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Post by Admin on May 8, 2021 23:17:55 GMT
In general, these migrations are seen as a part of a broader IE spread. Anthony
suggests a time around the 4th millennium BCE for the spread of pastoralists and proto-IE
language from the Pontic Caspian Steppe region north and east of the Black Sea (Anthony,
1995). Gimbutas suggested an earlier date with the Steppe people coming in three waves:
1) a first wave around the mid 5th millennium BCE (Srednji Stog Culture, Cucuteni A in
515 the northern Balkans, Vinça V, Rössen in Germany); 2) a second wave around the mid
4th millennium BCE (Maikop Culture, Baden in the Danube basin, Globular Amphora,
Ezero in Bulgaria); and 3) a third wave around the beginning of the 3rd millennium BCE
(Yamnaya and Pit Grave culture, Corded Ware culture in central Europe, Bell Beaker
in central and western Europe) (Gimbutas, 1997). The Steppe hypothesis links many
technological innovations thought to be consistent with the cultures north of the Pontic
Caspian Steppes with words that appear in common across all IE sub-families. These
include terms for ‘wheel’ (*rotho-, *kW(e)kWl-o-), ‘axle’ (*aks-lo-), ‘yoke’ (*jug-o-),
‘horse’(*ekwo-) and ‘to go, transport in a vehicle’ (*wegh) (Gray et al., 2011).For example,
the presence of wheeled vehicles in the IE vocabulary is a basic argument since these
do not appear in the European archaeological record before the 4th millennium BCE (Anthony, 1995), while in Greece, horses related to transportation and wheeled vehicle are not attested during the EBA (Coleman, 2000).
Supporters of this hypothesis accept the presence of the Anatolian linguistic substratum
observed in the Greek language. Coleman characterizes it as a "pre-Greek substrate
language" spoken by the Neolithic inhabitants. He suggests that this substratum came
as a loan into the Greek language spoken by proto-Greeks who migrated into mainland
Greece, at the beginning of EBA.
The Anatolian linguistic substratum has thus been explained by both hypotheses
under two different scenarios: 1) by the spread of Early Neolithic farmers from Anatolia;
or 2) by migration from the Pontic Caspian Steppe of people, who brought proto-Greek
but also integrated the Anatolian linguistic substratum. Although more detailed analysis
is beyond the scope of this paper, alternative scenarios could be plausible: e.g., the
presence of the Anatolian linguistic substratum as part of the Anatolian hypothesis
and a subsequent migration of IE speakers from the north that brought new linguistic
elements. This last suggestion is supported by a new approach to this highly debated
topic. Gray and Atkinson (2003), applying a computational phylogenetic method to 87
Indo-European languages, estimated the age of Proto IE at around 6,700 BCE. The nodes
on the phylogenetic tree of Gray and Atkinson (2003) and Gray et al. (2011) correspond
to the estimated divergence times of present-day languages (which correspond to tips
of the tree), assuming the split happened instantaneously (a simplifying assumption of
the model). In other words, the estimated divergence times indicate the period during
which languages accumulated differences. Note however that the linguistic innovations
underlying this separation may have taken centuries beforehand. According to their
analyses, Hittite is located at the base of the tree with an age of 6,700 BCE. In a later
study the divergence time was estimated around 5,000 BCE (Bouckaert et al., 2013).
Tocharian diverged from Hittite around 6,000 BCE and then gave rise to two branches,
one leading to Greek and Armenian and the second to the rest of the Indo-European
languages. Although the root of the tree goes back to around 6,700 BCE, much of the
diversification of the major IE subgroups happened around 5,000-4,000 BCE (Gray et al.,
2011). The authors therefore suggest that a proto-IE language was formed through the
Early Neolithic spread out of Anatolia (Anatolian hypothesis), but that 2,000 years later,
IE language sub-families expanded out of the Pontic Caspian Steppes, giving rise to the
major linguistic radiation we see today (Steppe hypothesis). The Steppe hypothesis was
also supported by other researchers using a similar phylogenetic analysis (Chang et al.,
2015). More genetic, linguistic, and archaeological evidence will be needed to better
disentangle the Anatolian and Steppe hypotheses, and their possible joint effect.
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Post by Admin on May 9, 2021 19:47:28 GMT
2 Population genetics
2.1 Mitochondrial DNA
2.1.1 mtDNA haplogroups
Martina Unterländer, Lucas Anchieri, Carlos Eduardo G. Amorim, Florian
Clemente, Diana I. Cruz Dávalos, Angelos Souleles, Elissavet Ganiatsou,
Anna-Sapfo Malaspinas, Christina Papageorgopoulou
We analyze in this section the data resulting for the mtDNA capture experiments (11
individual samples) as well as the mtDNA data from the six whole genomes (WGS data).
All mtDNA haplogroups can be found in Table S1 (tabs "WGS" and "mtDNA").
The mtDNA lineages of the individuals analysed belong to the haplogroups H, J, K,
L, U, X, which are among the most common in present-day populations of Europe and
the Near East. In present-day Greece those mtDNA haplogroups vary in frequency from
9.5% to to 40.5% of the population, respectively (eupedia.com, 2018).
Kou01, Kou03, PEL04, XER07: haplogroup K1
For the Cycladic individuals we found mtDNA haplogroups K1a (Kou03) and K1a2c
(Kou01), while XER07 and PEL04 individuals from northern Greece were associated
with K1a2 and K1a3a respectively. In the timespan preceding Kou01 and Kou03, a K1
individual was found in Greece at the Mesolithic site of Theopetra and haplogroup K1a2 to
the Late Neolithic site of Kleitos in northern Greece (Hofmanová et al., 2016). Haplogroup
K is present in Pre-Pottery Neolithic B individuals at the sites Tell Halula (6,800-6,000
BCE) and Tell Ramad (6,000-5,750 BCE) (Fernández et al., 2014). The haplogroup
K1a was found in a hunter-gatherer (HG) population from Serbia (Mathieson et al.,
2018), in individuals of the Early Neolithic Starčevo Culture in Hungary and Croatia
(Szécsényi-Nagy et al., 2015), in individuals of the Linear Pottery Culture (LBK) in
Hungary and Germany (Szécsényi-Nagy et al., 2015; Brandt et al., 2013) and in Neolithic
individuals from Turkey and Bulgaria (Kılınç et al., 2016; Mathieson et al., 2018). K1a2c
was inferred in individuals associated with the Bell Beaker culture from Czech Republic
and Germany (Mathieson et al., 2018; Olalde et al., 2018), whilst the haplogroup K1a3a
was found in an individual from the Neolithic period in Turkey (Mathieson et al., 2015).
AGI02, Log02, Pta08, XER02: haplogroup H
The mtDNA of individual Log02 from northern Greece was associated with haplogroup
H55a. Haplogroup H and its derived lineages are the most common in all European
populations—except in the Saami of Finland (0-7%) (Hay, 2017). It was also common
during the Neolithic in Europe (Brotherton et al., 2013), but haplogroup H55a has only
been reported in present-day Europeans to date (Hay, 2017). The Minoan individual
Pta08 from this study, along with individual XER02 from northern mainland Greece,
display haplogroup H, which has been found to be very common in individuals of Minoan
Crete (Hughey et al., 2013; Lazaridis et al., 2017) and was already present in Neolithic
Greece (Mathieson et al., 2018). Furthermore, haplogroup H was also found in individuals
from BA Anatolia (Lazaridis et al., 2017), in Hungary from the Mesolithic to the
late Copper Age and in the Balkans from the Neolithic onward (Gamba et al., 2014;
Szécsényi-Nagy et al., 2015; Mathieson et al., 2018).The mtDNA of individual AGI02
is associated with haplogroup H7c4. Haplogroup H7 is believed to represent lineages
descended from Mesolithic southern Europeans or Early Neolithic migrants from the Near
East (eupedia.com, 2018). It has been observed in individuals from the Neolithic and
Chalcolithic period in Bulgaria, while H7c in specific was found in an individual from the
Neolithic period in Croatia (Mathieson et al., 2018).
