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- Mesolithic and chalcolithic mandibular morphology: using geometric morphometrics to reconstruct incomplete specimens and analyse morphologyPublication . Godinho, Ricardo Miguel; Umbelino, Cláudia; Gonçalves, CéliaHuman skeletal remains are routinely used to examine cultural and biological aspects of past populations. Yet, archaeological specimens are frequently fragmented/incomplete and so excluded from analyses. This leads to decreased sample sizes and to potentially biased results. Digital methods are now frequently used to restore/estimate the original morphology of fragmented/incomplete specimens. Such methods include 3D digitisation and Geometric Morphometrics (GM). The latter is also a solidly established method now to examine morphology. In this study, we use GM-based methods to estimate the original morphology of incomplete Mesolithic and Chalcolithic mandibles originating from present Portugal and perform ensuing morphological analyses. Because mandibular morphology is known to relate to population history and diet, we hypothesised the two samples would differ. Thirty-seven specimens (12 complete and 25 incomplete) were CT-scanned and landmarked. Originally complete specimens were used as reference to estimate the location of absent anatomical landmarks in incomplete specimens. As predicted, our results show shape differences between the two samples which are likely due to the compounded effect of contrasting population histories and diets.
- 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.
- Changes in dental wear magnitude in the last ∼8000 years in southwestern IberiaPublication . Godinho, Ricardo Miguel; Umbelino, Cláudia; Garcia, Susana; Gonçalves, CéliaObjective: This study examines changes in dental wear magnitude in the past -8000 years, i.e., since Mesolithic until the 19th century, in southwestern Iberia. Thus, it encompasses the transition from hunting-gathering to agro-pastoralism, and then to the industrialization of food production and pre-processing. Design: Dental wear magnitude was scored in a total of 191 individuals and 1557 teeth from Mesolithic (individuals=56; teeth=643), Neolithic (individuals=35; teeth=169), Chalcolithic (individuals =35; teeth=221), Modern Age (individuals=17; teeth=209), and Late Modern Age (individuals=48; teeth=315) samples originating in southwestern Iberia (i.e., present central and southern Portugal) and according to the 8 levels ordinal scale of Smith (1984). Results: Results show a general trend for decreased wear magnitude in these two major transitions and during this timespan (although the hunting-gathering - agro-pastoralism transition had larger impact). The only meaningful differences in wear rate were found between the Late Modern Age and all remaining samples. Conclusion: Dental wear generally decreased during this timespan (although wear magnitude was less impacted by the industrialization of food production and pre-processing). Our results are consistent with studies documenting skull morphological gracilization associated with reduced masticatory demands due to the adoption of softer diets.
- The preburning condition of Chalcolithic cremated human remains from the Perdigoes enclosures (Portugal)Publication . Godinho, Ricardo Miguel; Goncalves, David; Carlos Valera, AntónioThe Iberian Chalcolithic displayed a remarkable variety of funerary practices, which has been related to interpopulation differences, intrapopulation social-cultural differences, and complex multistage funerary rituals. Perdigoes, a Chalcolithic set of ditched enclosures, reflects such diversity including a wide array of funerary practices. Among those practices is cremation, which, despite relatively rare, is represented in different structures in Perdigoes. One of these structures (Pit 40) presents an unparalleled high minimum number of individuals (n = 240), contrasting with nearby and coeval structures. In this study, we analyse heat-induced bone changes and other archaeothanatological variables to tentatively assess the preburning condition of the human remains. The results of Pit 40 are also compared with other comparable contexts to assess if this unique context presents further funerary differences relative to those other contexts in, for example, body processing. Our results suggest preferential cremation of fleshed human remains, but burning of at least a minority of skeletonised remains and deposition of possibly unburned remains also likely occurred. Body processing appears to be comparable with that of the cremation contexts of Perdigoes but contrasts with that of another nearby context (Dolmen of Olival da Pega 2b) in which burned bones were also found.
- Mandibular morphology and the Mesolithic–Neolithic transition in Westernmost IberiaPublication . Godinho, Ricardo Miguel; Umbelino, Cláudia; Valera, António Carlos; Carvalho, António; Bicho, Nuno; Cascalheira, João; Gonçalves, Célia; Smith, PatriciaNeolithic farming and animal husbandry were first developed in the Near East similar to 10,000 BCE and expanded westwards, reaching westernmost Iberia no later than 5500 BCE. It resulted in major social, cultural, economic and dietary changes. Yet, the impact of this change on human mandibular morphology in Iberia is yet to be assessed, which is regrettable because mandible form is impacted by population history and diet. In this study we used Mesolithic to Chalcolithic Iberian samples to examine the impact of this transition on mandibular morphology. We also compared these samples with a Southern Levantine Chalcolithic population to assess their relationship. Lastly, we assessed dental wear to determine if the morphological differences identified were related to the material properties of the diet. We found differences between samples in mandibular shape but not size, which we attribute to contrasting population histories between Mesolithic and later populations. Some differences in the severity of dental wear were also found between Mesolithic and later Iberian samples, and smaller between the Mesolithic Iberians and southern Levantines. Little relationship was found between wear magnitude and mandibular shape. Altogether, our results show that the Mesolithic-Neolithic Iberian transition resulted in a meaningful change in mandibular morphology, which was likely driven more by population history than by dietary change.
- Exploring the utility of geometric morphometrics to analyse prehistoric hand stencilsPublication . Fernández Navarro, V.; Godinho, Ricardo Miguel; García Martínez, D.; Garate Maidagan, D.Hand stencils are a remarkable graphic expression in Prehistoric rock art, dating back to 42 ka BP. Although these stencils provide direct impressions of the artists' hands, the characterization of their biological profile (i.e., biological sex and age) is very challenging. Previous studies have attempted this analysis with traditional morphometrics (TM), whereas little research has been undertaken using Geometric Morphometrics (GM), a method widely used in other disciplines but only tentatively employed in rock art studies. However, the large variation in relative finger position in archaeological hands poses the question of whether these representations can be examined through GM, or, in contrast, if this creates an unmanageable error in the results. To address this issue, a 2D hand scans sample of 70 living individuals (F = 35; M = 35) has been collected in three standardized positions (n = 210) and digitized with 32 2D conventional landmarks. Results show that the intra-individual distance (mean Procrustes distance between Pos. 1-2 = 0.132; 2-3 = 0.191; 1-3 = 0.292) is larger than the inter-individual distance (mean in 1 = 0.122; 2 = 0.142; 3 = 0.165). Finally, it has been demonstrated that the relative finger positions, as well as the inclusion of all hand parts in the analysis, have an overshadowing effect on other variables potentially involved in the morphometric variability of the hand, such as biological sex.
- Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identificationPublication . Mylopotamitaki, Dorothea; Harking, Florian S.; Taurozzi, Alberto J.; Fagernäs, Zandra; Godinho, Ricardo Miguel; Smith, Geoff M.; Weiss, Marcel; Schüler, Tim; McPherron, Shannon P.; Meller, Harald; Cascalheira, João; Bicho, Nuno; Olsen, Jesper V.; Hublin, Jean-Jacques; Welker, FridoHigh-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.
- Is enamel the only reliable hard tissue for sex metric estimation of burned skeletal remains in biological anthropology?Publication . Godinho, Ricardo Miguel; Ines, Oliveira-Santos; Pereira Manuel Francisco, C.; Antonio, Mauricio; Carlos Valera, António; David, GoncalvesSex diagnosis is a crucial element in the analysis of skeletal remains from forensic and archaeological contexts. Thus, researchers have developed several methods using different anatomical regions to estimate sex. Despite such variety of methods, sexing of collective cremated human skeletal remains is still challenging due to heat-induced size changes and fragmentation, along with the typical commingling of collective contexts. This study aims to examine the potential of burned tooth crowns for odontometric sex estimation. To that end, heat-induced size changes were quantified in experimentally heated teeth. Then, odontometric sex estimation was performed in a set of theoretical samples of pre and post-heated tooth crowns. Results show heated tooth crowns undergo variable but consistent and statistically significant expansion, which is due to micro-fracturing. Such heat induced size changes are of sufficient magnitude to impact odontometric sex diagnosis and sex ratios of the theoretical samples. Yet, sexing using heated/burned tooth crowns may still be useful to estimate the minimum number of females in a given sample. Further, the effect of heat-induced size changes may be calculated and removed using mu CT scanning.
- A lunate-triquetral coalition from a commingled funerary context from the Chalcolithic Perdigoes ditched enclosures of PortugalPublication . Godinho, Ricardo Miguel; Santos, Ana Luisa; Valera, António CarlosCarpal coalitions, resulting from a failure of separation of the cartilaginous precursors of the carpal bones during gestation, may be osseous or non-osseous. Even though lunate-triquetral coalitions are the most common of all carpal coalitions there is only one previous palaeopathological report of such a coalition. This study presents a non-osseous lunate-triquetral coalition found amongst the mostly cremated commingled bones from a Chalcolithic pit at Perdigoes (Portugal). The cremated bones show evidence of burning at varying but mostly at generally high temperatures. The perfect articulation between these right bones and pinpoint pitting in the lunate-triquetral joint were crucial for the identification of this congenital condition. Carpal coalitions are more frequent in African than European populations. Artifacts produced from ivory of African origin were found in Perdigoes, however it is not possible to establish the ancestry of this individual.
- Geometric morphometrics and finite elements analysis: assessing the functional implications of differences in craniofacial form in the hominin fossil recordPublication . O'Higgins, Paul; Fitton, Laura; Godinho, Ricardo MiguelThe study of morphological variation in the hominin fossil record has been transformed in recent years by the advent of high resolution 3D imaging combined with improved geometric morphometric (GM) toolkits. In parallel, increasing numbers of studies have applied finite elements analysis (FEA) to the study of skeletal mechanics in fossil and extant hominoid material. While FEA studies of fossils are becoming ever more popular they are constrained by the difficulties of reconstruction and by the uncertainty that inevitably attaches to the estimation of forces and material properties. Adding to these modelling difficulties it is still unclear how FEA analyses should best deal with species variation. Comparative studies of skeletal form and function can be further advanced by applying tools from the GM toolkit to the inputs and outputs of FEA studies. First they facilitate virtual reconstruction of damaged material and can be used to rapidly create 3D models of skeletal structures. Second, GM methods allow variation to be accounted for in FEA by warping models to represent mean and extreme forms of interest. Third, GM methods can be applied to compare FEA outputs the ways in which skeletal elements deform when loaded. Model comparisons are hampered by differences in material properties, forces and size among models but how deformations from FEA are impacted by these parameters is increasingly well understood, allowing them to be taken into account in comparing FEA outputs. In this paper we review recent advances in the application of GM in relation to FEA studies of craniofacial form in hominins, providing examples from our recent work and a critical appraisal of the state of the art.