UDK UDK 902(4/5)"633/634":577.2
Documenta Praehistorica XXXV (2008)
Phylogeography of Y chromosomal haplogroups as
reporters of Neolithic and post-Neolithic population
processes in the Mediterranean area
Fiorenza Pompei1, Fulvio Cruciani2, Rosaria Scozzari2, Andrea Novelletto1
1 Department of Biology, Universita "Tor Vergata", Rome, Italy
novelletto@bio.uniroma2.it
2 Department of Genetics and Molecular Biology, Sapienza Universita di Roma, Rome, Italy
ABSTRACT - The phytogeny of the human Y chromosome as defined by unique event polymorphisms
is being worked out in fine detail. The emerging picture of the geographic distribution of different
branches of the evolutionary tree (haplogroups), and the possibility of genetically dating their anti-
quity, are important tools in the reconstruction of major peopling, population resettlement and demo-
graphic expansion events. In the last 10 000years many such events took place, but they are so close
together in time that the populations that experienced them carry Y chromosomal types which can
hardly be distinguished genetically. Nevertheless, under some circumstances, one can detect departu-
res from the model of a major dispersal ofpeople over much of the territory, as classically claimed for
the European Neolithic. The results of three studies of haplogroups relevant for Southern European po-
pulations are discussed. These analyses seem to resolve the signal of recent post-Neolithic events from
the noise of the main East-toWest Palaeolithic/early Neolithic migrations. They also confirm that, pro-
vided an appropriate level of resolution is used, patterns of diversity among chromosomes which ori-
ginated outside Europe may often be recognized as the result of discontinuous processes which occur-
red within Europe.
IZVLEČEK - Filogenija človeškega kromosoma Y, kot jo lahko preberemo skozi zaporedje polimorfiz-
mov, je dobro poznana. Čedalje jasnejša slika geografskih distribucij posameznih vej evolucijskega
drevesa (haploskupin) in možnosti njihovega genetskega datiranja so pomembna orodja pri preuče-
vanju širjenja človeštva, premikov in širitev populacij. V zadnjih 10 000 letih se je zgodilo kar nekaj
takih dogodkov, ki pa so si časovno tako blizu, da populacije, ki so bile vanje vpletene, nosijo tako
zelo podobne Y kromosome, da jih genetsko le težko razločimo med seboj. Kljub temu je moč pod ne-
katerimi pogoji opaziti razlike, ki se ločijo od klasičnega modela širjenja populacij, ki velja za evrop-
ski neolitik. Predstavljamo rezultate treh študij haploskupin južnoevropskih populacij. Analize so po-
kazale, da je moč iz šuma glavnih paleolitskih in neolitskih migracij iz vzhoda proti zahodu razlo-
čiti nekatere po-neolitske demografske dogodke. Študija tudi potrjuje, da je mogoče - ob dovolj visoki
ločljivosti - nekatere vzorce kromosomov, ki izvirajo izven Evrope, pripisati seriji prekinjenih proce-
sov znotraj Evrope.
KEY WORDS - Y chromosome; Neolithic; peopling of Europe; population genetics; demographic
expansions
Introduction
The genetic characterization of human populations
has long been recognized as an important and often
indispensable complement to historical research for
the understanding of population stratification, the
reconstruction of migrations and the evaluation of
gene flow. A major leap forward in this field was re-
presented by the possibility of assembling and ana-
lysing genetic data into a phylogenetic perspective.
Here we are concerned with the application of this
approach to population processes that occurred in
the Neolithic and post-Neolithic, as inferred from the
current population distribution of genetic diversity
of the male-specific portion of the human Y chromo-
some (MSY).
The phylogenetic approach takes into account the
sequential accumulation of mutations in a given
stretch of DNA (in this case the MSY) over time. A
mutation in a given DNA position produces a so-cal-
led derived allele at that position. Whenever this
event can be considered unique, and subjects car-
rying the derived allele coexist in the population
with subjects carrying the non-mutated (ancestral)
allele, a so-called Unique Event Polymorphism (UEP)
can be observed (also called biallelic polymorphisms,
as typically only two alleles are observed at a given
position). In this situation, each derived allele be-
comes a genetic marker whose origin can be located
in a time when the 'parental' type already existed
and can, in turn, be considered 'parental' for other
mutations that appeared later. Graphs that summa-
rize the overall process are called phylogenetic trees,
and they display branches that diverge progressi-
vely, each new branch being defined by a new de-
rived allele in any position along the MSY.
