|
|
Post by Admin on May 3, 2021 21:18:08 GMT
 Figure S1 Images of archaeological site Elati-Logkas (Log02, Log04), related to Table 2 and Document S1 (A) Elati-Logkas, view of the cemetery with burials covered by stones known as “periboloi.” (B) Elati-Logkas, Burial 80.1 (Log04) is a pit-grave in the circumference of an inner enclosure built from rough stones. The buried individual was in crouched position lying to the left side, with the hands bent and the palms supporting the skull. Inside the same walls, four other similar burials were excavated with no grave goods apart from only one flint stone blade in tomb 80.5. (C) Elati-Logkas, Burial 22.1 (Log02) is the main among three pithos-inhumations and one secondary burial inside the “peribolos 22.” The grave itself is bordered by rough stones, with the buried individual laid on a ceramic “stretcher.” Several vertical lines are still visible on the skeletal remains. The individual of the burial 22.1 was found in a supine position with the hands crossed on the abdomen, the legs bent in a crouched position to the left, and the skull turned to the right side. There were no grave goods found in the burial 22.1. Photo credits: Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture, Greece. Courtesy of Dr. Georgia Karamitrou-Mentessidi. Six ancient Aegean whole genomes The resulting depth of coverage for the Aegean BA genomes ranged between 2.6× and 4.9× (average: 3.7×) (Tables 2 and S1; and STAR Methods). The number of SNPs covered by at least one read is considerably higher for the six Aegean BA genomes than for the Aegean BA SNP capture data from Lazaridis et al., 2017 when considering the “1240K” SNP capture set (Mathieson et al., 2015) but also across an “intergenic region” SNP set defined in this study (Figure S2A). The latter includes ∼5,270,000 SNP sites located at least 20 kb away from annotated genes and CpG islands (STAR Methods). Note that whole genomes from the populations studied hereafter have more low frequency variants in the intergenic regions than were detected in the 1240K SNP set for the same regions (Figure S2B). This likely owes to the SNP ascertainment scheme in the latter (Clark et al., 2005).  Figure S2 Comparison of SNP capture and WGS data, related to Figure 4 and Tables 2 and S1 (A) Number of single nucleotide polymorphisms (SNPs) in the nuclear genomic data from this study (WGS data) in comparison with previously published BA genomic data from the Aegean. The number of covered SNPs across BA Aegeans based on two SNP sets are shown. On the left: the number of SNPs based on the 1240K SNP set (Dataset I) defined by the array used in Lazaridis et al., 2017 to enrich the libraries. On the right: the number of SNPs based on the intergenic regions defined for the ABC-DL analysis below (Dataset IV, STAR Methods). The green box plots (median indicated by a horizontal line and interquartile range indicated by the box) correspond to the number of SNPs among the BA Aegean data from present-day Greece (Lazaridis et al., 2017); the blue box plots correspond to the number of SNPs among the whole genome sequence (WGS) data from this study. (B) One-dimensional Site Frequency Spectrum (SFS) for the seven whole genomes used for demographic analyses (ABC-DL). The seven genomes included here are: Mik15 and Log04 from this study, YamnayaKaragash_ EBA (3,018-2,887 BCE) (de Barros Damgaard et al., 2018), KK1 (CHG; 7,745-7,579 BCE) (Jones et al., 2015), Bar8 (Neolithic Barçın; 6,122-6,030 BCE) (Hofmanová et al., 2016), Sidelkino (EHG; 9,386-9,231 BCE) (de Barros Damgaard et al., 2018), and S_Greek-1 (SAME3302732; modern Greek from Thessaloniki) (Mallick et al., 2016).STAR Methods In blue ("WGS") the SFS for the regions included in Dataset IV (STAR Methods). In red ("1240K") the SFS for the regions in Dataset IV restricted to the sites overlapping with the SNPs included in the 1240K array. We observed typical ancient DNA damage patterns at the 5′ and 3′ termini of the DNA fragments, as well as short sequence reads (average length between 49.9 and 74.3 bases across genomes, after adaptor removal and mapping), attesting to the authenticity of the ancient data (Figure S3; STAR Methods). Across individuals, contamination rate estimates ranged between 0.6% and 1.1%, and between 0.01% and 1.49% when estimated using the X chromosome and mtDNA, respectively (Table 2).  