Log04 and Mik15: haplogroup J
We found no direct match for haplogroup J1c+16261 (Log04 ) in publications on ancient
populations from Greece or Central Europe prior to the Bronze Age; e.g., Brandt et al.,
2013; Haak et al., 2010; Haak et al., 2015; Gamba et al., 2014; Lazaridis et al., 2014;
Lazaridis et al., 2016; Lazaridis et al., 2017; Allentoft et al., 2015; Mathieson et al., 2018;
Szécsényi-Nagy et al., 2015. There are, however, reports for closely related haplogroups.
A J1c lineage could be found in Neolithic individuals of Germany and Bulgaria (Brandt
et al., 2013; Mathieson et al., 2018) and the Early Neolithic Starčevo Culture in Hungary
and Croatia (Szécsényi-Nagy et al., 2015). The closely related haplogroup J1c1 was found
in a Late Neolithic individual from the site of Paliambela in northern Greece (Hofmanová
et al., 2016). The BA individuals from the Paliambela site (this study) are associated
with the U2e2a1 haplogroup (see below).
The haplogroup J2b1 (Mik15 ) was also found in Neolithic individuals of Bulgaria and
Ukraine (Mathieson et al., 2018).
MIK08: haplogroup L
The MIK08 individual was associated with the African haplogroup L3d1b1. Haplogroup
L3 sits at the root of the mtDNA phylogenetic tree of haplogroups found outside of Africa,
and thus it is associated to the out of Africa expansion (Behar et al., 2008; Van Oven and
Kayser, 2009). A HG individual with the haplogroup L was found in the African Mota
Cave (Llorente et al., 2015) and in Iberia associated with the Bell Beaker culture (Olalde
et al., 2018).
XER01 and XER05: haplogroup X
The mtDNA of the individuals XER01 and XER05 was associated to haplogroup X2g.
Although haplogroup X is one of the rarest in Europe, it appears in Greece with a
frequency of 4% (eupedia.com, 2018). The haplogroup X was present in an Early Neolithic
individual from the site of Revenia in Northern Greece (Hofmanová et al., 2016), in
two Anatolian Neolithic individuals (Mathieson et al., 2015) and two individuals of the
Starčevo culture in Alsónyék-Bátaszék, Mérnöki telep archaeological site (Szécsényi-Nagy
et al., 2015). It was also found in a Middle BA Minoan individual (Hughey et al., 2013),
in an Armenian Early BA individual and in a Levant BA individual (Lazaridis et al., 2016).
PAL04, PAL05, PEL02, PEL03: haplogroup U
For the individuals belonging to haplogroup U, we found mtDNA haplogroups U2e2a1
(PAL04, PAL05 ), U3a1 (PEL03 ), and U4c1 (PEL02 ). Haplogroup U2 is a really "old
lineage" (going back 40,000 years), while U3 and U4 derived during the Last Glacial
Maximum at Mesolithic European HG and Middle Eastern HG populations respectively
(eupedia.com, 2018). The U2 haplogroup was found in individuals from Andronovo culture
(Allentoft et al., 2015) in addition to Motala HG and Latvia HG (Mathieson et al., 2018;
Mathieson et al., 2015). The U4 haplogroup was recorded in an Early Neolithic individual
from Samara (Mathieson et al., 2015), a HG from the Iron Gates (Mathieson et al., 2018),
as well as in individuals from the Andronovo and Yamnaya cultures (Allentoft et al.,
2015). On the other hand, haplogroup U3 is traced in Neolithic Anatolians (Mathieson
et al., 2015; Kılınç et al., 2016), Iberian and Iranian Chalcolithic individuals (Mathieson
et al., 2015; Lazaridis et al., 2016). There is also a Middle BA Minoan (2,210-1,680 BCE)
individual with this specific haplogroup (Lazaridis et al., 2017).