A direct extension of these concepts is that all MSY
copies (each carried by a different subject) bearing
the same derived allelic variant at a given position
can be considered, as a first approximation, descen-
dants of the first one in which that particular muta-
tional event occurred (i.e. have a monophyletic ori-
gin). When considering more than one position on
the same DNA molecule, the particular combination
of allelic variants (the haplotype) thus represents a
record of all the mutational
events that occurred on the li-
neage leading to that haplo-
type. Alleles shared by two
haplotypes testify to their com-
mon ancestry, whereas alleles
which differentiate two haplo-
types show that they belong
to lineages that diverged some
time in the past and, since
then, have accumulated a dif-
ferent series of mutations.
numbers from the deepest to the terminal branches
(Y Chromosome Consortium 2002) (Fig. 1). Each
lineage defined by biallelic markers is referred to
as a haplogroup, whereas the term haplotype has
been restricted to a combination of alleles at Short
Tandem Repeats (STRs, see below).
After a pioneering era, the search for biallelic mar-
kers exploited high-throughput methods that were
first applied to samples representative of the entire
world population and, later, oriented to resolve in
finer detail some specific lineages.
Another important class of markers is represented by
STRs. These include loci with different lengths of the
basic repeat, and extensive searches for developing
them as markers have been performed (Kayser et
al. 2004). Mutation at these loci occurs by the addi-
tion/subtraction of a number of repeats that is one
in the majority of cases. This latter feature fits the
theoretical 'Stepwise Mutational Model', which al-
lows us to create expectations for the rate of accu-
mulation of diversity and the distribution of allele
sizes. What matters here is that the overall amount
of STR diversity observed among the carriers of a
specific lineage defined by biallelic markers is a fun-
ction of the time elapsed since the origin of that li-
neage, and this property is exploited to arrive at an
evaluation of the antiquity of that lineage purely on
genetics grounds.
The genetic concepts and tools described above have
been used to search for the genetic signatures that
The principles and methods
of phylogenetic reconstruction
from experimental data can
be found in basic books. A ge-
neral consensus has been rea-
ched on the nomenclature of
lineages of the human MSY,
with alternating letters and
Fig. 1. Schematic representation of the human MSY phylogenetic tree.
Only the main branches found in Europe are shown. Mutations that iden-
tify each branch are reported above the corresponding line. Letters used
in the unified nomenclature for the main haplogroups are shown on the
right. The positions of the nodes are not proportional to age estimates.
the Neolithic revolution has left in the male gene
pool of populations of the Mediterranean region and
other areas nearby. However, it has to be empha-
sized that events that occurred in the last tenth of
millennia or later may have left traces that could
only modify the pre-existing repertoire of genetic
markers and their particular geographic distribu-
tions. These were the result of processes occurring
over a much longer time preceding the Neolithic. In
fact, even in the current description of the MSY
phylogenetic tree, most of the markers are older
than 10-15 ky BP, i.e. they were already present in
the populations that experienced the demographic
changes associated with the Neolithic revolution. In
conclusion, the question for the geneticist is whether
a DNA polymorphism which is able to mark a speci-
fic episode indeed exists and is known. In the phylo-
genetic framework, only under some circumstances
one can safely assume that a particular pattern of ge-
netic variation within a single or a group of popula-
tions can be the result of a Neolithic or post-Neolithic
event. These are:
O a biallelic marker near to the tip of a branch of
the MSY tree is dated at a time compatible or
younger than the Neolithic or,
© no such marker is known but, within an older li-
neage, a subset of populations display a limited
amount of STR variation, as if they had been foun-
ded at a more recent time and by a reduced num-
ber of founders.
We review and discuss here three studies (Di Gia-
como et al. 2004; Cruciani et al. 2007; Luca et al.
2007) that found genetic evidence of demographic
events which occurred after the spread of the Neo-
lithic culture from the Levant and involved Central
and South-Eastern Europe.
