
only statistically significant differences are reductions in U5, J1
and X, and a substantial increase in haplogroup H, which at a
frequency of 42%, dominates the western European mtDNA
gene pool today.
MtDNA haplogroup frequencies at these four time points are
illustrated in Figure 1. However, static images like these can-
not easily capture how haplogroup frequencies have changed
through time. In practice, it is likely that haplogroup frequent-
cies often changed quickly due to short, intense periods of mi-
gration and social upheaval, rather than varying regularly through
time. Nevertheless, we can see important dynamic facets of the
data, including the extensive diversification of mtDNA hap-
logroups between the Mesolithic and the Neolithic, and the
increasing dominance of haplogroup H from the Chalcolithic to
modern times.
This temporal analysis suggests that two of the three transi-
tional periods (Mesolithic/Neolithic and Neolithic/Bronze Age)
saw substantial change in the distribution of European mtDNA
haplogroup diversity. However, these changes likely had dif-
ferent proximate causes. During the Mesolithic/Neolithic tran-
sition, the appearance of new mtDNA haplogroups may have
been caused in part by the post-glacial recolonization of Europe
(e.g., H, K and T2) and/or by the expansion of Neolithic farm-
ers from the east (e.g., J2, N1 and T2). In either case, there
seems little doubt that Europe experienced some degree of gene
flow during this time period (Haak et al., 2010; Soares et al.,
2010). Conversely, the Chalcolithic transition (late Neolithic to
early Bronze Age transition) seems to reflect continuity of ex-
isting lineages rather than the appearance of new ones; few new
haplogroups are observed in the Chalcolithic, but many existing
haplogroups underwent substantial changes in allele frequency.
Finally, there is surprisingly little change in haplogroup diver-
sity from the Chalcolithic to the Modern period. While hap-
logroup frequencies altered substantially during the Neolithic,
they began to stabilize during the Chalcolithic and have re-
mained relatively static ever since.
These general patterns hold true when the analysis is re-
peated at regional scales; e.g., diachronic analyses for southern
Europe (essentially modern France, supplemental Table 2) and
northern Europe (essentially modern Germany, supplemental
Table 3). The main distinction being that there is little differ-
ence between Neolithic and Chalcolithic samples in the south,
while Neolithic and Chalcolithic populations are quite different
in the north. Conversely, three haplogroups (U5b, I and X)
have similar frequencies between the southern Neolithic sample
and the northern Chalcolithic sample (supplemental Table 4).
The northern Chalcolithic sample (Eulau, n = 9) is extremely
small, which may accentuate this difference. We note, however,
that the statistical procedure used here explicitly accounts for
small sample sizes. No haplogroups have similar frequencies
between the northern Neolithic and northern Chalcolithic sam-
ples (supplemental Table 3). We would not place too much
weight on this observed pattern given limitations of the avail-
able data. However, this may indicate relatively more continu-
ity between the southern Neolithic and northern Chalcolithic
populations (i.e., a signal of northward gene flow). This would
agree with some hypotheses regarding the northward spread of
the Bell Beaker culture during the late Neolithic/early Chalco-
lithic (Vander Linden, 2007; Guilaine et al., 2011), particularly
since Eulau is one of the few sites where both cultures (Bell
Beaker and Corded Ware) existed side by side (Haak et al.,
This statistical analysis highlights both continuity and change
in mtDNA diversity through western European prehistory. As
new samples become available, we expect that this first dia-
chronic synthesis of mtDNA change in Western Europe will
rapidly be improved upon. Broader geographical sampling will
fill in regional details, including the effects of spatially and
temporally restricted cultural processes, and will likely high-
light more detailed regional variability. Further, we anticipate
that technological advances will soon expand this story, mov-
ing it from solely a maternal perspective to instead capture
paternal and biparental aspects of European genetic prehistory.
For now, however, the main story is this. The Mesolithic period
was characterized by low mtDNA diversity, entirely dominated
by U haplogroups. The Neolithic saw the start of an ongoing
decline in these haplogroups, as farmers from the east intro-
duced a suite of new mtDNA haplogroups into Western Europe.
