Sex estimation is an important part of creating a biological profile for skeletal remains in forensics. The commonly used methods for developing sex estimation equations are discriminant function ...analysis (DFA) and logistic regression (LogR). LogR equations provide a probability of the predicted sex, while DFA relies on cutoff points to segregate males and females, resulting in a rigid dichotomization of the sexes. This is problematic because sexual dimorphism exists along a continuum and there can be considerable overlap in trait expression between the sexes. In this study, we used humeral measurements to compare the performance of DFA and LogR and found them to be very similar under multiple conditions. The overall cross‐validated (leave‐one‐out) accuracy of DFA (75.76–95.14%) was slightly higher than LogR (75.76–93.82%) for simple and multiple variable equations, and also performed better under varying sample sizes (94.03% vs. 93.78%). