Supplementary Note 1: Archaeological background 1.1. North Africa Youssef Bokbot, Jonathan Santana-Cabrera, Jacob Morales-Mateos and Abdeslam Mikdad 1.1.1. The Cave of Ifri n’Amr o’Moussa Ifri n'Amr ou Moussa is a cave located on the Zemmour Plateau in the Oued Beth Basin (Central Morocco). It presents a stratigraphic sequence ranging from Iberomaurusian to Chalcolithic1. Preliminary evidence suggests the arrival of the Neolithic package in this region during the last quarter of the 6th millennium cal BCE. A barley grain and an undetermined fruit have been radiocarbon dated between ca. 5,200 to 4,900 cal BCE, indicating the presence of an Early Neolithic occupation (Trench 2, SU 2006 and 2007; fruit, 5,207 - 4,944 cal BCE; Hordeum vulgare, 5,211 - 4,963 cal BCE) (Figure S1.1.). This evidence comes from deposits of ash and charcoal that included impressed-cardial ceramics and possibly domestic fauna1. Some disturbance of the archaeological layers was recorded during fieldwork. In order to confirm the antiquity of the skeletons analyzed in this study, we have dated them directly by means of 14C. The dates on the skeletons point to an Early Neolithic occupation in the late 6th and early 5th millennium BCE (Figure S1.1.). They also corroborate the stratigraphic relationship among burials, domesticated cereals, and Cardial pottery that was observed in archaeological fieldwork1. Finally, the cave yielded evidence of Bell-Beaker potteries2 and several Chalcolithic burials3. There are seven burial sites belonging to the Early Neolithic period in Ifri n’Amr o’Moussa. Funerary utilization of the caves, along with domestic activity, is also noticed in other sites of the same period in the region, including El Kiffen4, El-Mnasra5, and El Harhoura II3. During the 2006 and 2007 season, an adult human skeleton (IAM 1) and two infants (IAM 2 and IAM 3) were excavated. In 2010, four additional individuals were discovered (IAM 4, IAM 5, IAM 6 and IAM 7). Most individuals were laid on lateral and supine decubitus and oriented from East to West. Burials did not contain grave goods or any other type of artefact. Samples selected for this study are detailed in Table S1.1. 1 Figure S1.1. Calibrated dates of Ifri n’Amr o’Moussa human samples, barley seed, and undetermined fruit. Burial/Individual Age Sex Position Orientation IAM 1 30-40 years old Female Left lateral flexion East-West IAM 2 6 ± 2 months old - Supine North-South IAM 3 18 ± 2 months old - Left lateral decubitus East-West IAM 4 30-40 years old Female Left lateral decubitus East-West IAM 5 5 ± 1 years old - Left lateral decubitus East-West IAM 6 16 ± 2 years old Male? Supine East-West IAM 7 Infant (<5 years old) - Supine East-West Table S1.1. Demographic data and burial features of Ifri n’Amr o’Moussa Neolithic funerary customs. 1.1.2. The Cave of Kehf el Baroud The Kehf el Baroud cave is located about fifty kilometers east of the city of Casablanca. It takes its name from the reef-like massif into which it extends. The massif rises from Paleozoic shale formations with a rounded relief. The Oued Cherrat river, controlled by 2 the cave, follows its course between the Kehf-el-Baroud massif and the one called Sokhrat Echelh. It presents a human occupation ranging from Epipaleolithic to Bronze Age6. The cave consists of two halls connected by a small gallery7. The first hall, which opens to the east over the Oued Cherrat, has a length of 26 m and a width of 7 m at the entrance. The second room is a karst cave, the floor of which inclines steeply upwards and has an opening that leads directly to the plateau of the massif. At the bottom, the sediments are relatively loosely deposited, containing extensive archeological inventory as well as numerous faunal and human remains. De Wailly initially excavated this archaeological site in the 60’s and 70’s, and our team’s excavations continued in 1991, 1993 and 1994 (YB and AM)7,8. After analyzing the stratigraphic context, it seems clear that the sediments entered the cave by a flow process. In the main hall, despite the existence of strong disturbances caused by excavations6, archaeological research allows us to establish a preliminary stratigraphy sequence of two main occupational phases: 1) the Chalcolithic Age-Bronze Age phase, characterized by the presence of various types of ceramic styles, including Bell-Baker pottery, a copper point and a schist plate; and 2) the Neolithic phase, indicated by undecorated ceramic fragments, flint tools and domestic fauna. Human remains selected for this study come from this former phase. Antiquity of these remains was confirmed by means of 14C (4,850 +/- 30 BCE). The dates point to a Middle-Late Neolithic in the beginning of the 4th millennium BCE (Figure S1.2). Similar archaeological sites in the same area, such as of Rouazi-Skhirat and El Kiffen4, include burials from the same period. The Kehf el Baroud population used in this study is represented in eight samples belonging to the Neolithic phase (Table S1.2). Figure S1.2. Calibrated date of individual KEB 1. 