Post-Neolithic expansion from the Aegean de-
tected by haplogroup J2f1-M92
Haplogroup J has been considered to represent a sig-
nature of Neolithic demic diffusion associated with
the spread of agriculture (Semino et al. 1996). Di
Giacomo et al. (2004) provided population data
which give insights into the ways in which this ha-
plogroup spread.
Phylogenesis. Haplogroup J can be subdivided into
two major clades J1 and J2 - characterized by the
markers M267 and M172, respectively - plus the rare
paragroup J*(xJ1J2). Within J2, the analysis of a
multi-repeat deletion in the dinucleotide STR locus
DYS413 (Malaspina et al. 1998) resolves a major
multifurcation of six independent lineages, recently
increased to 11 (Sengupta et al. 2006). This additio-
nal mutational step within J2 enhances the possibi-
lity of performing phylogeographic studies of the
entire J2 sub-haplogroup in the Mediterranean area
(Fig. 2).
Population Data. Data on the overall occurrence of
the entire J haplogroup display an area of high fre-
quencies (>20%) stretching from the Middle East to
the central Mediterranean. A review of the frequency
data on Europe, the Caucasus, Iran, Iraq and North
Africa reveals that, in the Mediterranean, this haplo-
group is mainly confined to coastal areas. The high
frequencies in Turkey, Jewish and non-Jewish Middle
Eastern populations and in the Caucasus, identify
the fertile crescent and the east Mediterranean as
the focal area for the westward dispersal of the hap-
logroup. However, the data agree in showing that
this haplogroup did not leave a strong signature in
the peoples of the northern Balkans and central
Europe, this being the most likely route under the
demic diffusion model for the entry of agricultura-
lists into the European continent north to the Alps.
Instead, the raw frequency data from within the Ibe-
rian, Italian and Balkan peninsulas are more in line
with alternative routes of westward spread, possibly
maritime.
Internal J diversity. The highest UEP diversity is
observed in Turkey, Egypt and three locations in
southern Europe. The two most derived sub-haplo-
groups typed (J2f1-M92 and J2e-M12) were only
found in Turkey and locations west to it, boosting
the UEP internal diversity. The sub-haplogroup dis-
tribution found in Turkey is similar to that reported
by Cinnioglu et al. (2004).
The UEP diversity within J2 is lower in the Middle
East compared to both Turkey and the European lo-
cations. In conclusion, the UEP diversity of J in Tur-
key and southern Europe does not seem to be a sim-
ple subset of that present in the area where this ha-
plogroup first originated. This finding, also confir-
med in the data by Semino et al. (2004), points to
Turkey and the Aegean as a relevant source for the
J diversity observed throughout Europe.
The contribution of STRs for dating. When com-
bined with the results of 5 STRs, the age returned
for the entire J clade and its confidence interval fell
within the range reported in previous works (39.6
-10.5 ky BP). Conversely, two of the terminal bran-
ches (J2f-M67 and J2f-M92) turned out to be much
younger, with estimated ages of 4 and 2.6 ky BP, res-
pectively (C.I. 2.4-7.7 and 1.6-4.2, respectively).
Conclusion 1
The dating estimates obtained by Di Giacomo et al.
(2004) are in agreement with the appearance of J1
and J2 in the Levant at the time of the Neolithic agri-
culture revolution. Implicitly, these figures make
these haplogroups of little aid in identifying splits in
population that may have accompanied the west-
ward dispersal of the entire haplogroup.
The data by Di Giacomo et al. (2004) and Semino
et al. (2004) show that J2f1-M92 is predominantly
Fig. 2. Top. Phylogenetic arrangement of lineages within haplo-
group J, as analysed by Di Giacomo et al. (2004). Other internal
lineages (Y Chromosome Consortium 2002; Sengupta et al. 2006)
are not shown. The positions of the nodes of the tree are according
to age estimates (Di Giacomo et al. 2004) and are marked on the
lower bar (0 = present). Bottom. Same phylogenetic tree as above
superimposed onto geography, to show the main routes of disper-
sal of the different lineages. The origin of the entire J haplogroup
was arbitrarily placed in the fertile crescent and only south and
westward dispersals are outlined. For simplicity, J2-M12 and J2-
M47 are not shown. The endpoints of each line are schematic and
do not represent exclusive directions of migration (e.g. J1-M267 is
found not only in the Arabian Peninsula, but also in other areas
where J is present).
found in the northern Mediterranean, from Turkey
westward. In particular, the estimates for this latter
sub-haplogroup are barely compatible with its pre-
sence among the early Levantine agriculturalists.
Thus the most likely explanation is the emergence of
J2f1 in the Aegean area, possibly during the popula-
tion expansion phase also detected by Malaspina et
al. (2001), and coincident with the expansion of the
Greek world up to the European coast of the Black
sea. This scenario would agree with the clustering of
J2f1-M92 chromosomes in the north-west of Turkey
(Cinnioglu et al. 2004).
In summary, this set of data is in agreement with a
major discontinuity for the peopling of southern Eu-
rope. Here, haplogroup J constitutes not only the sig-
nature of a single wave-of-advance
from the Levant but, to a greater ex-
tent, also of the expansion of the
Greek world, with an accompanying
novel quota of genetic variation
produced during its demographic
growth. Recently Cadenas et al.
(2007) described similar evidence
concerning haplogroup J1-M267 as
a marker of the Neolithic spread
from the fertile crescent to the South
Arabian peninsula.
Post-Neolithic expansion from
within the Balkans detected by
haplogroup E-V13
Cruciani et al. (2007) provided de-
tailed population data on the distri-
bution of E-M78 binary sub-haplo-
groups defined by ten UEPs in 81
populations mainly from Europe,
western Asia and Africa. In order to
obtain estimates of the internal di-
versity and coalescence age of E-
M78 sub-haplogroups and their asso-
ciated human migrations and demo-
graphic expansions, a set of eleven
microsatellites was also analyzed.
The same set of microsatellites was
also analyzed in a sample of Y chro-
mosomes belonging to the haplo-
group J-M12. These results not only
provide a refinement of previous
evolutionary hypotheses based on
microsatellites alone, but also well
defined time frames for different mi-
gratory events that led to the disper-
sal of these haplogroups and sub-haplogroups in the
Old World.
Phylogenesis. By analyzing a worldwide sample of
6501 male subjects, 517 chromosomes belonging to
haplogroup E-M78 were identified, more than twice
the number found in a previous study (Cruciani et
al. 2004). These chromosomes have been further
analyzed for 10 biallelic markers. Four sub-haplo-
groups were either rare or absent in the global sam-
ple, while the other haplogroups/paragroups were
relatively common.
Population data and dating. The subdivision of
E-M78 in the six common major clades revealed a
pronounced geographic structuring: haplogroup E-
V65 and the paragroups E-M78* and E-V12* were
observed mainly in northern Africa, haplogroup E-
V13 was found at high frequencies in Europe, and
haplogroup E-V32 was observed at high frequencies
only in eastern Africa. The only haplogroup showing
a wide geographic distribution was E-V22, relatively
common in north-eastern and eastern Africa, but also
found in Europe, western Asia, up to southern Asia.
The peripheral geographic distribution of the most
derived sub-haplogroups with respect to north-east-
ern Africa, as well as the results of quantitative ana-
lysis of UEP and microsatellite diversity, are strongly
suggestive of a north-eastern African origin of E-
M78. The evolutionary processes that determined
the wide dispersal of the E-M78 lineages from north-
eastern Africa to other regions can then be addres-
sed.
Previous studies on the Y chromosome phylogeogra-
phy have revealed that central and western Asia
were the main sources of Palaeolithic and Neolithic
migrations contributing to the peopling of Europe
(Underbill et al. 2000; Wells et al. 2001). The mole-
cular dissection of E-M78 contributes to the under-
standing of the genetic relationships between north-
ern Africa and Europe. Several lines of evidence sug-
gest that E-M78 sub-haplogroups E-V12, E-V22 and
E-V65 were involved in trans-Mediterranean migra-
tions directly from Africa. These haplogroups are
common in northern Africa, where they probably
originated, and are observed almost exclusively in
Mediterranean Europe, as opposed to central and
eastern Europe. Also, among the Mediterranean po-
pulations, they are more common in Iberia and
south-central Europe than in the Balkans, the natu-
ral entry-point for chromosomes coming from the
Levant. Such findings are hardly compatible with
the south-eastern entry of E-V12, E-V22 and E-
V65 haplogroups into Europe. Upper limits for the
introduction of each of these haplogroups in Europe
are given by their estimated ages (18.0, 13.0 and 6.2
ky BP, respectively), while lower bounds should be
close to the present time, given the lack of internal
geographic structuring.
