Praia Rei Cortiço, Gruta Nova da Columbeira and Mira Nascente contain quartzite, quartz, chert, and other raw materials in trace amounts. However, Mira Nascente is dominated by chert, Praia Rei Cortiço by quartzite, and at all layers of Gruta Nova da Columbeira the amounts of the three main raw material change but are always balanced (Table 3).
Quartzite and quartz have some internal variability, appear always as rounded pebbles with very good and excellent knapping qualities. These raw materials are highly abundant in multiple and vast Cenozoic deposits widespread across the Lusitanian Basin region. They arrive by fluvial transport from the Iberian Massif Zone to the east, or by remobilization from the nearby outcropping Cretaceous conglomerates (Praia Rei Cortiço). They were most probably collected from local gravels, and for this reason they do not give relevant information about human mobility.
Chert, in contrast, is only present at some specific locations with different geochemical compositions. This allows a relatively good understanding of their distribution across the landscape as primary and secondary sources and, consequently, to infer human mobility and territoriality. However, it cannot be ruled out the possibility of other primary and secondary sources have been used but that are presently undersea, buried, eroded or unknown.
3.1. Macroscopic analysis
The macroscopic analysis of chert from Gruta Nova da Columbeira, following the methodology described above, identified five primary groups (Table 2).
The macroscopic characteristics of these chert assemblage shows diversity in texture, mineralogy, and color, suggesting different depositional and diagenetic conditions. Most samples are fine-grained, ranging from mud-supported (Mudstone, Wackestone) to grain-supported (Packstone, Boundstone).
Mud-supported cherts indicate low-energy sedimentation of the host limestone layers, while grain-supported types point to higher-energy environments or biogenic frameworks. Cherts are generally compact, indicating low primary porosity, or high diagenetic silicification though some semi-porous varieties (e.g., CH6, CH7, CH8, CH11) may show secondary porosity from diagenesis. Iron oxides, Liesegang rings, and geodes indicate post-depositional alteration, including fluid-rock interactions and oxidation, while chalcedony and bioclasts contribute to variability in luster.
Mud-supported cherts, such as CH1, CH6, and CH9, are compact to semi-porous with predominantly semi-opaque to translucent transparency. These samples exhibit dull to waxy luster, with some showing notable chalcedony content (e.g., CH1). CH6 is distinguished by the presence of geodes, suggesting a diagenetic overprint involving silica-filled void spaces. CH9, on the other hand, stands out for its high translucency, possibly indicating a high degree of silica purity and a lack of detrital impurities. The Munsell color values range from light grayish brown (10YR 6/2) to darker gray tones (5YR 4/1), suggesting generally low iron content with subtle variation, and potential organic matter influences.
Wacke-supported cherts (e.g., CH2, CH4, and CH5) are compact with low porosity, exhibiting semi-opaque transparency and a mix of dull, vitreous, and waxy lusters. CH2 is notable for the presence of geodes, which suggest cavity-filling silica precipitation during late-stage diagenesis. CH4 and CH5 contain bioclasts, indicating biological input and potential silica replacement of carbonate components. CH5 further distinguishes itself with the presence of chalcedony, reinforcing the interpretation of a mixed biogenic and chemically precipitated silica origin. Color variability within this group is significant, with hues ranging from reddish brown (10R 5/4) to light gray (5YR 8/1), likely reflecting iron variations and diagenetic oxidation processes.
A subset of samples, including CH3, CH10, and CH21, exhibit characteristics indicative of mixed mud-wacke compositions. These cherts maintain compact textures and semi-opaque transparency but display notable diagenetic features such as Liesegang rings (CH10, CH21) and iron concentrations. The Liesegang banding, particularly in CH10, suggests rhythmic silica precipitation influenced by fluctuating redox conditions. Iron-rich samples, such as CH21, exhibit darker hues (5R 3/4, 10R 2/2), consistent with ferruginous silica cementation.
Pack-supported cherts (CH7, CH14, and CH22) exhibit semi-porous to compact textures, with dull to waxy luster and moderate variability in bioclastic content. CH7, for instance, contains bioclasts and shows significant color heterogeneity (10YR 8/2 to 10R 2/2), potentially indicative of depositional variations in oxygenation levels. CH14 contains minor iron, which contribute to subtle reddish-brown tones (5Y 5/2, 10YR 8/6). These cherts may represent higher-energy depositional settings, where silica replacement of pre-existing carbonate frameworks was influenced by more dynamic diagenetic conditions.