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Post by Admin on May 10, 2021 0:45:42 GMT
2.1.2 mtDNA phylogenetic tree Lucas Anchieri, Carlos Eduardo G. Amorim, Florian Clemente, Vitor Sousa, Anna-Sapfo Malaspinas In order to investigate the relationship between individual samples and to reconstruct 5 a proxy for the "gene tree", we generated a phylogenetic tree (see below). We included the 17 mtDNA sequences in Table S1 (six under the "WGS" tab and 11 under the "mtDNA" tab) and added two San mitochondrial genomes (AY195783 and AY195789) (Mishmar et al., 2003) as outgroups. The sequences were first aligned using SeaView v5.0.4 (Gouy et al., 2010) and converted to phylip format using the R package ape v5.3 (Paradis and Schliep, 2019). We then used PhyML v3.1 (Guindon et al., 2010) and the R package phangorn v2.5.5 (Schliep, 2011) to determine the best model for our data. In our case, F84 + I + Γ was the best model. We then loaded the sequences on PhyML v3.1 and generated the tree using this model, with a BioNJ starting tree, SPR moves, and 10,000 bootstrap replicates. After collapsing all nodes with bootstrap support below 50%, we obtain the following tree:  sample was appended to its ID. Branch labels indicate bootstrap support. We can observe on the tree that in most cases, similar haplogroups tend to cluster together. The haplogroup topology is also mostly coherent with publicly available data (eupedia.com, 2018). However, individual samples from the same site/population/period are not strictly sister taxa. |
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Post by Admin on May 10, 2021 20:23:59 GMT
2.2 Y chromosome
Martina Unterländer, Diana I. Cruz Dávalos, Elissavet Ganiatsou, Florian
Clemente, Anna-Sapfo Malaspinas, Christina Papageorgopoulou
Y-haplogroup calls
The Y-haplogroups for Kou01 and Pta08 were found to be J2a-M410 and G2-L156, respectively. Details on how those haplogroups were called are given in the STAR METHODS,
see section "Uniparental markers".
The Neolithic transition was a major event in the construction of the European popu
lation, (Lacan et al., 2011a; Lacan et al., 2011b) and based on present-day data, the
Y-chromosomal haplogroups J and G have been associated with the Neolithic expansion
into Europe (Semino et al., 2000; Semino et al., 2004). Ancient DNA data confirm that
haplogroup G2a and its subgroups were very common during the Neolithic period in
general. These groups have been detected in Early Neolithic Turkey and Late Neolithic
Greece (Hofmanová et al., 2016) as well as Neolithic Germany (Haak et al., 2010; Haak
et al., 2015), Southern France (Lacan et al., 2011a) and Spain (Lacan et al., 2011b). They
were not detected in pre-Neolithic hunter gatherers from Central Europe (Mathieson et al.,
2018), which further supports the notion of a Neolithic expansion for the Y-chromosome
haplogroup G. The haplogroup G2, which has been detected in the Minoan sample Pta08,
has also been found in Eneolithic Bulgaria and Neolithic Ukraine (Mathieson et al., 2018).
This haplogroup was also found in Iberian individuals associated with the Bell Beaker
culture, which showed no Steppe-related ancestry (Olalde et al., 2018).
Ancient DNA evidence for haplogroup J in Central Europe is rare. It is suspected for
a WHG individual from France and the subgroup J2 was detected in Neolithic Austria for
an individual associated with the LBK (Mathieson et al., 2018). Ancient DNA analysis
could so far not provide clear evidence for a Neolithic expansion of haplogroup J that
was proposed based on present-day distribution of this haplogroup (Semino et al., 2004).
Derived lineages of haplogroup J2a, which has been found in the Cycladic individual
Kou01, seem to have been common in Bronze Age Greece. They were also detected in
Bronze Age Minoans from Crete and one Mycenaean individual from the Peloponnese
(Lazaridis et al., 2017). Haplogroup J2a has also been found in an CHG individual from
Georgia (Jones et al., 2015) and individuals dating to the Anatolian Neolithic and Early
Bronze Age (Mathieson et al., 2018; Barros Damgaard et al., 2018).
2.3 Multidimensional scaling analysis (MDS)
Florian Clemente, Frédéric Michaud, Diana I. Cruz Dávalos, Anna-Sapfo
Malaspinas
We explored the relationships among our six ancient genomes in the context of 259
previously published ancient and 638 primarily Eurasian modern genomes (Dataset II;
STAR Methods) with a classical multidimensional scaling (MDS) analysis. The results
can be seen in Figure 2.