Figure S3 Error rates, damage, and read length distributions for the WGS and nuclear capture data from this study, related to Figure 1 and Tables 2 and S1 (A) Error rate for whole genome sequencing before (lighter colors) and after (darker colors) trimming 5 bp from the extremities of the reads. Log02 was USERTM-treated. (B) Error rate for nuclear capture data for different mutation types. Columns 1 and 2 show transitions and column 3 shows transversions. (C) Read length distribution for whole genome sequencing. (D) Read length distribution for nuclear capture data. (E) Post-mortem damage pattern for whole genome sequencing (C to T and G to A substitutions). Dashed lines indicate partial data removal resulting from trimming 5 bp from the extremities of the reads. The color of each curve indicates the analyzed sample according to panel A. Log02 (dark green curve) was USERTM-treated. (F) Post-mortem damage pattern for nuclear capture data. Curves are colored according to panel B. See STAR Methods for details. |
|
|
|
Post by Admin on May 3, 2021 22:54:23 GMT
Population structure and demographic history Genomic homogeneity across the Aegean during the EBA despite distinct cultural backgrounds The overall genome-wide genetic relationship of the Aegean BA individuals was studied in the context of ancient and present-day Eurasian populations (STAR Methods). Despite their distinct cultures, the EBA Helladic, Cycladic, and Minoan genomes resemble one another in all analyses. Outgroup f3-statistics of the form f3(Yoruba;Y,X), where X is one of the present-day populations included in Dataset I (STAR Methods) and Y the ancient individuals from this study, show that the Helladic-Manika-EBA, Minoan-Petras-EBA, and Cycladic-Koufonisi-EBA have a similar profile, which contrasts with the Helladic-Logkas MBA. EBA Aegeans have higher genetic similarity with present-day southern Europeans, particularly present-day Sardinians (Figure S4). In the classical multidimensional scaling (MDS) analysis, the projected genetic dissimilarities between pairs of individuals estimated by an identity-by-state distance matrix in two dimensions (STAR Methods) show that the four EBA individuals (Mik15, Pta08, Kou01, Kou03) and the two MBA individuals (Log02 and Log04) form two groups (Figure 2) in agreement with the f3 profiles. In line with the results above, ancestry proportions estimated by ADMIXTURE for K > 2 using Dataset II (Table S2; STAR Methods) suggest that the EBA Aegeans are genetically similar to one another and distinct from the MBA Aegeans (Figures 3 and S5).  Figure S4 Genetic affinities between Neolithic, BA, and present-day Aegeans compared to other present-day Eurasian populations, related to Table 1 f3-statistics of the form f3(Yoruba; Y, X): Y corresponds to either Neolithic Anatolians or Greeks, Minoan-Petras-EBA individual from the island of Crete (Pta08), the Cycladic-Koufounisi-EBA individuals (Kou01, Kou03), the Helladic-Manika-EBA individual from the island of Euboea (Mik15), the Helladic-Logkas-MBA individuals from northern Greece (Log02, Log04), previously published BA Aegeans (Mycenaeans and Minoans), and present-day Greeks (incl. Cretans), Cypriots, while X are other present-day populations from Dataset I (Lazaridis et al., 2014, Lazaridis et al., 2016, Lazaridis et al., 2017) (STAR Methods). For clarity, we only show results for west Eurasian and north African populations and cap f3 values below 0.15. For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y). Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y (bars represent ~1.95 standard errors). In agreement with MDS and ADMIXTURE analyses, we observed that ancient and present-day Anatolians and Greeks share the most genetic drift with present-day central and southern European populations.  