Significance: The transition from a foraging subsistence strategy to a sedentary farming society is arguably the greatest innovation in human history. Some modern-day groups—specifically the Basques—have been argued to be a remnant population that connect back to the Paleolithic. We present, to our knowledge, the first genome-wide sequence data from eight individuals associated with archaeological remains from farming cultures in the El Portalón cave (Atapuerca, Spain). These individuals emerged from the same group of people as other Early European farmers, and they mixed with local hunter–gatherers on their way to Iberia. The El Portalón individuals showed the greatest genetic affinity to Basques, which suggests that Basques and their language may be linked with the spread of agriculture across Europe.

Significance: The gene pool of modern Europeans was shaped through prehistoric migrations that reached the Western Mediterranean last. Obtaining biomolecular data has been challenging due to poor preservation related to adverse climatic conditions in this region. Here, we study the impact of prehistoric (Neolithic–Bronze Age) migrations in Iberia by analyzing genomic and dietary data, demonstrating that farming practices were introduced by a population genetically distinct from the first farmers in central and northern Europe. After recovering from a founder bottleneck, these first farmers mixed with local hunter-gatherers. Finally, post-Neolithic migrations had a much smaller impact on the Iberian gene pool than they had in other parts of Europe. Stable isotope analysis reveals a homogenous terrestrial diet throughout this period.

Ancient DNA (aDNA) is the most informative biomolecule extracted from skeletal remains at archaeological sites, but its survival is unpredictable and its extraction and analysis is time consuming, expensive and often fails. Several proposed methods for better understanding aDNA survival are based upon the characterisation of some aspect of protein survival, but these are typically non-specific; proteomic analyses may offer an attractive method for understanding preservation processes. In this study, in-depth proteomic (LC-Orbitrap-MS/MS) analyses were carried out on 69 archaeological bovine bone and dentine samples from multiple European archaeological sites and compared with mitochondrial aDNA and amino acid racemisation (AAR) data. Comparisons of these data, including estimations of the relative abundances for seven selected non-collagenous proteins, indicate that the survival of aDNA in bone or dentine may correlate with the survival of some proteins, and that proteome complexity is a more useful predictor of aDNA survival than protein abundance or AAR. The lack of a strong correlation between the recovery of aDNA and the proteome abundance may indicate that the survival of aDNA is more closely linked to its ability to associate with bone hydroxyapatite crystals rather than to associate with proteins. Ancient biomolecule survival remains poorly understood, even with great advancements in 'omics' technologies, both in genomics and proteomics. This study investigates the survival of ancient DNA in relation to that of proteins, taking into account proteome complexity and the relative protein abundances to improve our understanding of survival mechanisms. The results show that although protein abundance is not necessarily directly related to aDNA survival, proteome complexity appears to be.

Aranbaltza is an archaeological complex formed by at least three open-air sites. Between 2014 and 2015 a test excavation carried out in Aranbaltza III revealed the presence of a sand and clay sedimentary sequence formed in floodplain environments, within which six sedimentary units have been identified. This sequence was formed between 137–50 ka, and includes several archaeological horizons, attesting to the long-term presence of Neanderthal communities in this area. One of these horizons, corresponding with Unit 4, yielded two wooden tools. One of these tools is a beveled pointed tool that was shaped through a complex operational sequence involving branch shaping, bark peeling, twig removal, shaping, polishing, thermal exposition and chopping. A use-wear analysis of the tool shows it to have traces related with digging soil so it has been interpreted as representing a digging stick. This is the first time such a tool has been identified in a European Late Middle Palaeolithic context; it also represents one of the first well-preserved Middle Palaeolithic wooden tool found in southern Europe. This artefact represents one of the few examples available of wooden tool preservation for the European Palaeolithic, allowing us to further explore the role wooden technologies played in Neanderthal communities.