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The biological life history of infants from archaeological contexts can provide a unique insight into past human populations. Dental mineralized tissues contain a permanent record of their growth that can provide access to the prenatal and early infant life, and mortality, of human skeletons. This study focuses on the histomorphometric analysis of deciduous teeth from the ‘Archaic Necropolis’ of Motya (7th–6th century BCE, Sicily–Italy). The histomorphometric analysis is conducted on prenatal and postnatal enamel of eight anterior deciduous teeth from seven individuals from this Phoenician population to estimate their chronological age-at-death, health, and enamel growth parameters. Proteomic analysis has been used to determine the sex of the infants. The presence of the Neonatal Line in all specimens indicates that the seven individuals survived birth. The occurrence of at least one Accentuated Line in prenatal enamel in four out of seven individuals suggests the foetuses and/or their mothers experienced a stress-related event during pregnancy. As expected, there was limited variation in Daily Secretion Rates near the Enamel Dentine Junction. These rates increase toward the outer enamel surface and decrease toward the cervix. Our findings illustrate the importance of dental histology for reconstructing perinatal and early infancy mortality and morbidity patterns at Motya, which sheds light on the socio-cultural perception of new-borns and infants in an ancient Phoenician community.

Acknowledgements: The authors thank G. Marciani and O. Jöris for comments on archaeology; C. Jeong, M. Spyrou and K. Prüfer for comments on genetics; M. O’Reilly for graphical support for Fig. 5 and Extended Data Fig. 9; the entire IT and laboratory teams at the Department of Archaeogenetics of MPI-SHH for technical assistance; M. Meyer and S. Nagel for support with single-stranded library preparation; K. Post, P. van Es, J. Glimmerveen, M. Medendorp, M. Sier, S. Dikstra, M. Dikstra, R. van Eerden, D. Duineveld and A. Hoekman for providing access to human specimens from the North Sea (The Netherlands); M. D. Garralda and A. Estalrrich for providing access to human specimens from La Riera (Spain); J. Górski and M. Zając for providing access to human specimens from Maszycka cave; C. Di Patti for providing access to human specimens from San Teodoro 2 (Italy); P. Blaževičius for providing access to the Donkalnis human remains and the new radiocarbon dates; the Italian Ministry of Culture and Soprintendenza Archeologia Belle Arti e Paesaggio for the Provinces of Verona, Rovigo, and Vicenza for granting access to the human remains of Tagliente 2; F. Fontana, who carries out investigations of the Riparo Tagliente site (Italy); the Friuli Venezia Giulia Superintendency for providing access to the human tooth Pradis 1; and the Soprintendenza Archeologia Belle Arti e Paesaggio for the Provinces of Barletta-Andria-Trani and Foggia for providing access to the Paglicci human remains. This project has received funding by the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreements no. 803147-RESOLUTION (to S.T.), no. 771234-PALEoRIDER (to W.H.), no. 864358 (to K.M.), no. 724703 and no. 101019659 (to K.H.). K.H. is also supported by the Deutsche Forschungsgemeinschaft (DFG FOR 2237). E.A. has received funding from the Van de Kamp fonds. PACEA co-authors of this research benefited from the scientific framework of the University of Bordeaux’s IdEx Investments for the Future programme/GPR Human Past. A.G.-O. is supported by a Ramón y Cajal fellowship (RYC-2017-22558). L. Sineo, M.L. and D.C. have received funding from the Italian Ministry of University and Research (MUR) PRIN 2017 grants 20177PJ9XF and 20174BTC4R_002. H. Rougier received support from the College of Social and Behavioral Sciences of CSUN and the CSUN Competition for RSCA Awards. C.L.S. and T. Saupe received support from the European Union through the European Regional Development Fund (project no. 2014-2020.4.01.16-0030) and C.L.S. received support from the Estonian Research Council grant PUT (PRG243). S. Shnaider received support from the Russian Science Foundation (no. 19-78-10053)., Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

The northern coast of Trapani is characteristed by a series of phenomena linked to Quaternary glaciations. These phenomena have modeled esplanades, terraces, cliffs, leaf grooves and caves of great natural beuaty. The extreme strip of the Peninsula of S. Vito lo Capo, the Piana di Sopra, is made up of parareciphal limestones with Orbitoline and Rudist from the Cretaceous. This area has a strong density of cavities of marine origin estimated at four cavities per kilometer. These cavities are an important anthropological testimonly to a continual human presence from deep prehistory onwards. A fundamental prerequisite for a study of the prehistory of an area is its geomorphologic description which includes the mapping of sites of paleontological and anthropological interest. Here we present the unpublished research of this territory carried out in 1987-88 by Giovanni Mannino and his collaborators. This research, although it makes a signficant contribution to our knowledge of the prehistory of this region, was unfortunately never published. Now, a few months after Giovanni's death we are offer, with its publication here, a sign of our fond memory and our esteem.

