Genetic history of Italy
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The genetic history of the Italians is greatly influenced by geography and history. The ancestors of Italians are identified as Italic peoples (of which the most notable are the Latins/Romans but also Umbrians, Sabines and others) and it is generally agreed that the invasions that followed for centuries the Fall of the Roman Empire did not significantly alter their gene pool because of the relatively small number of Germanic or other migrants compared to the large population of what constituted Roman Italy.
Multiple DNA studies confirmed that genetic variation in Italy is clinal going from the Eastern to the Western Mediterranean (with Sardinians as outliers) and that all Italians are made up of the same ancestral components, but in different proportions, related to Mesolithic, Neolithic and Bronze Age settlements of Europe. In their admixture ratios all Italians are similar to other Southern Europeans and that is being of Early Neolithic Farmer ancestry. The only exception are certain northeastern Italian populations who cluster with Germanic and Slavic speaking Central Europeans.
There is a noticeable genetic difference between the Northern Italians and Southern Italians, with the former being close to the French population, while the latter overlap with both Balkan and other southern European populations. Yet, the genetic distance between Northern and Southern Italians, although pretty large from a single European 'nationality' point of view, is only roughly equal to the one between Northern Germans and Southern Germans. The genetic gap between Northern and Southern Italians is filled by an intermediate Central Italian cluster, creating a continuous cline of variation down the peninsula and the islands (with Sardinians as outliers) that mirrors geography.
Molecular anthropology found no evidence of significant Northern geneflow into the Italian peninsula over the last 1500 years. On the other hand, the bulk of Italian ethnogenesis occurred prior to Germanic or non European invasions. Dna studies show that only the Greek colonization of Sicily and Southern Italy had a lasting effect on the local genetic landscape.
Historical population of Italy
Modern man appeared during the Upper Paleolithic. Specimens of Aurignacian age were discovered in the cave of Fumane and dated back about 34,000 years ago. During the Magdalenian period the first men from the Pyrenees populated Sardinia.
During the Neolithic farming was introduced by people from the east and the first villages were built, weapons became more sophisticated and the first objects in clay were produced. In the late Neolithic era the use of copper spread and villages were built over piles near lakes. In Sardinia, Sicily and part of Mainland Italy the Beaker culture spread from Western Europe.
During the Late Bronze Age the Urnfield or Villanovan culture appeared in Italy, characterized by the typical rite of cremation of dead bodies originating from Central Europe, and the use of iron spread. In Sardinia the Nuragic civilization flourished.
From the 8th century BC, Greek colonists settled on the southern coast and in Sicily and founded cities, initiating what was later called Magna Graecia. The Etruscan civilization developed on the coast of Tuscany and Latium. In the 5th century Celtic tribes from continental Europe settled in Northern Italy and parts of Central Italy. With the fall of the Western Roman Empire, different populations of German origin invaded Italy, the most significant being the Lombards.  Iapygian tribes, possibly Illyrian, populated Apulia.
Y-DNA genetic diversity
The majority of Italians, Sicilians and Corsicans belong to Haplogroup R1b, common in Western and Central Europe. The highest frequency of R1b is found in Garfagnana (76.2%), Tuscany. This percentage lowers at the extreme south of Italy in Sicily (34%). On the other hand, the majority of Sardinians belong to Mesolithic European haplogroup I2a1a.
A study from the Università Cattolica del Sacro Cuore found that while Greek colonization left little significant genetic contribution, data analysis sampling 12 sites in the Italian peninsula supported a male demic diffusion model and Neolithic admixture with Mesolithic inhabitants. The results supported a distribution of genetic variation along a North-South Axis and supported demic diffusion. South Italian samples clustered with South east and south central European samples, and Northern groups with West Europe.
A 2004 study by Semino et al. contradicted this study, and showed that Italians in North-central regions had a higher concentration of J2 than their Southern counterparts. North-central had 26.9% J2, whereas Calabria (a far Southern region) had 20.0%, Sardinia had 9.7% and Sicily had 16.7%.
Y-DNA introduced by historical immigration
The so-called barbarian migrations that occurred on Italian soil following the fall of the Western Roman Empire have probably not significantly altered the gene pool of the Italian people. These migrations generally consisted of relatively small groups of people that either did not remain on the peninsula or settled in densely populated areas of Italy, therefore becoming genetically diluted and assimilated into the predominant genetic population within a relatively short amount of time. Despite the lengthy Goth and Lombard presence in Italy, the I1 haplogroup associated with the Norsemen is present only among 6-7% of mainland Italians, peaking at 11% in the northeast (20% in Udine and 30% in Stelvio). An average frequency of 5% I1 has been detected in Sicily, 8% in the western part and 2% in the eastern.
