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- SPIN enables high throughput species identification of archaeological bone by proteomicsPublication . Rüther, Patrick Leopold; Husic, Immanuel Mirnes; Bangsgaard, Pernille; Gregersen, Kristian Murphy; Pantmann, Pernille; Carvalho, Milena; Godinho, Ricardo Miguel; Friedl, Lukas; Cascalheira, João; Taurozzi, Alberto John; Jørkov, Marie Louise Schjellerup; Benedetti, Michael; Haws, Jonathan; Bicho, Nuno; Welker, Frido; Cappellini, Enrico; Olsen, Jesper VelgaardSpecies determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
- The early Aurignacian dispersal of modern humans into westernmost EurasiaPublication . Haws, Jonathan; Benedetti, Lucilla; Talamo, Sahra; Bicho, Nuno Gonçalo Viana Pereira Ferreira; Cascalheira, João; Ellis, M. Grace; Carvalho, Milena M.; Friedl, Lukas; Pereira, Telmo; Zinsious, Brandon K.Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.
- Human adaptive responses to climate and environmental change during the Gravettian of Lapa do Picareiro (Portugal)Publication . Haws, Jonathan; Benedetti, Michael; Carvalho, Milena; Ellis, Grace; Pereira, Telmo; Cascalheira, João; Bicho, Nuno; Friedl, LukasOn the Iberian Peninsula, abrupt climate shifts during the Late Pleistocene impacted human and natural systems. Our knowledge of human adaptive responses to these climatic perturbations has improved in recent years with the development of new radiocarbon techniques that have increased the temporal resolution of cultural chronologies. At the same time, new high-resolution paleoclimatic records from Greenland ice cores, deep-sea sediment cores, speleothems, and microfaunal assemblages have permitted detailed paleoenvironmental reconstructions. Combined with the archaeological record of culture change, these data sets allow for a better understanding of the nature of human socio-ecological systems during the Late Pleistocene. Here we present new data on the Gravettian occupations at Lapa do Picareiro, a cave site in Portugal with a long continuous stratigraphic sequence spanning MIS 3 and 2. The ongoing excavation of Lapa do Picareiro has revealed at least three Gravettian levels with very different patterns of raw material use and technological reduction. The Early Gravettian levels contain a quartzite flake assemblage with several refitting clusters and a small chert assemblage with nosed endscrapers and bladelet technology. The Late or Terminal Gravettian level contains carinated endscraper/core-bladelet technology, mainly quartz, with chert blade production, and a few bone tools. The faunal assemblages also have a different character. Both contain a similar range of medium and large ungulates but the earlier Gravettian has a much richer and more diverse assemblage of small animals. These combined archaeological data sets provide a new perspective on Gravettian human adaptations in response to climate shifts, especially Heinrich Event 3 and Greenland Interstadials 4 and 3.
- Impact of 3D surface scanning protocols on the Os coxae digital data: implications for sex and age-at-death assessmentPublication . Koterova, Anezka; Kralik, Vlastimil; Rmoutilova, Rebeka; Friedl, Lukas; Ruzicka, Pavel; Veleminska, Jana; Marchal, Francois; Bruzek, JaroslavThe 3D imaging technologies have become of paramount importance for example in disciplines such as forensic anthropology and bioarchaeology, where they are being used more and more frequently. There are several new possibilities that they offer; for instance, the easier and faster sharing of data among institutions, the possibility of permanent documentation, or new opportunities of data analysis. An important requirement, however, is whether the data obtained from different scanning devices are comparable and whether the possible varying outputs could affect further analyses, such as the estimation of the biological profile. Therefore, we aimed to investigate two important questions: (1) whether 3D models acquired by two different scanning technologies (structured light and laser) are comparable and (2) whether the scanning equipment has an effect on the anthropological analyses, such as age-at-death estimation and sex assessment. 3D models of ossa coxa (n = 29) were acquired by laser (NextEngine) and structured light (HP 3D Structured Light Scanner PRO 2) scanners. The resulting 3D models from both scanners were subjected to age-at-death analyses (via the quantitative method of Stoyanova et al., 2017) and sex analyses (via Diagnose Sexuelle Probabiliste 2 of Brůžek et al., 2017). Furthermore, high quality scans of a small sample (n = 5) of pubic symphyseal surfaces with the RedLux Profiler device were acquired as reference surfaces to which the outputs from both scanners were compared. Small deviations between surfaces were more evident in more rugged surfaces (in areas of depression and protrusion). Even though small differences from the reference surfaces were found, they did not have a significant effect on the age and sex estimates. It never resulted in the opposite sex assignment, and no significant differences were observed between age estimates (with the exception of those with the TPS/BE model).