Putting dental calculus under the microscope

Dental calculus. This small, hard, inconspicuous substance that forms on the teeth of humans and animals contains a surprising amount of information about our lives. During its formation and growth as a living biofilm, it accumulates a wide variety particles, especially bacteria and food debris.What makes this so interesting to archaeologists is that, when plaque hardens and forms dental calculus, these particles become trapped and well-protected against removal and degradation during hundreds to thousands of years, preserving a picture of past activities.The major problem—one of the major problems, for there are several—one of the many major problems is that this picture was never a complete picture of a lifetime of activities, and that picture fades over time. We know that these problems exist and that they limit our interpretations of past activities. What we need to do is approach these problems at a fundamental level. In my dissertation I introduce a protocol for growing artificial dental calculus. Working with a very controlled model allows me to explore the influence of a wide range of factors that may affect the uptake of particles into dental calculus, and better explain why and how our picture is incomplete.Bioarchaeolog

Investigating biases associated with dietary starch incorporation and retention with an oral biofilm model

Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited to in vivo studies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted on in vitro dental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25 days growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06% to 0.16%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules (>20 μm) consistently being under-represented. We also found a positive correlation between the absolute granule counts and dry-weight of the biofilm (r = 0.659, 90%CI[0.463, 0.794]), meaning the absolute quantity of starch granules will increase as the size of the calculus deposit increases. A similar, but weaker correlation was found between the concentration (count per mg) of granules and dry-weight (r = 0.3, 90%CI[0.0618, 0.506]). Our results complement and reinforce previous in vivo studies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20 μm in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus.Horizon 2020(H2020)STG–677576Bioarchaeolog

European Society for the Study of Human Evolution 2017: old sites, new methods

Horizon 2020(H2020)ERC-STG 677576Bioarchaeolog

Dog Days on the Plains: A Preliminary aDNA Analysis of Canid Bones from Southern Alberta and Saskatchewan

Dogs were an important component of lifeways on the Northern Plains until the reintroduction of the horse following European contact. There has been little investigation into the variability of domesticcanids on the Prairies and the potential of that variability as a proxy for identifying relationships between culture-historic entities. Distinguishing between sympatric canids using morphological characteristics can be challenging with degraded specimens that have high intra-specific variability, and where wolf-dog hybridization can result in transitional morphologies. Here, we present preliminary ancient DNA data on archaeological canids recovered from FM Ranch (EfPk-1) and Cluny (EePf-1) in Alberta, as well as fromLake Midden (EfNg-1) in Saskatchewan. Using the mitochondrial control region, we taxonomically reclassify zooarchaeological remains, find potential evidence of European dogs in a protocontact component, and identify preliminary indications of a distinct dog population at the Cluny site that may beof interest for determining the origin of the One Gun phase.Bioarchaeolog

Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 1; peer review: 1 approved, 1 approved with reservations]

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.Bioarchaeolog

The real deal?: Validation of a dental calculus model using FTIR

Dental calculus is increasingly used by researchers looking at diet in past populations. These studies employ a range of methods including microscopy, and DNA and protein extraction. Despite the promise of these methods little attention has been given to the potential biases associated with the accumulation of dietary compounds into dental calculus during the lifetime of an individual. Our recently-developed oral biofilm model has the potential to elucidate these biases by growing in vitro dental calculus in a controlled environment. Here we report on one validation test of the system, which explored whether our model calculus mineralizes in a manner similar to actual calculus. FTIR was conducted on multiple samples across 25 days of model calculus growth. Results show an overall increase in the inorganic component relative to organic over the course of the experiment. This is especially evident in the hydroxyapatite peak at 1040 and doublet at 605 and 565 wave-numbers (cm -1), and a reduction in intensities of the peaks at 1546 and 1654 wavenumbers (cm-1). IR splitting factors (IRSF) ranged from 2.38–3.30, indicating a similar level of crystallinity to modern human-derived calculus samples (IRSF 3.46–3.76). The final model calculus consisted mainly of carbonated hydroxyapatite, the principal component of real calculus, although with a higher organic component than the comparative modern samples. This and prior validation of the model dental calculus suggests that it is a viable method to supplement the analysis of fossil dental calculus.Horizon 2020(H2020)StG-677576Bioarchaeolog

Getting rid of dichotomous sex estimations: why logistic regression should be preferred over discriminant function analysis

Bioarchaeolog

Age estimation using vertebral bone spurs: testing the efficacy of three methods on a European population

Age-at-death estimation is an essential step in both bioarchaeological and forensic studies when human remains are found, as this can also contribute to the identification of the individual. It is critical that age-at-death methods be tested verified in various populations, to obtain the most accurate estimation, making research into new age-at-death methods also imperative. Since osteophyte formation on the vertebral column increases with age, this can be used as a possible method of age-at-death estimation. Snodgrass (2004), Watanabe and Terazawa (2006) and Praneatpolgrang et al. (2019) have tested this method before and have provided promising results. We test the efficacy of Snodgrass (2004), Watanabe and Terazawa (2006), and Praneatpolgrang et al. (2019) on a 19th-century archivally recorded Dutch population. A total of 88 individuals, 40 males, and 48 females were scored for the degree of osteophyte formation on the vertebral column. In addition to testing the three methods above, population-specific regression equations were developed and tested. Accuracy percentages for estimating the age-at-death based on the mean osteophyte score of the entire vertebral column were obtained for all three methods (73.86%, 76.14%, and 72.73%, respectively). In this study, a general pattern of osteophyte formation could be established, which is useful for estimating the age at death. We therefore recommend that this method can be used, cautiously as a means of age-at-death estimation.Bioarchaeolog