Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily

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Marieke S.van de Loosdrecht119Marcello A.Mannino2318SahraTalamo34Adam B.Rohrlach15AinashChildebayeva1VanessaVillalba-Mouco16FranziskaAron1GuidoBrandt1MartaBurri1CäciliaFreund1RitaRadzeviciute1RaphaelaStahl1AntjeWissgott1HelenFewlass3AntonioTagliacozzo7MarcelloPiperno8SebastianoTusa9JohannesKrause12021 rights and content
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1.Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers.
2.A near-complete genetic turnover during the Mesolithic-Neolithic transition.
3.Exchange of subsistence practices between hunter-gatherers and early farmers.


Sicily is a key region for understanding the agricultural transition in the Mediterranean, due to its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, while Late Mesolithic HGs carry ∼20% ancestry related to northern and (south)eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP, however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.

Grotta dell’Uzzo in northwestern Sicily is a unique site for understanding human prehistory in123
the Central Mediterranean. The cave stratigraphy at Grotta dell’Uzzo covers the late Upper124
Palaeolithic, a continuous occupation during the Mesolithic, and up to the Middle Neolithic
, with125
traces of later occupation (STAR Methods) (Mannino et al., 2015). This provides direct and126
unprecedented insights into the cultural, subsistence and dietary changes that took place in the127
transition from hunting and gathering to farming (Mannino et al., 2015, 2007; Tagliacozzo,128
1993). In addition, two Impressa Ware horizons associated with elements of Early Neolithic129
farming appeared rapidly in a timeframe of ~500 years. The first horizon of Impressa Wares130
appeared 8,000-7,700 cal BP followed by the Impressed Ware of the Stentinello group131
(Stentinello/Kronio) around 7,800-7,500 cal BP
(Binder et al., 2017; Guilaine, 2018; Mannino et132
al., 2015; Natali and Forgia, 2018).

Here, we provide population genomic and dietary isotope analyses for 19 individuals166
that cover a time transect of over 6,000 years, from the Early Mesolithic (EM; ~10,700 cal BP)167
to the Early Bronze Age (EBA; ~4,100 cal BP) (Data S1.1). An Epigravettian HG individual168
(OrienteC) from the Grotta d’Oriente on Favignana island in western Sicily (14,200–13,800 cal169
BP, 14C date on charcoal from the deposit) is co-analysed with our data

The two oldest groups fall within a cluster of western European Mesolithic hunter-gatherers [...]
These three individuals all carried mitogenome lineages that fall within the187
U2'3'4'7'8’9 branch (Data S1.1), which was closely related to an Epigravettian-associated188
Sicilian from San Teodoro and also reported for an older Gravettian-associated Paglicci108 from189
the Italy peninsular (Modi et al., 2021; Posth et al., 2016). They also shared a large amount of190
genetic drift with each other, compared to other individuals in the WHG cluster (Data S5.3,191
Figure S3). We labelled this group Sicily Early Mesolithic (Sicily EM, n=3).

The second, chronologically younger HG group includes nine individuals dated to ~8,650-7,790193
cal BP. Seven of them correspond archaeologically to the Late Mesolithic and probably for part194
of the Castelnovian, a variety of the Late Mesolithic blade-and-trapeze horizon in southern195
France, Italy and Dalmatia, as well as Sicily [...]
Moreover, the mitogenome haplogroups carried by these individuals are all typical for205
European Late Mesolithic WHG (Bramanti et al., 2009; Posth et al., 2016), falling in206
haplogroups U4 and U5, different from the first group (Data S5.2). As a consequence, we207
grouped UZZ71 and UZZ88 with the Sicily LM HG individuals, and labelled this group as Sicily208
Late Mesolithic (Sicily LM, n=9).

The third group contains individuals directly dated to ~7,430-6,660 cal BP, overlapping210
chronologically with Early Neolithic to Middle Neolithic farmer horizons at Grotta dell’Uzzo,211
characterised by Impressed Wares (Sicily EN, n=7). In PC space, these individuals group with212
early farmers from southeastern Europe and Anatolia, and not with the preceding Sicilian HGs213
(Fig. 1C). All the farmer individuals with sufficient coverage on the mitogenome carried214
haplogroups characteristic for European early farmers: U8b1b1 (n=2), N1a1a1 (n=1), J1c5 (n=1),215
K1a2 (n=1) and H (n=1)

The fourth and youngest group includes one individual (UZZ57) dated to 4,150-3,970 cal BP and220
is attributed to the Early Bronze Age (Uzzo EBA). This individual is displaced from the Early221
Neolithic towards the direction of individuals associated with the Bell Beaker phenomenon and222
other Late Neolithic and BA groups that carry the so-called “steppe”-related ancestry. This223
ancestry was characteristic for the steppe-nomads from western Eurasia, and spread across224
Europe during the Bronze Age (Haak et al., 2015). A similar shift was also found in published225
Early Bronze Age individuals from Sicily (Fernandes et al., 2020). This individual UZZ57226
carried the Y-haplogroup R1b1a1b1a1a2, commonly found in Bronze Age Europe, and also227
previously reported in Sicilian Bronze Age individuals (Data S1.4, Data S5.2) (Fernandes et al.,228