3 1.2. Southern Spain Dimas Martín-Socas, María Dolores Camalich Massieu, Jonathan Santana Cabrera , Francisco Javier Rodríguez-Santos and Aioze Trujillo Mederos 1.2.1. El Toro site El Toro (36º 57’ 26” N; 4º 32’ 10” W) is a cave site located in Antequera (Málaga), concretely in the Sierra del Torcal, at an elevation of 1,190 meters above sea level. Sierra del Torcal is a wide karstic mountain range that separates Mediterranean Andalusia from the Sub-Betic System of southern Iberian Peninsula. The morphogenesis of this region is characterized by calcareous rocks and diaclastic systems that have conditioned the directions of karst flow (Figure S1.3). Numerous pits have been identified, some of which have provided evidence of occupation during the Neolithic period9. Figure S1.3: View of Sierra del Torcal (Málaga, Spain) Today, the cave of El Toro shows an internal structure characterized by large fallen blocks, which collapsed prior to the Neolithic occupation. During the first quarter of the 4th millennium, the structure of the cave changed, possibly as the result of a tectonic movement or a collapse of the karst system. These changes included the closure of the original entrance, the configuration of a new entrance, the formation of a 17-meter pit, and the modification of the sedimentary fill in the southern sector. 4 Two of the authors of the present study (D.M-S. and M.D.C.) carried out five excavation campaigns in the cave (1977, 1980, 1981, 1985 and 1988), in the immediate area of the entrance (Figure S1.4). A stratified 2.40 m depth sequence was identified, divided into a series of archaeological units following the Harris Matrix10. These units were grouped into four chrono-cultural phases and one sterile phase9,11 (Figure S1.5): - Phase I: Superficial layer, where evidence of the more recent occupation of the cave has been identified (Roman, medieval and modern times). - Phase II: Layer dating to the end of the third millennium BC9, which is characterized by a decrease in occupation with less evidence of material remains and domestic activities. Although this layer is by more recent occupations, the presence of raptor droppings suggests a discontinuity and reduction of human occupancy. - Phase III: Layer corresponding to the Late Neolithic period, dated 5,320 - 5,170 BP (4,250 - 3,950 cal BCE)12. This layer is subdivided into Phases IIIB and IIIA, depending on the differences in the occupancy characteristics and, consequently, in the distribution of archaeological remains. These differences are related to the structural changes produced in the cave after its collapse, which, as indicated, involves the closing of the original entrance and a reduction of the interior space. - Sterile phase, probably associated with a period of abandonment of the site, based on the absolute radiocarbon dates that establish an estimated hiatus around 600 years. - Phase IV: Layer corresponding to the Early Neolithic phase, dated between 6,200 - 5,980 BP (5,280 - 4,780 cal BCE)12,13 (Table S1.2, Figure S1.6). Regarding phase IV, the archaeological complex includes lithic remains, bones and ceramics. Associated fauna remains are mainly those of ovicaprids, while seeds excavated correspond mostly to cereals. Functional analysis highlights a predominance of meat processing activities, along with evidence of bone, wood, leather and clay work. Also, the production of ceramic in situ has been evidenced14. Pottery remains from phase IV in El Toro cave, are characterized by the use of highly diverse decoration techniques. Ceramics from El Toro were decorated including incise, printed, plastic, “boquique” and “almagra” techniques (Figure S1.6). The element that standardizes and 5 particularizes this production is the widespread use of the almagra and the plastic decoration based on embossed cords. The use of the almagra is not only restricted to the surface finishes, total or partial, but is also used to fill the negatives of the different decorative techniques15 (Camalich & Martín-Socas, 2013) (Fig. S1.5). Figure S1.4: Structure of El Toro cave Figure S1.5: Stratigraphic sequence of El Toro cave Human remains were excavated in the Early Neolithic phase. The remains appeared scattered and without anatomical connection. They were distributed in two well- differentiated areas: contexts A and B. Context A is associated with the area of domestic occupation and is the source of most of the human remains. Context B is a ritual area that is located in a small hollow, and it is spatially independent of the domestic space.