Figure 2 Multidimensional scaling analysis (MDS) Included are the six Aegean Bronze Age individual samples from the present study, 259 ancient genomes, and 638 modern individuals (gray shapes) of Eurasian ancestry (Table S2; STAR Methods). Population labels are given in Table 1.  Figure 3 ADMIXTURE analysis for modern and ancient Eurasian individuals Shown are a subset of individuals for K = 3, which has the lowest cross validation error (CV = 0.974). Results for the full dataset and statistical support are shown in Figure S5. The six BA individuals whole genome sequenced in this study are highlighted with an asterisk. Abbreviations for chronological periods and population names are given in Table 1.  Figure S5 ADMIXTURE analysis using ancient and modern populations with the number of ancestry components ranging from K = 2–6 and cross-validation error, related to Figure 3, Table 1, and Document S1 (A) For this analysis we consider a total of 969 individuals (638 modern and 331 ancient) and 165,447 SNPs (Dataset II, STAR Methods). Each bar represents one individual. Individuals from the same population were grouped. For all K > 2, red represents the component mostly present in “European Neolithic-like,” light blue in “Neolithic Iran/Caucasus HG-like” and orange for “European HG-like.” (B) Cross-Validation error (CV error) for K ranging from 2 to 6. The CV-error is plotted for the ten runs for each value of K (STAR Methods). Compared to other ancient Eurasian populations, the EBA Aegeans are similar to other Aegean BA and Anatolian populations, but are quite distinct from all Balkan populations. For instance, in the MDS analysis, they fall within or near Minoan-Lasithi-MBA, Mycenaean-Peloponnese-LBA, and Anatolian populations such as Anatolia_Tepecik_Ciftlik (Figure 2). Similarly, in the ADMIXTURE analysis, the EBA Aegeans show similar ancestry proportions to other Aegean populations, such as the Minoan-EMBA and Anatolia_Kumtepe, as well as Anatolian populations spanning the Chalcolithic and the EMBA (e.g., Anatolia_ChL, Anatolia_BA) (Figure 3). The genomic EBA homogeneity across cultures in the Aegean and parts of Anatolia may indicate that Aegean populations used the sea as a route to interact not only culturally but also genetically. This could have been the result of an intense network of communication in the Aegean, which has been well documented on the archaeological level and has been dubbed the “International Spirit of the Aegean” (Renfrew, 1972). Moreover, given the high similarity between Minoan-Petras-EBA and the Cycladic-Koufonisi-EBA, the genomic data also informs debates related to the formation of colonies from the Cycladic islands to Crete (Doumas, 2010; Papadatos, 2007). |
|
|
|
Post by Admin on May 4, 2021 3:01:16 GMT
Ancestry components of EBA Aegeans indicating gene flow from a source related to the CHG during the Neolithic
ADMIXTURE results indicate that the EBA Aegean population consists mostly of an ancestry component shared with Neolithic Aegeans (accounting for >65%), whereas most of the remaining ancestry can be assigned to Iran Neolithic/Caucasus HG-related populations (17%–27%) (Figure 3). These results were replicated with qpWave/qpAdm (STAR Methods) using Dataset I (Tables 3 and S3). When considering early Neolithic populations and HG populations as potential sources, EBA individuals were in general found to be consistent with the majority of their ancestry deriving from populations related to Anatolia_N (∼69%–84%) (Table 3). This suggests that the people behind the Neolithic to BA transition largely had ancestors from the preceding Aegean farmers, in line with archaeological theories for the EBA transformation (Dickinson, 2016; Renfrew, 1972; Tsountas and Manatt, 1897) (Document S1). The second component in qpWave/qpAdm could be assigned to Iran_N/CHG-related populations (∼16%–31%) (Table 3). In line with this result, in the MDS analysis (Figure 2), the Aegean EBA individuals are on an axis connecting Neolithic Aegeans to the Iran Neolithic/Caucasus HG (“Caucasus-axis”).