La Grotta di San Teodoro (ST) è uno dei siti preistorici più importanti del Mediterraneo cen-trale. Da pochi anni il sito è oggetto di una ripre-sa delle attività di analisi stratigrafica, geologica, geochimica e paleontologia, alla luce di una colla-borazione tra il Parco Archeologico di Tindari e l’Università degli Studi di Palermo.

Objectives: The developmental origins of health and disease (DOHaD) hypothesis describes how early childhood stress affects morbidity and mortality later in life. The role of early childhood stress in mortality from infectious disease is understudied. Stressors in early childhood that weaken the immune system may result in increased susceptibility to infectious disease in adulthood. Weaning is one of the earliest potential periods of significant stress in early childhood. This research investigates the effect of weaning after ~6months of age on cholera mortality among 18th-19th-century Italian populations by determining if earlier breastfeeding cessation is associated with earlier mortality, analyzing childhood dietary variation and physiological stress markers, and determining if age-at-weaning completion differs between catastrophic and attritional populations. Methods: Serial dentin stable carbon and nitrogen isotope analyses from canines are compared between catastrophic (n=45) and attritional groups (n=23). Canines are sectioned serially from crown to apex, and the increment's δ15 N and δ13 C are used to estimate age-at-weaning completion. Results: Catastrophic and attritional groups exhibit similar age-at-weaning completion (~2.8 years). Seventy-four percent of individuals lack elevated δ15 N values in dentin that formed during infancy. Conclusions: Age-at-weaning completion was not a predisposing factor in cholera mortality in adulthood in this sample. Age-at-weaning completion may not be significantly associated with infectious disease mortality because weaning completion likely occurred after infants had adapted to consuming contaminated weanling foods. Individuals without detectable weaning curves may represent infants who received supplementary foods since birth or were weaned before the age of 6-9months.

Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.

Grotta d’Oriente, a small coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. The individual known as Oriente C was found in the lower portion of an anthropogenic deposit containing typical local Late Upper Palaeolithic (Late Epigravettian) stone assemblages. Two radiocarbon dates on charcoal from the deposit containing the burial are consistent with the archaeological context and refer Oriente C to a period spanning about 14,200-13,800 cal. BP. Anatomical features are close to those of Late Upper Palaeolithic populations of the Mediterranean and show strong affinity with Palaeolithic individuals of San Teodoro. Here we present new ancient DNA data from Oriente C. Our results, confirming previous genetic analysis, suggest a substantial genetic homogeneity among Late Epigravettian hunter-gatherer populations of Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the Last Glacial Maximum (LGM).

The first undisputed colonization of the island has been linked to Late or Final Epigravettian groups after the Last Glacial Maximum (LGM), as evidenced by the fossil record. Two significant sites to investigate this issue are the Grotta di San Teodoro (Acquedolci, Messina) and the Grotta d’Oriente (Favignana island). The Grotta di San Teodoro has yielded the oldest and largest human skeletal sample yet found in Sicily. Inside the cave, during field excavations carried out in the 1937-1947 years, seven human adults have been discovered (ST1-ST7). In the Grotta d’Oriente four prehistoric burials assigned to Late Upper Paleolithic (Oriente A and C) and Mesolithic (Oriente B and X) were unearthed during two campaign of ex-cavations (1972 and 2005). Thanks to the recent development of new methods for the analysis of ancient DNA (aDNA) coupled with Next Generation Sequencing technologies (NGS), it is nowadays possible to go deep inside the migration movements of human past populations. In order to better understand the peopling dynamics of Sicily during the Late Upper Paleolithic and Mesolithic, we analyzed and compared three complete mitochondrial genome sequences of ST2, Oriente C and Oriente B specimens. ST2 is an almost complete cranium attributed to a male, housed at the “G.G. Gemmellaro” Geo-logical Museum of the University of Palermo. The ST2 individual was buried near the ST1 skeleton, which was radiocarbon dated to 15,232-14,126 cal. BP. Oriente C individual was found during excavations of 2005. Two radiocarbon dates on char-coals are consistent with typical Late Epigravettian stone assemblages and refer Oriente C, a female only represented by the upper half of the skeleton, to a period spanning about 14,200-13,800 cal. BP. The Mesolithic Oriente B was unearthed in 1972. This individual, an almost complete skeleton attributed to an adult female, has been directly dated to 10,683-10,544 cal. BP. Paleogenetic analysis reveals a significant homogeneity in Sicilian Paleo-Mesolithic hunter-gatherers, and our data suggest a strong genetic relationship with Upper Paleolithic hunter-gatherers from Southern Italy, supporting the hypothesis that the first humans to arrive in Sicily could have originated from Epigravettian groups that migrated from the Italian pen-insula soon after the LGM.