Boundstone-associated cherts (e.g., CH8, CH24) exhibit a more massive texture, typically with opaque to semi-opaque transparency and waxy or dull luster. These samples occasionally contain geodes (CH8), suggesting synsedimentary or early diagenetic silicification of carbonate-rich sediments. Their color profiles, ranging from white (N9) to reddish-brown (5YR 5/6), indicate a combination of primary mineral composition and later diagenetic alteration.
Overall, the chert assemblage reflects a spectrum of silica diagenetic processes, from primary biogenic sources to secondary chemical precipitation and silica replacement of pre-existing carbonate substrates. Variability in iron content, Liesegang banding, and porosity characteristics further suggest differential diagenetic histories, likely controlled by localized geochemical conditions and fluid-rock interactions.
It was possible to detect secondary patinas reflected mostly on the lustre of the assemblage. The great majority of the pieces analysed present a waxy to dull lustre. Thermal alterations caused thermal domes, cracking and a waxy sheen. Likewise, these elements may have alterations in their colouring and fracture pattern which partly limit the correct correlation of these pieces with macroscopic groups. When thermic alterations were evident, these elements were excluded from the raw material identification analysis. However, their presence is important to note because it confirms the occurrence of fires inside the cave, as suggested by the ash detected during the excavation (Cardoso et al. 2002).
3.2. pXRF results
The pXRF analysis (Supplementary information Table 1 and Fig. 6a) was only performed in the assemblage from Gruta Nova da Columbeira and a wider number of samples from LusoLit. Results show the predominance of silica often with values close to 100% but shifting in some cases down to 81,5%. Phosphate, sulfur, and chlorine are present in all samples. Calcium is present in all archaeological samples from Gruta Nova da Columbeira and in several geological samples from primary outcrops and gravels nearby them, reflecting the environmental inputs from the cave and their original association with limestone or dolostone.
Nickel is present in very few specimens, and it only appears in the samples from further north in the eastern façade of the Serra d’Aire and Candeeiros (Arneiro da Milhariça and Espinheiro). Au appears in several archaeological and geological samples, the latter from the eastern drainage of Serra d’Aire and Candeeiros. Other samples to the west of this mountain are associated with quartzite, quartz, and chert cobbles in the gravels of Leiria and Nazaré, but never in primary position. Tungsten, barium, and silver appear in geological samples from this same region on either side of the Serra d’Aire and Candeeiros. Some of the geological samples from this area may have moved North-South due to the river dynamics, but they seem to be relatively consistent in their position. The samples with less silica are those that tend to have higher magnesium. Aluminum is present in most but not all specimens, which is a common feature of several sources in western Iberia.
The cluster analysis of single readings and mean values of multiple readings show several branches linking the Gruta Nova da Columbeira specimens with the Cesaredas at west, the Nazaré outcrop and Leiria at north, some sources from the top the Serra d’Aire and Candeeiros, and with gravels from the western parts of Rio Maior and Alenquer.
3.3. PIXE results
Silica is dominant but its frequency shifts between 99,9% and 61,4%. Phosphorus, sulfur, chlorine, potassium, calcium, titanium and manganese are the most common elements while cobalt, nickel, copper, zinc, bromine and strontium are present in lesser amounts. Bromine (usually associated with evaporitic deposits) and strontium are only present in archaeological specimens from Praia de Rei Cortiço and Gruta Nova da Columbeira, which might indicate a local chemical signal that is not from the western face of Cesaredas from where two of the several geological samples already taken were analyzed. Nickel is only present in Nazaré and cobalt is only present in Nazaré and Montes (12 km inland from Nazaré), both areas more than 30 km from the cave.
The cluster analysis shows two major branches. One includes archaeological specimens from Gruta Nova da Columbeira and a single specimen from Praia Rei Cortiço that is chemically and macroscopically distinct from the others recovered from this site, and another with only archaeological specimens from Praia Rei Cortiço and Mira Nascente (Supplementary information Table 2 and Fig. 6b).