Haplogroup E-V13 is the only E-M78 lineage that
reaches the highest frequencies outside Africa. In
fact, it represents about 85% of European E-M78
chromosomes, with a clinal pattern of frequency di-
stribution from the southern Balkan peninsula
(19.6%) to western Europe (2.5%) (Fig. 3). The same
haplogroup is also present at lower frequencies in
Anatolia (3.8%), the Near East (2.0%) and the Cau-
casus (1.8%). In Africa, haplogroup E-V13 is rare,
being observed only in northern Africa at a low fre-
quency (0.9%). The European E-V13 microsatellite
haplotypes are related to each other to form a near-
ly perfect, star-like network, a likely consequence of
rapid demographic expansion (Jobling et al. 2004).
The age of the European E-V13 chromosomes turns
out to be 4.0-4.7 ky BP. On the other hand, when
only E- V13 chromosomes from western Asia are
considered, the resulting network does not show
such a star-like shape, and a much earlier age of
11.5 ky BP (95% C.I. 6.8-17.0) is obtained. These re-
sults present the possibility of recognizing time win-
dows for i) population movements from the E-M78
homeland in north-eastern Africa to Eurasia, and ii)
population movements from western Asia into Eu-
rope and, later, within Europe.
The most parsimonious and plausible scenario is that
E-V13 originated in western Asia about 11 ky BP,
and its presence in northern Africa is the result of a
more recent introgression. Under this hypothesis, E-
V13 chromosomes sampled in western Asia and their
coalescence estimate detect a likely Palaeolithic exit
from Africa of E-M78 chromosomes devoid of the
V13 mutation, which later occurred somewhere in
the Near East/Anatolia. The refinement of location
for the source area of such movements and associ-
ated chronologies attained by Cruciani et al. (2007)
may be relevant to controversies on the spread of
cultures (and languages) between Africa and Asia in
the corresponding timeframes (Bellwood 2004; Ehret
et al. 2004).
Two haplogroups support the same scenario.
As to a western Asia-Europe connection, the data
suggest that western Asians carrying E-V13 may
have reached the Balkans anytime after 17.0 ky ago,
but expanded into Europe not earlier
than 5.3 ky ago. Accordingly, the allele
frequency peak is located in Europe,
whereas the distribution of microsatel-
lite allele variance shows a maximum
in western Asia. Based on previously
published data discussed above, Cru-
ciani et al. (2007) observed that ano-
ther haplogroup, J-M12, shows a fre-
quency distribution within Europe si-
milar to that observed for E-V13. In
order to evaluate whether the present
distribution of these two haplogroups
can be the consequence of the same
expansion/dispersal microevolutionary
event, the two frequency distributions
in Europe were compared. A high and
statistically significant correspondence
between the frequencies of the two ha-
plogroups (r = 0.84, 95% C.I. 0.70-
0.92) was observed. A similar result
(r = 0.85, 95% C.I. 0.70-0.93) was ob-
tained when the series was enlarged
with the J-M12 data from Bosnia, Cro-
atia and Serbia (Marjanović et al.
2005) matched with the frequencies
of E-M78 cluster a (Peričić et al. 2005) as a proxy
for haplogroup E-V13.
Finally, tetranucleotide microsatellite data were used
in order to obtain a coalescence estimate for the J-
M12 haplogroup in Europe. By taking into conside-
ration two different demographic expansion models,
age estimates very close to those of E-V13 were ob-
tained, i.e. 4.1 ky BP (95% C.I. 2.8-5.4 ky BP) and
4.7 ky BP (95% C.I. 3.3-6.4 ky), respectively.
The overall view was confirmed by subsequent works
aimed at clarifying the peopling of Crete. According
to Martinez et al. (2007) E-M78 cluster a chromo-
somes (which largely overlap E-V13) may have rea-
ched Crete as a result of gene flow from mainland
Greece during and/or after the Neolithic. King et al.