The Egadi archipelago includes three islands: Favignana, Levanzo and Marettimo. The island of Favignana is the closest to Sicily, about 7 km from the mainland coast and about 13 km from Trapani. Levanzo and Marettimo are roughly 13 and 36 km from Trapani, respectively. During the last glacial, Favignana and Levanzo were reachable by land since they were joined to the mainland as a result of glacial marine regression. On the other hand, Marettimo was never connected to Sicily, even during the last glacial maximum, due to a sea channel about 1.8 km wide and very deep. According to the most recent and reliable reconstructions, the island of Favignana was separated from Sicily around 7.35 thousand years ago (calibrated dating - 7.35 ka cal BP) and Levanzo around 9.2 thousand years ago (calibrated dating - 9.2 ka cal BP). The finding at the Cave of Thunder, on Marettimo Island, of Patella (spp.) and the remains of Cervus elaphus opens an intriguing debate regarding the first human peopling on the island and its navigational activities towards Marettimo from a period between 8.9 and 8.6 ka cal BP. Due to the high scientifi c value of the fi ndings and to valorize the impressive sea cave and the faunal remains discovered, a joint sampling and study intervention was planned involving several specialists.

Introduzione al Volume

Description of the Second Stop in The Excursion at the SanTeodoro Cave

Lipari, the largest of the Aeolian Islands, is located in the southern Tyrrhenian Sea. Archeological evidence suggests an early human occupation starting from the Neolithic period. The island, favored by its volcanic history, was an important crossroads of cultures and commerce exchanges during prehistory up to Greek and Roman dominations. In this study, we present multidisciplinary analysis results on four skeletal remains from the necropolis of Contrada Diana attributed to the Roman period. By using Next Generation Sequencing technology we identified the biological sex and reconstructed the complete mitochondrial genome for two individuals. We retrieved the first ancient L3e5a lineage that is today present only in North and Central Africa. In addition, a 14C dating of 2,030 ± 45 years BP was obtained for one individual. A previous ancient DNA study has highlighted a genetic link between Sicily and the African continent at least from the Bronze Age. Our results, documenting the existence of contacts between Lipari and Africa during Roman influence, are particularly relevant to better understand the peopling of the Aeolian Archipelago when the island was a sea route of primary importance for the trade in the Mediterranean.

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.

Interpreting depositional settings of cave sites is generally problematic, especially in absence of palaeontological/archaeological evidence. This is the case of some deposits at San Teodoro Cave (Sicily), a key site for the Mediterranean Palaeolithic. In a stratigraphic level interrupted by a carbonatic concretion, phosphatic nodules are present only in the part enclosed between the concretion and the cave wall. The discovery of these nodules combined with the punctual lack of fossils had initially suggested an erosion phenomenon and subsequent formation of nodules at a vadose level. Here we show the usefulness of an integrated, geochemical-palaeoecological approach in defining stratigraphy and palaeoenvironmental reconstructions. XRD, ICP-OES, ATR-FTIR and EDS analyses allowed the formulation of a new hypothesis regarding the origin of the nodules, the depositional dynamics, and the role played by the guano produced by an extensive colony of bats. The role of barium and rubidium in detecting taphonomical processes has been highlighted.