In two villages in Lazio and Abruzzo (Cappadocia and Vallepietra) I1 was recorded at levels 35% and 28%. In Sicily, further migrations from the Vandals, Normans and Saracens have only slightly affected the ethnic composition of the Sicilian people. However, Greek genetic legacy is estimated at 37% in Sicily. Norman civilization proliferated for several centuries on the island, with a strong impact on the culture of the place and different populations as Normans, Bretons, Anglo-Saxons, Swabians and Lombards have repopulated the island with a male contribution, e.g. 8% haplogroup I1.
The Norman Kingdom of Sicily was created in 1130, with Palermo as capital, and would last until 1198. Nowadays it is in north-west Sicily, around Palermo and Trapani, that Norman Y-DNA is the most common, with 8 to 15% of the lineages belonging to haplogroup I. In the thirteenth century Frederick II turned against the Muslims in Sicily (during the preceding century most had converted to Catholicism) and between 1221 and 1226 he moved all to the city of Lucera in Puglia. Ultimately, the North African male contribution to Sicily was estimated between 6% and 7.5%. Overall the estimated Balkan and North Western European paternal contributions in South Italy and Sicily are about 63% and 26% respectively.
A 2015 genetic study of six small mountain villages in eastern Lazio and one mountain community in nearby western Abruzzo found some genetic similarities between these communities and Near Eastern populations, mainly in the male genetic pool. The Y haplogroup Q, common in Western Asia and Central Asia, was also found among this sample population, suggesting that in the past could have hosted a settlement from Central Asia. But Q-M242 is distributed across most European countries at low frequencies, and the frequencies decrease to the west and to the south.
Genetic composition of Italians mtDNA
In Italy as elsewhere in Europe the majority of mtDNA lineages belong to the haplogroup H. Several independent studies conclude that haplogroup H probably evolved in West Asia c. 25,000 years ago. It was carried to Europe by migrations c. 20–25,000 years ago, and spread with population of the southwest of the continent. Its arrival was roughly contemporary with the rise of the Gravettian culture. The spread of subclades H1, H3 and the sister haplogroup V reflect a second intra-European expansion from the Franco-Cantabrian region after the last glacial maximum, c. 13,000 years ago.
African Haplogroup L lineages are relatively infrequent (less than 1%) throughout Italy with the exception of Latium, Volterra, Basilicata and Sicily where frequencies between 2 and 3% have been found.
A study in 2012 by Brisighelli "et al." stated that an analysis of ancestral informative markers "as carried out in the present study indicated that Italy shows a very minor sub-Saharan African component that is, however, slightly higher than non-Mediterranean Europe." Discussing African mtDNAs the study states that these indicate that a significant proportion of these lineages could have arrived in Italy more than 10,000 years ago; therefore, their presence in Europe does not necessarily date to the time of the Roman Empire, the Atlantic slave trade or to modern migration." These mtDNAs by Brisighelli "et al." were reported with the given results as "Mitochondrial DNA haplotypes of African origin are mainly represented by haplogroups M1 (0.3%), U6 (0.8%) and L (1.2%)" for the 583 samples tested. The haplogroups M1 and U6 can be considered to be of North African origin and could therefore be used to signal the documented African historical input. Haplogroup M1 was observed in only two carriers from Trapani (West Sicily), while U6 was observed only in Lucera, South Apulia, and another at the tip of the Peninsula (Calabria).
A 2013 study by Alessio Boattini et al. found 0 of African L haplogroup in the whole Italy out of 865 samples. The percentages for Berber M1 and U6 haplogroups were 0.46% and 0.35% respectively.
A 2014 study by Stefania Sarno et al. found 0 of African L and M1 haplogroups in mainland Southern Italy out of 115 samples. Only two Berber U6 out of 115 samples were found, one from Lecce and one from Cosenza.
Close genetic similarity between Ashkenazim and Italians has been noted in genetic studies, possibly due to the fact that Ashkenazi Jews have a high degree of European admixture (30%–60%), a lot of which came from Italy when diaspora males migrated to Rome and found wives among local women who then converted to Judaism. More specifically, Ashkenazi Jews could be modeled as being 50% Levantine and 50% European, with an estimated mean South European admixure of 37,5%. Most of it (30,5%) seems to derive from an Italian source.
A 2010 study of Jewish genealogy found that with respect to non-Jewish European groups, the population most closely related to Ashkenazi Jews are modern-day Italians, followed by the French and Sardinians.
The contribution in rebuilding Europe's mtDNA
Recent studies have shown that Italy has played an important role in the recovery of "Western Europe" at the end of the Last glacial period. The study focused mitochondrial U5b3 haplogroup discovered that this female lineage had in fact originated in Italy and that then expanded from the Peninsula around 10,000 years ago towards Provence and the Balkans. In Provence, probably between 9,000 and 7,000 years ago, it gave rise to the haplogroup subclade U5b3a1. This subclade U5b3a1 later came from Provence to the island of Sardinia by obsidian merchants, as it is estimated that 80% of obsidian found in France comes from Monte Arci in Sardinia reflecting the close relations that were at the time of these two regions. Still about 4% of the female population in Sardinia belongs to this haplotype.