Table 3 qpWave/qpAdm admixture models
Period Test Ref1 Ref2 Ref3 Mixture Prop. Ref1 ± SE Mixture Prop. Ref2 ± SE Mixture Prop. Ref3 ± SE p value
EBA Kou01 Anatolia_N CHG 0.75 ± 0.03 0.25 ± 0.03 0.67
Kou01 Anatolia_N Iran_N 0.75 ± 0.03 0.25 ± 0.03 0.90
Kou03 Anatolia_N CHG 0.69 ± 0.03 0.31 ± 0.03 0.10
Mik15 Anatolia_N CHG 0.84 ± 0.03 0.16 ± 0.03 0.08
Mik15 Anatolia_N Iran_N 0.84 ± 0.03 0.16 ± 0.03 0.07
Pta08 Mik15 Iran_N 0.98 ± 0.03 0.02 ± 0.03 0.09
Pta08 Mik15 CHG 0.99 ± 0.03 0.01 ± 0.01 0.07
Kou01 Anatolia_N CHG EHG 0.74 ± 0.04 0.25 ± 0.03 0.01 ± 0.02 0.67
Kou01 Anatolia_N Iran_N EHG 0.74 ± 0.03 0.24 ± 0.03 0.02 ± 0.02 0.88
Kou03 Anatolia_N Iran_N EHG 0.67 ± 0.03 0.25 ± 0.03 0.08 ± 0.02 0.82
MBA Log02 Kou01 EHG 0.81 ± 0.02 0.19 ± 0.02 0.07
Log02 Kou03 WHG 0.91 ± 0.02 0.09 ± 0.02 0.06
Log02 Anatolia_N Balkans_LBA CHG 0.22 ± 0.05 0.65 ± 0.06 0.12 ± 0.04 0.08
Log02∗ Kou01 Steppe_MLBA 0.61 ± 0.03 0.39 ± 0.03 0.20
Log02∗ Kou01 Europe_LNBA 0.56 ± 0.04 0.44 ± 0.04 0.05
Log04 Kou01 Balkans_LBA 0.21 ± 0.06 0.79 ± 0.06 0.08
Log04 Kou03 Balkans_LBA 0.26 ± 0.07 0.74 ± 0.07 0.07
Log04 Mik15 Balkans_LBA 0.21 ± 0.06 0.79 ± 0.06 0.06
Log04 Anatolia_N CHG EHG 0.58 ± 0.03 0.16 ± 0.03 0.27 ± 0.02 0.12
Log04∗ Anatolia_N Steppe_EMBA 0.53 ± 0.03 0.47 ± 0.03 0.35
Log04∗ Anatolia_N Steppe_MLBA 0.38 ± 0.03 0.62 ± 0.03 0.13
Log04∗ Pta08 Balkans_LBA 0.15 ± 0.04 0.85 ± 0.04 0.06
Log04∗ Pta08 Steppe_MLBA 0.44 ± 0.03 0.56 ± 0.03 0.36
LBA Mycenaean Log04 Minoan_Lasithi 0.36 ± 0.04 0.64 ± 0.04 0.35
Mycenaean Log04 Minoan_Odigitria 0.21 ± 0.04 0.79 ± 0.04 0.45
Mycenaean Anatolia_N Kou03 0.37 ± 0.09 0.63 ± 0.09 0.40
Present-day Crete Log02 Iran_N 0.82 ± 0.04 0.18 ± 0.04 0.08
Cypriot Pta08 CHG Villabruna 0.64 ± 0.02 0.32 ± 0.02 0.04 ± 0.01 0.31
Cypriot Pta08 CHG WHG 0.65 ± 0.02 0.32 ± 0.02 0.03 ± 0.01 0.23
Greek Log02 EHG 0.93 ± 0.02 0.07 ± 0.02 0.16
Greek Log02 MA1 0.96 ± 0.02 0.04 ± 0.02 0.10
Greek Log02 Kostenki14 0.93 ± 0.02 0.07 ± 0.02 0.07
For a test population, the estimated admixture proportions (±1 standard error, SE) for n = 2 or n = 3 source populations (Ref1, Ref2, and Ref3) are shown. Ancestry was inferred from both “ultimate” sources representing the earliest populations, and “proximate” sources (row labeled with a ∗ symbol) representing populations down to the Bronze Age (STAR Methods). Only a subset of the results with p values ≥0.05 are depicted. See also Tables 1 and S3.