A petrographic characterization has been used here, for the first time, in the study of lithic raw materials exploited in prehistoric Sicily. Our research interests one of the oldest archaeological sites with evidence of the early human peopling of the island (∼15kyr ago): San Teodoro Cave, in northeastern Sicily. Two geological Formations, Numidian and Monte Soro Flysch gave origin to well-rounded pebbly quartzite elements scattered in the marine terraces surrounding the cave and likely exploited as one of the sources of the raw materials for the production of lithic tools by the Epigravettian communities having settled the place. The preference for one of the two qualities of quartzite is hypothesized thanks to the results of the petrographic analysis and a naked eye recognition of the differences between the two varieties of sandstone by the Epigravettian groups is also speculated.

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 bc, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 bc. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 bc) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 bc, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium bc, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island’s early farmers until the first millennium bc, with the exception of an outlier from the third millennium bc, who had primarily North African ancestry and who—along with an approximately contemporary Iberian—documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium bc and, at present, no more than 56–62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people., D.M.F. was supported by an Irish Research Council grant GOIPG/2013/36. Radiocarbon work was supported in part by the NSF Archaeometry program BCS-1460369 (to D.J.K. and B.J.C). C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015-64699-P and PGC2018-095931-B-100). D.C. was supported by grant 20177PJ9XF MIUR PRIN 2017. D.Reich is an Investigator of the Howard Hughes Medical Institute, and his ancient-DNA laboratory work was supported by National Science Foundation HOMINID grant BCS-1032255, a National Institutes of Health grant GM100233, an Allen Discovery Center grant, and grant no. 61220 from the John Templeton Foundation.

Studio relativo ai primi risultati della ricerca antropologica condotta sui contesti ossei umani rinvenuti nella necropoli punica e romana di Tharros Capo San Marco (Cabras - OR).

The Mediterranean islands and their population history are of considerable importance to the interpretation of the population history of Europe as a whole. In this context, Sicily, because of its geographic position, represents a bridge between Africa, the Near East, and Europe that led to the stratification of settlements and admixture events. The genetic analysis of extant and ancient human samples has tried to reconstruct the population dynamics associated with the cultural and demographic changes that took place during the prehistory and history of Sicily. In turn, genetic, demographic and cultural changes need to be understood in the context of the environmental changes that took place over the Holocene. Based on this framework, this paper aims to discuss the cultural and demographic dimension of the island by reviewing archaeogenetic studies, and lastly, we discuss the ecological constraints related to human peopling in times of change in landscapes that occurred on the island in various periods. Finally, possible directions for future archaeogenetic studies of Sicily are discussed. Despite its long human history, Sicily is still one of the world’s biodiversity hotspots. The lessons we learn from the past use of landscape provide models for sustainable future management of the Mediterranean’s landscapes.

In two publications from 1967 and 1971, M. Masali described human skeletal remains presumed to have been found in the Balzi Rossi caves (Ventimiglia, Italy), based on a signed note dated to 1908. Since then, the remains - dubbed "Conio's Finds" and preserved at the University of Torino - had not been further studied. We performed a multidisciplinary investigation aimed at clarifying the geographical and chronological attribution of these specimens. Collagen extraction for AMS dating was unsuccessful, but we obtained two direct dates on the best- preserved crania via 231Pa/235U direct gamma-ray spectrometry (10,500±2,000 years BP and 12,500±2,500 years BP). We analyzed the metrics and morphology of the crania and femora by comparing them with samples belonging to the Upper Paleolithic, Mesolithic, and Neolithic periods, and evidenced that the "Conio's Finds" are morphologically more compatible with a Late Pleistocene rather than Holocene attribution. We analyzed the literature regarding the history of excavations at Balzi Rossi, and we propose that - if any credence should be given to the note accompanying the material - the remains may have been found in front of Grotta dei Fanciulli or Grotta del Caviglione, in the redeposited soil dug up during the installation of lime kilns carried out between the late 18th and the early 19th centuries. These hypotheses may be tested in the future by comparing the speleothem deposited on one of the crania and the remaining deposit at the site.

The prehistoric peopling of Sicily has left scattered traces of symbolic activities through well-known rock art expressions in caves and rock shelters located all around the island (among the most significant, the sites of Addaura, Racchio and Genovese). A peculiar phenomenon is the incision of linear signs, often grouped on the same rocky walls, hidden in fissures or placed at the entrance of the underground chambers of caves. In this report, we investigate a sample of these graphic expressions from a spatial and technical point of view. A GIS-based approach presents the territorial pattern providing insight, on a macroscale, into the intentional positioning of the sign complexes. A 3D model of the rock panels, coupled with the spatial analysis performed in a GIS environment, is presented here as a research protocol to ascertain and comprehend the physical gestures involved in the production.

