Pax Augusta
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Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes
September 2022 Frontiers in Genetics 13
DOI: 10.3389/fgene.2022.945227
https://www.frontiersin.org/articles/10.3389/fgene.2022.945227/full
Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of preIron Age populations, that should be further investigated.
Discussion
The study of ancient complete mitochondrial genomes from Sicily presented in this paper has generated insight into the diachronic level of population genetic structure of one of the main islands of the Mediterranean Sea. The analysis of mitogenomes from the Mediterranean allowed us to contextualize the Sicilian genetic variation with that of possibly related groups from Early Neolithic to Iron Age. Whereas the comparison with modern Sicilian variation marked the first step towards the understanding the genetic impact of ancient cultures on the modern inhabitants of the Island.
The 36 sequences we analyzed belong to five different archaeological sites, and the haplogroups composition revealed a wide range of variation, even within the same necropolis. The high mitochondrial genetic variation of ancient Sicily is evident also when compared with other ancient European populations, as shown by the PCA in Figure 2B and by MDS plot in Figure 4A. The FST heatmap in Figure 4B further confirms this pattern, highlighting a higher differentiation among Sicilian groups with respect to what is present in other Mediterranean islands (e.g., Sardinia), or in Continental Europe. Indeed, we observed a statistically significant genetic structure within Sicilian groups (AMOVA FST: 0.08947; p-value: 0.00139 + −0.00035) whereas in Sardinia, the other main island in the Mediterranean basin, the genetic differentiation is not significant (AMOVA FST: 0.00158; p-value:0.42158 + −0.00459). The mitochondrial genetic structure we identify in Sicily is in agreement with the documented historical migrations of populations belonging to different cultures, which made the Island a major Mediterranean crossroad for different populations from Europe, North Africa, and the Levant for a long time (Sarno et al., 2017), and deserves to be further investigated. It also supports that these cultural exchanges were actually accompanied by movements of people, with a possible following exchange of genes.
The eleven individuals sequenced in the necropolis of Motya clustered in two different subgroups, with the three individuals attributed to the Phoenician culture that genetically clustered together and separated from the Bronze Age samples from the same necropolis. These three samples also show similarities with the Phoenician individual from Lilibeo, whose sampling location in the main Island postulates a migration between the two areas or a recent shared ancestry, and further confirms the Phoenician presence within the island of Motya. Another noteworthy pattern of genetic similarities come from the analysis of Baucina and Polizzello samples. In Baucina the individuals have been attributed to the Sicanian culture (26 individuals) and to the Greek culture (3 individuals); the haplogroups compositions and the FST heatmap (Figures 2, 4) actually show the presence of genetic differentiation between these two groups, thus reflecting their different cultural attribution. The observed genetic structure within the Baucina settlement could suggest that a certain social and ethnic distinction was maintained during the Greek colonization. This scenario is also supported by the archaeological records that show a strong Hellenization of the settlements and necropolises starting from the second half of the sixth century BCE, as a consequence of the arrival and establishment of Greeks in the region living alongside the local people (Lyons, 1996; Morgan, 1999).
As highlighted in Figures 2B, 4A, the Sicanians of Baucina show rather more genetic links with the Iron Age samples from Polizzello (Diroma et al., 2021), coming from a necropolis located in the heart of Sicania, and dated ninth-seventh century BCE, than with their Greek neighbors. The genetic closeness of mitochondrial genomes of Sicanians from Baucina and Iron Age indigenous from Polizzello may support the attribution of Polizzello individuals to the Sicanian culture (de Miro, 1988). Additionally, these results reveal a certain genetic homogeneity of the inhabitants of central and western Sicily associated with the same culture.