To further test for gene flow events from outside of the Aegean, D-statistics were computed. In particular, we tested whether an H3 population (e.g., Iran_N or CHG—the blue component in ADMIXTURE) (Figure 3) shares more alleles with H1 = Anatolia_N (D > 0) or with Aegean/Anatolian populations from different time periods (H2 = Greece_N, BA Aegeans/Anatolians, present-day Greeks and Cypriots) (D < 0), using the ancient Ethiopian Mota (Gallego Llorente et al., 2015) as an outgroup D(Anatolia_N, H2; H3, Mota) (Figure S6). The EBA Aegean genomes were found to be similar to one another. Although EBA Aegeans carry the “Iran Neolithic/Caucasus HG-like” component in other analyses (e.g., Figure 3), no statistically significant evidence for gene flow from Iran_N or CHG was detected. However, a visible trend suggests that Aegeans dating to ∼4,000 BCE onward (from Anatolia_ChL to Mycenaean) share more alleles with Iran_N/CHG than with Anatolia_N (Figure S6). This trend is replicated in the ADMIXTURE results (Figure 3), where small proportions of CHG-like components were observed from the Neolithic onward in individuals on both sides of the Aegean and in Anatolia but not in the Balkans. This CHG-like component increases in frequency during the early Neolithic in Anatolia (e.g., Boncuklu, Tepecik-Ciftlik) (Kılınç et al., 2016), the late Neolithic in the Aegean (e.g., Greece_N) (Hofmanová et al., 2016; Omrak et al., 2016), and during the BA in Anatolia (Anatolia_BA) (Lazaridis et al., 2017). This is not seen in the Balkans, where the transition from Neolithic to BA is mostly associated with an increase in “European HG-like” ancestry (Figure 3).
|
|
|
|
Post by Admin on May 4, 2021 5:53:57 GMT
 Figure S6 Exploring differential allele-sharing in Aegean/Anatolian populations through time with D-statistics, related to Table 1 D-statistics of the form D(Anatolia_N, H2; H3, Mota) were computed, testing whether Anatolia_N (H1), or ancient/modern Anatolian and Aegeans (H2) share more alleles with CHG, Iran_N, EHG, or Steppe_EMBA (H3, STAR Methods). For this analysis, the genome of an Ethiopian individual (Mota) was used as an outgroup. Points represent D-statistics, and horizontal error bars represent ~3.3 standard errors (SE corresponding to a p-value of ~0.001 in a Z-test). Vertical bars represent upper and lower bounds of the dates available for the populations. In this figure, the populations are ordered chronologically, using either radiocarbon dates (when available) or dated archaeological context. Horizontal dashed lines indicate time periods. Vertical dashed lines mark the zero. A value of D = 0 indicates no gene flow or ancestral population structure (Durand et al., 2011), thus H1 and H2 are symmetrically related to H3 and Mota. In this case, D < 0 would indicate potential gene flow between H3 and H2, and D > 0 would indicate potential gene flow between H3 and H1. Abbreviations for chronological periods and population names are given in Table 1. To compare competing scenarios, and to infer the mode and tempo of potential gene flow events into the Aegean while accounting jointly for the population history of Neolithic, BA, and present-day populations from Greece, we performed ABC-DL (Mondal et al., 2019) (Document S1; STAR Methods). To determine the relationship between HG and Aegean Neolithic, we first contrasted 3-leaf models (Figure 4A; Table S4) of the three ancestral populations: CHG, EHG, and Aegean Neolithic. In this analysis, the 3-leaf model (EHG, CHG, and Aegean Neolithic) had the greatest posterior probability (P(M|D) = 0.999). This result is in agreement with Jones et al., 2015, who found a closer relationship between CHG and “Early Farmer” from Stuttgart, than with WHG. We used this tree for the more complex 7-leaf models (Figure 4B; Table S4). In line with all of the above results, 7-leaf models without a CHG-like pulse of gene flow (models B1, B2, and B3) (Figure 4B) were associated with lower posterior probabilities (0.000–0.014). In contrast, a model including such gene flow, estimated at 16% (0.2%–29%, 95% highest posterior density interval) (Table S4) at ∼5,700 BCE (8,299–2,881 BCE, 95% highest posterior density interval) (Table S4) was assigned much higher support (posterior probability of 0.98 for model B4) (Document S1; STAR Methods). Taken together, these results suggest that a population related to the Caucasus HG had either directly influenced the Aegean through migration, or a CHG-like component was indirectly introduced through exchanges with Neolithic Anatolian populations.  Figure 4 Model comparison in ABC-DL analysis (A) Posterior probabilities P(M|D) of different 3-leaf models (models A1–A4) calculated with ABC-DL to establish the topology of the three ancestral populations: CHG, EHG and Aegean Neolithic. (B) Seven-leaf demographic models (models B1–B6) extending the tree from (A) with the highest posterior probability, each including Neolithic, EBA and MBA Aegeans, present-day Greeks, CHG, EHG, and Pontic-Caspian Steppe_EMBA populations. Yellow (EHG-like), light blue (CHG-like), and dark blue (Steppe-like) arrows indicate a single pulse of gene flow from simulated “ghost” populations diverged from EHG, CHG, and Steppe_EMBA. Posterior probabilities are listed below each schematic topology (Document S1; STAR Methods). See also Figure S2 and Tables 1 and S4. |