Scenarios for the dispersal of Homo sapiens in Southern Europe and in the Mediterranean basin have been uncertain, given the scarceness of osteological samples and the simplicity of the proposed archaeologically-based settlement hypotheses. According to available data, the first anatomically modern humans entered Sicily during the Late Pleistocene, coming from the Italian peninsula. A presumably small Late Epigravettian population colonised coastal sites. Later, North-Western archaeological horizons gave hospitality to a significant Mesolithic expansion. In order to verify a hypothesis of continuity in the peopling of the island, we analyzed Sicilian skulls from the Late Epigravettian site of San Teodoro, Eastern Sicily (AMS 14C dated at 14,500 BP) and from the Mesolithic period (14C dated from 9,500 to 8,500 BP) coming from various sites (Uzzo, Molara, Grotta d'Oriente) located on the North Western coast of the island. The aims were to test the biological variability through time within the island as well as to evaluate the relationships of Sicilian Pleistocene hunter-gatherers with Old World populations. We also evaluated the Sicilian Mesolithic uniformity especially between the Uzzo and Grotta d'Oriente sites, given their vicinity and accessibility during the Early Holocene. We applied 3D geometric morphometric methods to assess shape variation as well as geographic and diachronic morphological patterns. All analyzed specimens, plus a comparative sample from the Old World dated from the Upper Paleolithic to recent periods, were transformed in digital images and standard craniofacial landmarks were extracted from the 3D models. Our results underline a high variability among the Mesolithic specimens, as well as a large craniometric distance from the presumed founder Paleolithic settler representatives (San Teodoro specimens) that have closer morphological affinities with other European Upper Paleolithic specimens.

This paper deals with a monument that is, up to this date, unique in Sicily and in the Italian peninsula: the Mycenaean-type tholos tomb of the Gazzi necropolis in Messina. A recent excavation in the alluvial deposits revealed extensive traces of a funerary area with a tholos tomb and several enchytrismos tombs with skeletal remains, presumably dated back to the end of the Early or the initial stage of the Middle(?) Bronze Age. The present multi-disciplinary investigation has been developed to analyse new data related to sediments, building stones and skeletal remains of this funerary area. The stratigraphic succession hosting the necropolis was formed by overbank sediments deposited on the alluvial floodplain of the Gazzi palaeostream and developed during a regressive trend. The tholos building stones were opportunely selected and distributed in the different sectors of the tomb. The crystalline building stones are unworked stones derived from the alluvial pebbles of the palaeostream, whereas the worked stones are derived from local quarries of limestones located in the surrounding hills. The osteological remains are ascribable exclusively to Homo. The minimum number of individuals inside the tholos was calculated to consist of one adult, whereas one adult and one infant were found in the enchytrismos burials. The Gazzi necropolis discovery demonstrates the important role played by the Messina settlements during the Bronze Age, when relationships between the Aegean and Western world became closer.

Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-020-1102-0, published online 24 February 2020., D.M.F. was supported by an Irish Research Council grant GOIPG/2013/36. Radiocarbon work was supported in part by the NSF Archaeometry program BCS-1460369 (to D.J.K. and B.J.C). C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015-64699-P and PGC2018-095931-B-100). D.C. was supported by grant 20177PJ9XF MIUR PRIN 2017. D.Reich is an Investigator of the Howard Hughes Medical Institute, and his ancient-DNA laboratory work was supported by National Science Foundation HOMINID grant BCS-1032255, a National Institutes of Health grant GM100233, an Allen Discovery Center grant, and grant no. 61220 from the John Templeton Foundation.

Equus hydruntinus was a small equid that ranged from the Iberian Peninsula to Middle East. In Italy it has been considered present from the Middle Pleistocene to its extinction in the Middle-Late Holocene. E. hydruntinus shares plesiomorphic traits with other known Pleistocene equids. As a consequence, its classification has always been problematic. Genetic analyses on few fossil remains from Iran and Crimea have revealed that E. hydruntinus was more closely related to extant hemiones. To further investigate its systematic position, using target-enrichment capture and next-generation sequencing, we reconstructed a near complete mitogenome of a specimen from San Teodoro Cave from Sicily radiocarbon dated at 23-21 ka cal. BP. Comparisons with extant and extinct equids demonstrate close relationship between this specimen and the Asian wild asses, supporting previous genetic and morphological studies. Furthermore, our findings confirm the occurrence of E. hydruntinus species in Sicily, that presumably might have represented a typical glacial refugium during the LGM.