When ancient Sicilians were contextualized within the Mediterranean domain, we did not find any genetic link between Sicanians individuals (both from Baucina and Iron Age Polizzello) and other Iberian populations. Fernandes et al. (2020) identified Iberia as a key ancestry source for Bronze Age people of Sicily, but the explicit demographic analyses of Sicanian sequences show that this ancestry may not be directly linked to the origin of the Sicanian culture, as originally postulated by Thucydides (VI, 2, 2). The resemblance between Iberia and Sicily seems instead to trace back to Late Neolithic, as emerging also from the low FST values reported in Figure 4B. Our inferential model-based analysis through Approximate Bayesian Computation further supports these results, favoring a local development of Sicanian individuals with a genetic continuity in Central/Western Sicily at least since the Early Bronze Age. Bearing in mind that we are only considering the evolution of the maternal lineage and cannot test other models that may be compatible with the observed genetic variation (such as demographic scenarios that account for sex-biased migrations), our model-based analysis still represents a first step toward a comprehensive and inferential reconstruction of past evolutionary and demographic dynamics in Sicily.
Another interesting similarity pattern came from the Phoenicians in Motya, that showed large resemblance with Levant Late Bronze Age, and the highest FST values (about 0.3) with Phoenicians from Iberian islands. Among the haplogroups identified in the new sequenced samples the most notable is undoubtedly the L3, currently present at high frequency in Northeast Africa (Soares et al., 2012). This L3 sequence found in a Bronze Age individual of Motya explicitly confirmed that the widespread human mobility from North Africa to Europe during the Chalcolithic and Bronze Age, involved also the most remote part of the Island, as emerged also in Fernandes et al. (2020).
Finally, we compared the ancient Sicilian genetic structure with that of modern individuals with known Sicilian ancestry, coming from nine cities around the Island. From the comparison of frequency distribution of mitochondrial haplogroups of ancient and modern Sicilian populations, as well as from the structure emerging from the PCA of Figure 5, we cannot exclude the possibility that Bronze/Iron Age Sicilians made a modest ancestry contribution to modern Sicilians, at least for the maternal lineage. The Y chromosome variation, indeed, has proven to overlap between current and Bronze Age inhabitants of Sicily (Fernandes et al., 2020), postulating a different demographic and evolutionary history for the females and males inhabitants of the Island. A more comprehensive analysis of sex biased processes and of the underlying demographic and evolutionary forces would benefit from an increased and extensive sequencing of modern populations, that would allow to perform explicit comparison between continuity/isolation models from Bronze Age to current time. While our data are indeed consistent with a nearly complete replacement (at least for the mitochondrial lineage) of the pre-Iron Age populations of Sicily by modern inhabitants of the Island, we cannot exclude the hypothesis that locally we may still find a degree of continuity that deserves to be investigated.
This study is restricted to the analysis of a uniparental marker, the mitochondrial genome. Focusing on this marker gave us the opportunity to extend the sampling and the sequencing to a higher number of individuals, so as to adequately representing different cultures dwelling in Sicily in different time periods, and allowing us to identify a structured genetic variation and quantify genetic distances among groups. Albeit limited to the maternal lineage, the present study indeed emphasizes the complex genetic scenario of Sicily since its colonization. The structured genetic variation in culturally defined groups actually supports that cultural processes and exchanges within the Island have been accompanied and promoted by movement of people, and that these dynamics left a footprint on the genetic background of ancient individuals. Modern populations present a rather different pattern of maternal genetic variation; the more homogeneous composition of contemporary uniparental gene pool within Sicily (also reported by Sarno et al., 2014) points towards a recent genetic replacement of pre-Iron Age populations that should be further explicitly addressed.
We acknowledge that the amount of genetic information as well as the inferential power of this uniparental marker is limited with respect to genome-wide ancient DNA data. The analysis of whole-genome variation of different ancient populations from Sicily would provide a more accurate and comprehensive source of information to make inference about past dynamics, such as the time and the origin of principal migration events within the island, the extent of genetic links among contemporary and diachronic groups, and will allow us to explicitly test the hypothesis of a genetic turnover within the island in the last two to three thousand years.