Copyright © 2012 SciRes. 17
Although not previously appreciated, the Chalcolithic (late Neo-
lithic to early Bronze Age transition) was also a time of sub-
stantial genetic change, which did more to shape current mt-
DNA diversity than any subsequent time periods. However,
rather than the arrival of new mtDNA lineages, the Chalcolithic
is characterized by major fluctuations in the frequencies of
existing haplogroups. During this period, southern Europe ex-
perienced regional continuity, although there may be evidence
of northward population movements as the Neolithic gave way
to the Chalcolithic. Apart from the ongoing expansion of hap-
logroup H, there were few major changes from the Chalcolithic
period to modern times, and it appears that the basic profile of
modern western European mtDNA diversity was largely estab-
lished by the Bronze Age. In this context, the well-documented
narratives of the historic period seem to have played out on a
background of European genetic diversity that was ultimately
laid down thousands of years earlier.
This research was supported by grants from the French De-
partment of Research and the CNRS-département INNE to
F.X.R., and a Rutherford Fellowship awarded to M.P.C. by the
Royal Society of New Zealand (RDF-10-MAU-001). We are
grateful to Patrice Gerard and Rebecca Coles for constructive
comments on the manuscript.
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Supplemental Materials
Supplemental Movie 1.
Dynamic illustration of mtDNA haplogroup frequencies changing through the four sampled time points.
(supplemental Tables 1-4 see the following pages)
Note : Mesolithic (Germany, Russia, Poland, Lithuania; Bramanti et al 2009); Neolithic (Austria, Hungary, Germany, Spain, France; Sampietro et al 2007, Haak et al 2005, 2006, Deguilloux et al 2010); Chalcolithi c (Germany,
France; Lacan et al 2011; Haak e t al 2008); Modern (Germany, France; Dubut et al 2004; Tetzlaff et al 2007). ND : not determined.
Increase i n frequency through tim e No change in freque ncy through time Decrease in frequency through time .
Supplemental Table 1.
Significance of changes in mtDNA haplogroup frequencies between the Mesolithic, Neolithic, Chalcolithic and Modern periods for all European samples.
Copyright © 2012 SciRes.
ote: Mesolithic (Germany, Russia, Poland, Lithuania; Bramanti et al 2009); Neolithic (Austria, Hungary, Germany, Spain, France; Sampietro et al 2007, Haak et al 2005, 2006, Deguilloux et al 2010); Chalcolithic (Germany,
France; Lacan et al 2011; Haa k et al 2008); Modern (Germany, France; Dubut et al 2004; Tetzlaff et al 2007). ND : not determined.
Increase i n frequency through tim e No change in freque ncy through time Decrease in frequency through time .
Supplemental Table 2.
Significance of changes in mtDNA haplogroup frequencies between the Mesolithic, Neolithic, Ch alcolithic and Modern periods in Southern Europe.
Copyright © 2012 SciRes. 21
Note : Mesolithic (Germany, Russia, Poland, Lithuania; Bramanti et al 2009); Neolithic (Austria, Hungary, Germany, Spain, France; Sampietro et al 2007, Haak et al 2005, 2006, Deguilloux et al 2010); Chalcolithic (G ermany,
France; Lacan et al 2011; Haa k et al 2008); Modern (Germany, France; Dubut et al 2004; Tetzlaff et al 2007). ND : not determined.
Increase i n frequency through tim e No change in frequency through time Decrease in frequency through time .
Supplemental Table 3.
Significance of changes in mtDNA haplogroup frequencies between the Mesolithic, Neolithic, Ch alcolithic and Modern periods in Northern Europe.
Copyright © 2012 SciRes.
Copyright © 2012 SciRes. 23
Note: Mesolithic (Germany, Russia, Poland, Lithuania; Bramanti et al 2009); Neolithic (Austria, Hungary, Germany, Spain, France; Sampietro et al 2007, Haak et al 2005, 2006, Deguilloux et al 2010); Chalcolithic (Germany,
France; Lacan et al 2011; Haak e t al 2008); Modern (Germany, France; Dubut et al 2004; Tetzlaff et al 2007). ND : not determined.
Increase in fr
quency through time
No change in fr
quency throughtime
crease in frequency through time
Supplemental Table 4.
Significance of changes in mtDNA haplogroup frequencies between the Neolithic (Southern Europe) and the Chalcolithic (Northern Europe).