Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils

We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca. 6300 to 15 600 cal BP all showed B haplotypes, closely related or even identical to those found on Sardinia. Genetic diversity in the mainland population was considerably higher than on the islands. Together with palaeontological evidence our genetic results identify the Italian Peninsula as the ultimate origin of the B lineage and thus the Tyrrhenian and North African red deer. This is in line with previous biogeographic findings that uncovered distinct intraspecific phylogeographic lineages in Italian mammals, underlining Italy’s status as a hotspot of European mammalian diversity.

. List of red deer samples used in aDNA analyses. Calibrated ages are given in years before present, i.e. years before AD 1950. The Corsican material used in this study is temporarily located at the Muséum National d'Histoire Naturelle in Paris (more specifically, the laboratory "Archaeozoology, archaeobotany") and will eventually be deposited at the Musée archéologique de Sartène in Corsica.

Sardinia
Sardinian samples came from sites 2-13 (Fig 1) which were dated, based on archaeological context, from the Neolithic to the Middle Ages 4 . The Grotta Verde, the most ancient cave site, is located on the cliff on the northwestern coast near Alghero. The faunal remains in the cave are abundant, although deer remains are scarce 5 . One of the antler fragments found at this site had processing marks.
Also within the territory of Alghero are the Nuragic villages of Flumenelongu, Talia and Sant'Imbenia. Flumenelongu and Talia were built during the Bronze Age and were inhabited until the Roman Empire. At the latter site the remains of an important villa rustica were found. The nuragic village of Sant'Imbenia was a port settlement that must have been of great importance for trade and was frequently visited by Phoenician sailors. At the site Bronze Age and Iron Age levels were excavated, yielding, among other things, fragments of elephant ivory, a shell from northwestern Africa and many red deer remains.
The Nuraghe Santu Antine near Torralba, one of the largest and most important nuraghe of Sardinia, is located in the northern part of the island, far from the coast. The faunal remains that were studied have been attributed to the late Bronze Age and come from one of the smaller towers.
During the Iron Age Sardinia was colonized by the Phoenicians and later by the Punics. Some samples were examined from a site in the northern part, Santu Pedru near Olmedo in the territory of Alghero, but the most important sites, Monte Sirai and Nuraghe Sirai, are in the Sulcis area, in the southeastern part of the island. The former Sulcis site was a town founded by Phoenicians on a hill near the sea, while the latter is a site dated to the Bronze Age which was successively occupied by Phoenicians. The sites are located very close to each other. It is assumed that red deer was an animal of great importance for meat and antler processing at both sites.
For the Roman period, in addition to the already mentioned Nuraghe Flumenelongu and Talia sites, we also analysed samples from the well-sanctuary of the Purissima near Alghero. It is dated to the Bronze Age and was frequented until the Roman Imperial age. A cult linked to water was practiced at the sanctuary and numerous ex-votos representing human feet were recovered. The animal remains found at the site are likely to be connected to sacrificial practices.
The Roman villa of Santa Filitica is located on the northern coast. In the first centuries of the Middle Ages, on the ruins of the villa a village was built exploiting the area's resources. Red deer were hunted both for meat and antler processing. Some combs and buckles made of deer antler, of best craftsmanship, were recovered.
The most recent sample is from the urban excavations in the city of Sassari, but unfortunately its quality is poor. All samples from Sardinia are from faunal remains studied by the Archaeozoological Laboratory of the University of Sassari.
The Sardinian material of this study is kept in Sardinia, at the cultural superintendencies in Alghero and Sassari and at the Museo Archeologico Villa Sulcis in Carbonia.

Mainland Italy
On the Italian Peninsula (sites nos 14-23) it was possible to recover more ancient samples 6 . The Cave Polesini is located near Tivoli in the Lazio region and provided a large number of animal remains dating back to the Upper Palaeolithic (epigravettiano). Red deer bones were very abundant. The fauna from this cave has never been studied in depth.
The grotta Azzurra of Samatorza near Trieste 7 is the only site located in northeastern Italy. The excavations of the University of Pisa revealed Mesolithic and Neolithic levels. The study of the Mesolithic fauna highlighted the presence of many wild species, including red deer.
In central and southern Italy, Latronico and grotta Continenza are two important sites showing continuity of life from the Mesolithic to the Neolithic and beyond. Latronico, in the Basilicata region, is a site consisting of a cave system, very rich in faunal remains. The site lies in a hilly position, in an area rich in forests and waters. Hunting was still of great importance in the Neolithic, and red deer remains are frequent.
Grotta Continenza was a cave overlooking the Fucino lake, now dried up, in the Abruzzo region. In the Mesolithic its inhabitants lived on trout fishing and mammal hunting, while in the Neolithic these activities became less important.
For the Neolithic we have samples from some sites in central Italy: San Pietrino Tolfa in the Lazio region; Ripoli, San Callisto di Popoli, grotta dei Piccioni di Bolognano e Fossacesia in the Abruzzo region. With the exception of a cave (grotta dei Piccioni) all sites were village settlements. Domestic mammals prevail in all these sites, but hunting was still practiced, and red deer remains were found.
The most recent site is the village of Punta Le Terrare near Brindisi in the Puglia region, dating back to the Bronze Age. At this time red deer hunting had regained great importance, perhaps as a result of the introduction of the horse, and the percentages of red deer remains are very high.
The material from the Italian mainland used in this study is temporarily stored in the laboratory of archaeozoology of the University of Pisa and will be sent back to the cultural superintendencies of the regions from which it originates.