|
|
|
Post by Admin on May 4, 2021 20:23:41 GMT
Unlike for most European populations, little EHG contribution is seen during the EBA
In central, western, and northern BA Europe, the CHG component is generally accompanied by an EHG component (Allentoft et al., 2015; Haak et al., 2015; Jones et al., 2015) – which would be expected to appear in similar proportions if transmitted through Steppe-related populations (de Barros Damgaard et al., 2018). In contrast, EBA Aegeans carry little to no EHG ancestry. Based on the D-statistics analysis, we cannot reject that most EBA Aegean genomes and Anatolia_N are equally close to EHG (Figure S6). Moreover, when considering three potential sources in qpWave/qpAdm, EBA individuals carry only ∼1%–8% EHG versus 24%–25% CHG ancestry (i.e., substantially less EHG ancestry) (Table 3). This is further supported by ADMIXTURE results (Figure 3), indicating that changes from Neolithic to EBA were mostly associated with increases in IranN/CHG-like ancestry in the Aegean and Anatolia, whereas the Balkans and the rest of Europe were mostly associated with increases in EHG-like ancestry (Figure 3). Finally, all ABC-DL models including an EHG pulse into the ancestor of EBA Aegeans (models B5 and B6) (Figure 4) have negligible posterior probability support (0.000–0.002). Taken together, these results suggest little influence of populations related to EHG during the EBA in the Aegean, further implying that the Caucasus component arrived in the Aegean independently.
Genomic heterogeneity during the Aegean MBA, likely owing to gene flow from a Steppe-like population prior to 2,000 BCE
Considerably more population structure is observed in the Aegean during the MBA compared to the EBA. MBA individuals from northern Greece are quite distinct from the EBA Aegeans, as can be seen across all analyses. For example, in the f3 analysis, unlike the EBA Aegeans, they are equally distant to a much larger set of populations across Europe (Figure S4). In MDS (Figure 2) and ADMIXTURE (Figure 3) analyses, they form a separate group distinct from the EBA Aegeans, sharing the same components as the present-day Greeks. In contrast, the Minoan-Lasithi-MBA are very similar to the EBA Aegean populations (Figures 2 and 3).
The primary feature distinguishing the Helladic-Logkas-MBA from the contemporary Minoan-Lasithi-MBA, as well as from the EBA populations, is the higher proportion of “European HG-like” ancestry. For instance, in ADMIXTURE, the “European HG-like” component accounts for 26%–34% of the overall Logkas ancestry, more than four times greater than the 2%–6% found in the Aegean EBA individuals (Figure 3). Similarly, in qpWave/qpAdm, a Helladic-Logkas-MBA individual (Log04) was consistent with a 3-way admixture model, deriving ∼58% of her ancestry from Aegean Neolithic populations; the remaining ancestry can be attributed to CHG-like and EHG-like sources (accounting for ∼16% and ∼27%, respectively)—that is, having a much greater contribution from EHG as compared to the EBA Aegeans (Table 3). Because EHG and CHG are the major components of Steppe-related populations (e.g., Steppe_EMBA with 66% EHG-like and 34% IranN/CHG-like0 (Figure 3), consistent with previous results (de Barros Damgaard et al., 2018), this supports the hypothesis that populations from the Pontic-Caspian Steppe contributed to the ancestry of the Helladic-Logkas-MBA individuals. This combined ancestry has been observed in central, western, and northern BA Europeans and interpreted as the result of a “massive” Steppe migration (Allentoft et al., 2015; Haak et al., 2015; Jones et al., 2015; Mathieson et al., 2018; Olalde et al., 2019). Our ADMIXTURE estimates are consistent with an increase of EHG components in the Late Neolithic and EBA in most regions of Europe, including in the Balkans (Figure 3; Document S1). Yet, in Anatolia, such an increase in EHG-like ancestry is residual, and in the Aegean, it is only seen later in the MBA (Helladic-Logkas-MBA) and LBA (Mycenaean) individuals, suggesting a later arrival of Steppe-related ancestry in the Aegean.