From the first two dimensions of variation, we see that our EBA individuals (Kou01,
Kou03, Mik15, Pta08 ) can be distinguished from the Neolithic farmers by being slightly
drawn towards Caucasus HG/Iran Neolithic related populations. This is consistent with
our ADMIXTURE, qpAdm, ABC-DL results, which indicate a Caucasus HG/Iran Neolithic
influence starting in Greece at around 3,000 BCE. More recent individuals (Minoans and
Mycenaeans (Lazaridis et al., 2017) and modern Cypriots) are further drawn towards
Caucasus HG/Iran Neolithic related populations, which suggests a gradual increase of this
component over time. The MBA Logkas individuals (Log02 and Log04 ) are distinct from
the EBA Aegean individuals as well as from all other previously studied ancient Greek
individuals. They lie on the axis between Neolithic Anatolian/Greek farmers and Steppe
populations and are the ancient individuals closest to the modern Greeks. This is also in
line with our ADMIXTURE, qpAdm, D-statistics and ABC-DL results, which suggest
an impact of Steppe related populations on our Logkas individuals (i.e., on mainland
Greece by 2,000 BC). Moreover, the proximity between the Logkas individuals and modern
Greeks on the MDS plot is consistent with the qpAdm results where the modern Greeks
could be modelled with >90% Logkas ancestry and another source. The structure among
European/Aegean Neolithic, Steppe populations, and Greek individuals (modern/ancient)
becomes less visible in dimensions three and four (results not shown), which respectively
1090 explain 0.46% and 0.4% of the variation.
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Post by Admin on May 11, 2021 2:33:35 GMT
2.4 Admixture analysis
Francisco Coroado-Santos, Florian Clemente, Carlos Eduardo G. Amorim,
Anna-Sapfo Malaspinas, Vitor C. Sousa
To estimate the average genomic ancestry proportions, we used the software ADMIXTURE
v1.31 (Alexander et al., 2009) (STAR Methods).
As missing data can affect the admixture proportion estimates, we computed the
amount of missing data using VCFTools v.0.1.17 (Danecek et al., 2011) for the final SNP
set for each of the 969 individuals. In Table S2 ("Percentage_of_missing_SNPs" tab) we
show the number and percentage of missing SNPs for the individuals from ancient and
present-day Greece and Cyprus, and the ancient samples used in the ABC-DL analyses.
For modern samples (Greek and Cypriot), the missing data ranged from 0.04% to 0.23%,
while for the ancient samples the proportion of sites with missing data ranged from
0.08% (a 20X Steppe_EMBA genome) to 94% (Minoan Odigitria). Among the Aegean
BA individuals, the newly sequenced genomes from this study (Mik15, Kou01, Kou03,
Pta08, Log02, Log04 ) have considerably less missing data than the other ancient Aegeans
(Mycenaeans and Minoans Lasithi/Odigitria) from previous studies with amounts ranging
from 1.2 to 13.0% for the data from this study versus amounts than 29% (Table S2).
Results for K = 3, the K value with lower CV error (0.97391 for K = 3, Figure
S6), estimate that the set of ancient and modern individuals from Eurasia can be described by three main ancestry components: "European Neolithic - like" (red), "Iranian
Neolithic/Caucasus HG - like" (light blue) and "European HG - like" (orange) (Figure
S6). We found that in comparison with Aegean Neolithic, which have on average 91%
of "European Neolithic - like" and 7.5% of "Iranian Neolithic/Caucasus HG - like", the
Aegean EBA individuals (Mik15, Kou01, Kou03, Pta08 ) have a higher proportion of the
"Iranian Neolithic/Caucasus HG - like" component, larger than 17%. This is consistent
with previously reported results for younger Aegean BA individuals (Mycenaean and
Minoan Lasithi) (Lazaridis et al., 2017). The newly sequenced Aegean EBA individuals
from this study are from three different cultures: Cycladic (Kou01 and Kou03 ), Minoan
(Pta08 ) and Helladic (Mik15 ). The Cycladic (Kou01 and Kou03 ) are estimated to have
on average 70% of "European Neolithic - like", 25% of "Iranian Neolithic/Caucasus HG -
like" and 5% of "European HG - like". The Minoan individual is estimated to have 76%
of "European Neolithic - like", 22% of "Iranian Neolithic/Caucasus HG - like" and 2% of
"European HG - like". The Helladic individual is estimated to have 78% of "European
Neolithic - like", 17% of "Iranian Neolithic/Caucasus HG - like" and 5% of "European HG
- like". The estimated admixture proportions are thus similar across the three cultures,
indicating that they were not genetically isolated. This is in accordance with the MDS
analysis, which clusters them together, and with the qpWave/qpAdm results, which suggest
that the Cycladic-Koufonisi individuals (Kou01, Kou03 ) and the Minoan-Petras individual
(Pta08 ) can be modelled as a mixture of the same source populations, suggesting reduced
genetic barriers to gene flow between these populations.