(2008) dated the expansion of E-V13 chromosomes
in Crete at 3.1 ky BP, "arguably reflecting the pre-
sence of a mainland Mycenaean population in
Crete". Also, the V13 marker is able to rule out re-
cent genetic affinities between Crete and Egypt,
where E chromosomes are mainly devoid of V13.
Conclusion 2
The congruence between frequency distributions,
shape of the networks, pair-wise haplotypic differ-
ences and coalescent estimates point to a single
Fig. 3. Map of the observed haplogroup E-V13 frequencies (Cru-
ciani et al. 2007).
evolutionary event at the basis of the distribution
of haplogroups E-V13 and J-M12 within Europe, a
finding never appreciated before. These two hap-
logroups account for more than one fourth of the
chromosomes currently found in the southern Bal-
kans, underlining the strong demographic impact of
the expansion in the area.
At least four major demographic events have been
envisioned for this geographic area, i.e. the post-Last
Glacial Maximum expansion (about 20 ky BP) (Ta-
berlet et al. 1988; Hewitt 2000), the Younger Dryas-
Holocene re-expansion (about 12 ky BP), the popu-
lation growth associated with the introduction of
agricultural practices (about 8 ky BP) and the de-
velopment of Bronze technology (about 5 ky BP).
Though large, the confidence intervals for the coale-
scence of both haplogroups E-V13 and J-M12 in
Europe exclude the expansions following the Last
Glacial Maximum, or the Younger Dryas. The esti-
mated coalescence age of about 4.5 ky BP for haplo-
groups E-V13 and J-M12 in Europe (and their C.I.s)
would also exclude a demographic expansion asso-
ciated with the introduction of agriculture from Ana-
tolia and would place this event at the beginning of
the Balkan Bronze Age, a period that saw strong
demographic changes as clearly seen in the archaeo-
logical record. The arrangement of E-V13 and J-M12
frequency surfaces appears to fit the expectations
for a range expansion in an already populated terri-
tory. Moreover, similarly to what Peričić et al. (2005)
found for the E-M78 network, the dispersion of E-
V13 and J-M12 haplogroups seems to have mainly
followed the rivers connecting the southern Balkans
to north-central Europe, a route that had already has-
tened by a factor of 4-6 the spread of the Neolithic
to the rest of the continent (Davison et al. 2006).
Post-Neolithic expansion within Central Europe
detected by three haplogroups
Luca et al. (2007) explored the MSY diversity in five,
closely spaced Czech population samples. The hap-
logroups P-DYS257*(xR1a) and R1a-SRY10831 estab-
lish a major divide across central Europe, initially
identified with a line roughly extending from the
Adriatic to the Baltic (Malaspina et al. 2000). This
line separates high frequencies of R1a-SRY10831 to
the East from low frequencies to the West, with an
opposite trend for P-DYS257*(xR1a). Kayser et al.
(2005) found this sharp genetic boundary to coin-
cide with the German-Polish border, and interpreted
it as the result of massive population movements as-
sociated with World War II, superimposed on pre-exi-
sting continent-wide clines. The Czech Republic ap-
pears to be affected by a much smoother frequency
shift, if any, supporting the interpretation of a very
recent origin of the German-Polish discrepancy.
Overall, the haplogroup frequencies identify the
Czech population as one influenced to a very mode-
rate extent by genetic inputs from outside Europe in
the post-Neolithic and historical times. It thus may
represent an ideal population to draw inferences on
geographically confined processes that might also
have occurred in other parts of central Europe.
Inferences based on STR variation in the three most
common haplogroups obtained with coalescent me-
thods deserve careful evaluation. First, even though
sampling was carried out in a limited geographic
area, it returned age estimates for I-M170, P-
DYS257*(xR1a) and R1a-SRYW831 similar to those
obtained in reports with a wider geographical cove-
rage (approximately 500, 400 and 350 generations
ago, respectively). Conservatively, one can simply
conclude that the Czech population harbours a large
part of the STR variation generated in each haplo-
group. The ages of the three most common haplo-
groups turned out to be largely overlapping, and
compatible with their presence during or soon after
the Last Glacial Maximum.