Grotta d’Oriente, a coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. Inside the cave, during different field excavations, three burials attributable to the Late Upper Palaeolithic and Mesolithic were found. The Mesolithic Oriente B individual, directly dated at 9,377 ± 25 uncal BP, was previously assigned to HV1 haplogroup using a traditional approach. However, it is well known that PCR based methods are prone to erroneous haplotype or haplogroup determination. In order to redefine the mitochondrial lineage of this Mesolithic hunter-gatherer and explore its phylogenetic position, we target-enriched and sequenced the complete mitochondrial genome of Oriente B. Moreover, we conducted a morphometric analysis to assess its phenetic affinities. Oriente B individual was classified into U2′3′4′7′8′9 haplogroup. In Sicily, this lineage has also been found on the Upper Palaeolithic Oriente C and Early Mesolithic individuals from Grotta dell’Uzzo. Our results show significant genetic and morphological similarities in Sicilian Early Mesolithic hunter-gatherers, presumably because of genetic drift processes. Furthermore, dating the emergence of the “Sicilian clade”, we speculate that Epigravettian hunter-gatherers carrying U2′3′4′7′8′9 haplogroup might be the first settlers of Sicily arrived from the Italian peninsula by the crossing of a temporary land-bridge around the Last Glacial Maximum.

In the Cercopithecini ancestor two chromosomes, homologous to human chromosomes 20 and 21, fused to form the Cercopithecini specific 20/21 association. In some individuals from the genus Cercopithecus, this association was shown to be polymorphic for the position of the centromere, suggesting centromere repositioning events. We set out to test this hypothesis by defining the evolutionary history of the 20/21 association in four Cercopithecini species from three different genera. The marker order of the various 20/21 associations was established using molecular cytogenetic techniques, including an array of more than 100 BACs. We discovered that five different forms of the 20/21 association were present in the four studied Cercopithecini species. Remarkably, in the two Cercopithecus species, we found individuals in which one homolog conserved the ancestral condition, but the other homolog was highly rearranged. The phylogenetic analysis showed that the heterozygosity in these two species originated about 8 million years ago and was maintained for this entire arc of time, surviving multiple speciation events. Our report is a remarkable extension of Dobzhansky's pioneering observation in Drosophila concerning the maintenance of chromosomal heterozygosity due to selective advantage. Dobzhansky's hypothesis recently received strong support in a series of detailed reports on the fruit fly genome. Our findings are first extension to primates, indeed to Old World monkeys phylogenetically close to humans of an analogous situation. Our results have important implications for hypotheses on how chromosome rearrangements, selection, and speciation are related.

The San Teodoro Cave is considered the most significant witness of the first, Epigravettian, human colonization of Sicily from the Italian continent. Furthermore the site is a paradigmatic horizon in the Pleistocene faunal record, demonstrating a progressive transition from mega faunas to smaller-sized, Boreal, faunas. The site has been repeatedly studied and excavated, with different aims and approaches, leading to an interpretation of Epigravettian burial site and daily attendance. Here we propose a reappraisal of the study of the stratigraphy of the site, and in particular of the bone-rich layer (PAL) accumulated over the red ochre layer that apparently sealed all the different burials, with the exception of one. The study has been conducted starting from a new, consistent collection of materials from the PAL layer previously identified by Bonfiglio and co-authors, and moved from the morphological and microscopical identification of faunal remains and their taphonomy, to the accurate geological, petrographical and pedological definition of the sediments by stereomicroscope (SM), polarized light microscope (PLM) and X-Ray diffractometry (XRD) analyses. We propose the first 14C AMS dating of the layer PAL, performed on a Bos primigenius sample that has been dated to 12624 ± 59 BC, 15224–14708 cal yr BP. This date does not differ much from the dates obtained with analogous methodology on buried human remains. Despite the difficulty of a reconstruction of biological times and human behaviours that are not chronologically traceable, we can nonetheless state that the site had at least two main moments of attendance in the late Upper Palaeolithic: one linked to burials, excavated in a cave still sporadically visited by humans, and a second period of intense attendance, industrial production of quartz arenite lithics and rare flint, intensive slaughter of late-glacial Boreal fauna and presence of many combustion residues.