- In 2008, Dutch geneticists determined that Italy is one of the last two remaining genetic islands in Europe (the other being Finland.) This is due in part to the presence of the Alpine mountain chain which, over the centuries, has prevented large migration flows aimed at colonizing the Italian lands.
- Recent genome-wide studies have been able to detect and quantify admixture like never before. Li et al. (2008), using more than 600,000 autosomal SNPs, identify seven global population clusters, including European, Middle Eastern and Central/South Asian. All the Italian samples belong to Central-Western group with minor influences dating to Neolithic period.
- López Herráez et al. (2009) typed the same samples at close to 1 million SNPs and analyzed them in a Western Eurasian context, identifying a number of subclusters. This time, all of the European samples show some minor admixture. Among the Italians, Tuscany still has the most, and Sardinia has a bit too, but so does Lombardy (Bergamo), which is even farther north.
- A 2012 study by Di Gaetano et al. used 1,014 Italians with wide geographical coverage. It showed that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population.
By using the ADMIXTURE software, the authors obtained at K = 4 the lowest cross-validation error. The HapMap CEU individuals showed an average Northern Europe (NE) ancestry of 83%. A similar pattern is observed in French, Northern Italian and Central Italian populations with a NE ancestry of 70%, 56% and 52% respectively. According to the PCA plot, also in the ADMIXTURE analysis there are relatively small differences in ancestry between Northern Italians and Central Italians while Southern Italians showed a lower average admixture NE proportion (43,6%) than Northern and Central Italy, and a higher Middle East ancestry of 28%. The Sardinian samples display a pattern of crimson common to the others European populations but at a higher frequency (70.4%).
The average admixture proportions for Northern European ancestry within current Sardinian population is 14.3% with some individuals exhibiting very low Northern European ancestry (less than 5% in 36 individuals on 268 accounting the 13% of the sample).
- A 2013 study by Peristera Paschou et al. confirms that the Mediterranean Sea has acted as a strong barrier to gene flow through geographic isolation following initial settlements. Samples from (Northern) Italy, Tuscany, Sicily and Sardinia are closest to other Southern Europeans from Iberia, the Balkans and Greece, who are in turn closest to the Neolithic migrants that spread farming throughout Europe, represented here by the Cappadocian sample from Anatolia. But there hasn't been any significant admixture from the Middle East or North Africa into Italy and the rest of Southern Europe since then.
- Ancient DNA analysis reveals that Ötzi the Iceman clusters with modern Southern Europeans and closest to Italians (the orange "Europe S" dots in the plots below), especially those from the island of Sardinia. Other Italians pull away toward Southeastern and Central Europe consistent with geography and some post-Neolithic gene flow from those areas (e.g. Italics, Greeks, Etruscans, Celts), but despite that and centuries of history, they're still very similar to their prehistoric ancestor.
- A 2013 study by Botigué et al. 2013 applied an unsupervised clustering algorithm, ADMIXTURE, to estimate allele-based sharing between Africans and Europeans. Regarding Italians, the North African ancestry does not exceed 2% of their genomes. On average, 1% of Jewish ancestry is found in Tuscan HapMap population and Italian Swiss, as well as Greeks and Cypriots. Contrary to past observations, Sub-Saharan ancestry is detected at <1% in Europe, with the exception of the Canary Islands.
- Haak et al. (2015) conducted a genome wide study of 94 ancient skeletons from Europe and Russia. The study argues that Bronze Age steppe pastoralists from the Yamna culture spread Indo-European languages in Europe. Autosomic tests indicate that the Yamnaya-people were the result of admixture between two different hunter-gatherer populations: Eastern Hunter-Gatherers from the Russian Steppe and either Caucasus Hunter-Gatherers or Chalcolithic Iranians (who are very similar). The authors estimated a 21% ancestral contribution of the Yamnaya in the DNA of modern Italians, excluding Sardinians (7.1%), and to a lesser extent Sicilians (11.6%).
- A 2016 study Sazzini et al., confirms the results of previous studies by Di Gaetano et al. (2012) and Fiorito et al. (2015) but has much better geographical coverage of samples, with 737 individuals from 20 locations in 15 different regions being tested. The study also for the first time includes a formal admixture test that models the ancestry of Italians by inferring admixture events using all of the Western Eurasian samples. The results are very interesting in light of the ancient DNA evidence that has come out in the last couple years:
In addition to the pattern described in the main text, the SARD sample seemed to have played a major role as source of admixture for most of the examined populations, especially Italian ones, rather than as recipient of migratory processes. In fact, the most significant f3 scores for trios including SARD indicated peninsular Italians as plausible results of admixture between SARD and populations from Iran, Caucasus and Russia. This scenario could be interpreted as further evidence that Sardinians retain high proportions of a putative ancestral genomic background that was considerably widespread across Europe at least until the Neolithic and that has been subsequently erased or masked in most of present-day European populations.
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