Evidence for such a Steppe contribution is provided, for example, in MDS (Figure 2), where the Helladic-Logkas-MBA fell on a “Steppe-axis” connecting Neolithic Aegeans with Steppe populations. In ADMIXTURE (Figure 3), the Helladic-Logkas-MBA carries similar relative amounts of the “Iran Neolithic/Caucasus HG-like” (∼1/3) and “European HG-like” (∼2/3) components as Steppe_EMBA. Moreover, unlike the Neolithic and the EBA Aegeans and Anatolians, as well as the Minoan-Lasithi-MBA, the Helladic-Logkas-MBA share significantly more alleles with CHG, EHG and Steppe_EMBA compared to Anatolia_N (Figure S6). In addition, the Helladic-Logkas-MBA Log04 individual could also be directly modeled as 2-way admixture (proximate sources) of Anatolia_N (∼53%) and Steppe_EMBA (∼47%), or Anatolia_N (∼38%), and Steppe_MLBA (∼62%), consistent with a strong genetic contribution from the Steppe (Table 3). Furthermore, demographic modeling suggests that gene flow (8%–45%, 95% highest posterior density interval) (Table S4) from a ghost population related to Steppe_EMBA, prior to the MBA split, considerably improves the fit of the model to the data (model B4 versus model B1) (Figure 4B). The timing of such gene flow into the ancestors of the Helladic-Logkas-MBA ought to have occurred by ∼1,900 BCE, based on the radiocarbon dates of the Logkas individuals, and was estimated at ∼2,300 BCE (2,616–2,003 BCE 95% highest posterior density interval) (Table S4) in the ABC-DL analysis. This suggests that a Steppe-like migration wave may have reached the Aegean by the MBA. Because Steppe-related ancestry is essentially absent in Sardinia (Fernandes et al., 2020; Marcus et al., 2020), and because we have no evidence of Steppe-like or EHG-like ancestry among Minoans, this may suggest that Steppe-related populations did not cross the sea during the BA. Supporting this hypothesis, the archaeological record does not indicate that BA populations from the Pontic-Caspian Steppe were sea-faring people (Anthony, 2010).
Note, however, that the Steppe-like ancestry observed in the Logkas individuals may have been brought directly by migrating populations originally from the Pontic-Caspian Steppe or indirectly by populations with substantial Steppe-like gene flow (e.g., Balkans_LBA or Europe_LNBA) (Table 3). Alternatively, the Steppe-like component may have been brought by an unsampled, genetically similar, population (e.g., MBA Balkans). The indirect contribution is supported by ADMIXTURE estimates that suggest an earlier influence of Steppe-related ancestry in the Balkans than in the Aegean (Figure 3), and by qpWave/qpAdm modeling of the MBA Log04 individual as 2-way admixture involving Balkan LBA (Table 3). This finding is consistent with the suggestion of intermittent genetic contact between the Balkans and the Steppe populations during the BA (Mathieson et al., 2018) and is in line with archaeological evidence of cultural contacts between southeastern Europe and the Pontic-Caspian Steppe around 2,500 BCE (Anthony, 2010). This may further be related to previous hypotheses based on both archaeological and linguistic evidence that populations with Steppe-like ancestry contributed to the formation of the Helladic culture (Coleman, 2000) (Document S1).
|
|
