We hypothesize two simple historical scenarios leading to the observed genetic variability across Italy: (a) continuous ancient gene flow amplified by isolation-by-distance in recent times; (b) different ancestral origins of the main Italian macroareas whose distinguishability has been attenuated by genetic exchange in recent times.
Monmonier's algorithm revealed no evidence of the presence of genetic barriers across the peninsula. Instead, results from the Mantel test provide evidence of a correlation between genetics and geographical distance. The observed higher average length of the segments with shared IBD within regions compared with those shared between regions (Supplementary Table S2B) suggests recent isolation-by-distance across the wide range of latitude of the Italian peninsula. Moreover, a North to South gradient of increasing ancestral Ne was inferred for the three main macroareas (Northern, Central and Southern), coinciding with increased heterozygosity in Southern Italy. A similar trend was previously described for the rate of inbreeding and genome-wide similarity across Central Europe, and could be interpreted as a signature of the 'Out of Africa' migration during Palaeolithic expansions from refugia after the ice age and of ancient South-to-North migratory waves that occurred at the times of European colonization by Neolithic farmers. The ancestry and IBD analyses provided evidence of admixture in Italy with three major ancestries detected, most represented in Northern Europeans, Southern Europeans and Middle Eastern, respectively (with a small percentage of a North African component found in South Italy and Sardinia), with different prevalence across the peninsula. None of these components is fixed in any population, meaning that there is a poor fit with a strict admixture model, as assumed by the algorithm used, and supporting a process of continuous gene flow in multiple directions (migratory waves to and from Italy). According to previous studies on the Y chromosome and mtDNA, the Middle Eastern ancestry in Southern Italians most likely originated at the time of the Greek colonization and, with a smaller percentage, of the subsequent Arabic domination, whereas in Central-Northern Italy it is possibly because of the admixture of the indigenous residents with Middle Eastern populations spreading from the Caucasus to Central Europe. Our results agree with previously published reports describing a possible maritime route of colonization across Europe, including Italy, although we cannot exclude the occurrence of more recent demographic events leading to a similar scenario. Finally, the homogenous ancestral effective population size across Italian regions could be interpreted as reflecting common genetic origins, taking also into account previous considerations, although the same results might also occur in comparing populations without common origins.
Our study supports the notion that genetic variability across Italy is likely to represent continuous gene flow leading to differences in the proportion of ancestry from different sources, along with genetic exchange among neighbouring populations (eg, Northern Italian with European countries, Southern Italian with Middle Eastern and North African ones). Previous studies, analysing uniparental markers, found Y-chromosome genetic discontinuity across Italy. This contrasts with a general lack of structure for mitochondrial DNA, and with a higher homogeneity for maternal than paternal genetic contributions, suggesting different demographic and historical dynamics for females and males in Italy.
One issue is that the samples are still unevenly distributed, with a big gap between North-Center and South — which is reflected in the PCAs — and almost nothing from the eastern part of the country. (Note: the genetic gap between Aosta Valley and its very close neighbor regions is due to some of it being ethnically French).
This time they do include a few Iberians for comparison, and that's who Northern Italians cluster with. But besides a few Cypriots, there are still no Greeks, which Paschou et al. (2014) and many other studies show Southern Italians clustering with. Sardinians, as always, are the closest to Ötzi the Iceman.
Fiorito et al. "The Italian genome reflects the history of Europe and the Mediterranean basin". Eur J Hum Genet, 2016.