Through 40,000 years of human presence in Southern Europe: the Italian case study

Abstract

The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.

Fig. 1

Ancient Italian individuals discussed in this review. A Geographical location of ancient individuals from Italy and surrounding areas. The Italian ancient individuals are divided into four main categories: Continental Italy (yellow), Peninsular Italy (orange), Sicily (red), and Sardinia (pink); B Principal component analysis (PCA) projecting the ancient Italian individuals onto the genetic variation of present-day individuals (in grey). C Chronological distribution (x-axis) and the number of autosomal SNPs of the ancient Italian individuals (y-axis, proxied by the number of available SNPs from the standard 1240K+HO (Human Origin array) SNP set)

Fig. 2

PCA and outgroup f₃ multidimensional scaling (MDS) for samples dated back to Paleo-Mesolithic (hunter-gatherers) and Neolithic periods (A–D, respectively). Samples were divided into four groups according to their chronological and cultural affiliation and projected onto the genetic variation of modern West Eurasians (left column, panels A, C) along with a number of modern reference samples from neighbouring regions. Samples within the dashed grey polygons were also used to construct a pairwise matrix of outgroup f₃ distances in the form of f₃ (Mbuti; X, Y) on which an MDS was performed, hence providing a complementary visualization to the PCA. The chronological dating, based on mean date BP (before present), was used to color-code the samples (right column, panels B, D)

Fig. 3

PCA and outgroup f₃ multidimensional scaling (MDS) for Bronze and Iron Age samples (A–D, respectively). Samples were divided into four groups according to their chronological and cultural affiliation and projected onto the genetic variation of modern West Eurasians (left column, panels A, C) along with a number of modern reference samples from neighbouring regions. Samples within the dashed grey polygons were also used to construct a pairwise matrix of outgroup f₃ distances in the form of f₃ (Mbuti; X, Y) on which an MDS was performed, hence providing a complementary visualization to the PCA. The chronological dating, based on mean date BP (before present), was used to color-code the samples (right column, panels B, D)

Fig. 4

Derived allele frequencies across the four Italian macro-areas for five genetic variants reported to be the strongest significant signals of selection in (Mathieson et al. 2015). The name of the variant (in bold), the allele for which the genetic frequencies are computed (the derived one), the name of the gene, and the associated function are shown above each plot

Fig. 5

Timeline summarizing the main demographic events experienced by the ancient Italian populations from the Palaeolithic to the Middle Ages. The time range for each period is relative to Italy or, more generally, to Southern Europe