The Helladic-Manika individual (Mik15 ) represents one of the oldest samples from
Early Bronze Age in Greece. Given that Mik15 shows an increase of approximately 9%
in the "Iran Neolithic/ Caucasus HG" - like component when compared with Neolithic
Greek individuals (17% in Mik15 vs 8% in Greece N and Peloponnese N), it suggests that
by 3,000 BC the Aegean was influenced by a demographic transition period, during which
the component related to Iran Neolithic and CHG was increasing and spreading in the
Aegean. Thus, the newly sequenced EBA individuals provide the earliest evidence for the
influence of "Iran Neolithic/ Caucasus HG - like" genetic ancestry for the demographic transition to Bronze Age in Greece. Note that the older evidence for this has been
reported in Anatolia (Lazaridis et al., 2016), and we confirm those previous results, as
admixture proportion estimates indicate an increase in "Iran Neolithic/Caucasus HG -
like" proportions from Anatolia Neolithic (average of 2%) to Anatolia BA (average of
28%), despite higher estimates in some Neolithic individuals (16-27% in Anatolia Tepecik
Ciftlik and 23-28% in Anatolia Kumtepe, Figure S6).
Age, as the admixture proportions of Aegean EBA individuals (Mik15, Pta08, Kou01,
Kou02 ) were consistently different from the admixture proportions of Aegean MBA
individuals (Log02, Log04 ) for all K > 2. For K = 3, ancestry estimates for the Aegean
MBA individuals are 48% "European Neolithic - like", 22% of "Iranian Neolithic/Caucasus
HG - like" and 30 % of "European HG - like". In comparison with Aegean EBA individuals,
as well as Aegean BA individuals from other studies, the Aegean MBA individuals (Log02,
Log04 ) showed a higher proportion of the "European HG - like" component (orange) for
all K > 2, except for K = 6 (but note that K = 6 has the higher CV error). Furthermore,
for K > 3 the main components of Steppe_EMBA individuals (estimated to have on
average 50% of "European HG - like" for K = 4 − 5, or a specific "Steppe EMBA - like"
component for K = 6), are found in higher proportion in Aegean MBA than in EBA
individuals. Given that "European HG - like" is the major component of Steppe-related
populations at K = 3 (i.e. the K with lower CV error), and that at K > 3 the components
of Steppe-EMBA are found in higher proportion in Aegean MBA than in EBA Aegean, it
suggests that by the Middle Bronze Age the influence of Steppe populations extended
to the Aegean. The increase of this ancestry component in Aegean MBA individuals
is in agreement with their location on the MDS plot, as they are closer to the Steppe
individuals (see Figure 2 of main text) than Aegean EBA individuals, which are closer to
European and Aegean Neolithic. These ADMIXTURE results are also in agreement with
the qpWave/qpAdm analysis, which estimate a Steppe-related ancestry for the Aegean
MBA individuals of up to 50% (Figure 3). Furthermore, these ADMIXTURE results are
consistent with the previously reported Steppe related influence in Europe (Haak et al.,
2015; Olalde et al., 2019), and provide evidence that this was already seen on mainland
Greece by 2,000 BCE.
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