However, a local signal emerged from the distribu-
tion of this diversity, i.e. that of a fast and recent po-
pulation growth, which persists even after relaxing
the prior assumptions of the dating method and is
similar for the three haplogroups. This is summari-
zed by the parameters alpha (rate of population
growth, 0.023, 0.031 and 0.032 for I-M170, P-
DYS257*(xR1a) and R1a-SRYW831, respectively) and
beta (beginning of population growth, 97, 150 and
125 generations ago, respectively) and their relati-
vely narrow confidence intervals (up to 1.5 fold the
average). Estimation of the beta parameter most li-
kely locates the beginning of this process in the 1st
millennium BC, with confidence intervals that are
barely compatible with the archaeologically docu-
mented introduction of Neolithic technology in this
area (Haak et al. 2005). At least for the female lin-
eage, these authors found a little genetic contribu-
tion to the present European gene pool from the
first farmers settled in the area. Independently of
the relevance of these data for reconstructing the ge-
netics of Europe in the early Neolithic (Barbujani
and Chikhi 2006), the central value for population
growth coincides with a later period of repeated
changes in the material cultures in this geographic
region, driven by the development of metal techno-
logies and the associated social and trade organiza-
tion.
Conclusion 3
The combined use of UEP and STR markers
allowed the exploration of different time horizons
for the age of molecules and for the process of pop-
ulation growth (Torroni et al. 2006). In fact, the
data for the Czech population favour a model in
which the age of the most common MSY molecules
could be separated from consistent population
growth. Similar results have been obtained for
Lithuania (Kasperaviciute et al. 2004). Both regions
lie at the north-western and northern edge, respecti-
vely, of the putative homeland (central and south-
eastern Europe) of an aboriginal quota of the mole-
cular MSY diversity. This offers an unprecedented
opportunity to test alternative models for a continen-
tal pattern of diversity which is arranged along the
southeast-to-northwest axis. The question of whether
this could be the result not only of a single demic dif-
fusion, but also of the demographic increases affec-
ting pre-existing local gene pools is still open. Exam-
ples of the recent growth of pre-existing gene pools
that add complexity to the simple demic diffusion
models, are provided by mtDNA haplogroup HV and
H1 (Achilli et al. 2004), as well as Y chromosomal
haplogroup R-SRY2627 (Hurles et al. 1999).
Concluding remarks
The build-up of present day male-specific Y chromo-
some (MSY) diversity can be viewed as an increase
in complexity, due to the repeated addition of new
variation to the pre-existing background by two main
mechanisms: the immigration of differentiated MSY
copies from outer regions, and the accumulation of
novel MSY variants generated by new mutations in
loco. Recently, Sengupta et al. (2006) pointed out
that combining highly resolved phylogenetic hierar-
chy, haplogroup internal diversification, geography
and expansion time estimates can lead to the appro-
priate diachronic partition of the MSY pool. The DNA
content of the MSY ensures that abundant diversity
exists to proceed a long way in this process of phylo-
geographic refinement, eventually leading to a level
of resolution for human history comparable with, or
even greater than, that achieved by mitochondrial
DNA (Torroni et al. 2006).
In addition, environmental or cultural transitions are
usually considered to be the basis of dramatic chan-
ges in the size of human populations. These changes,
too, are expected to leave a distinct signature in the
genetic pools of the populations that experienced
them. Even in the absence of known markers that
are able to qualitatively mark these episodes, quanti-
tative analysis is feasible and can sometimes lead to
robust inferences.
Here we show that a growing body of work conver-
ges in disclosing a further level of complexity in the
genetic landscape of central and south-eastern Eu-
rope. This appears to be, to a large extent, the conse-
quence of a recent population increase in situ, rather
than the result of a mere flow of western Asian mi-
grants during the early Neolithic.
-ACKNOWLEDGEMENTS-
This work was supported by grants Grandi Progetti
Ateneo, Sapienza Universita di Roma (to R.S.), and the
Italian Ministry of the University - Progetti di Ricer-
ca di Interesse Nazionale 2007 (to R.S. and A.N. grant
numbers 20073RH73W_002 and 20073RH73W_003).
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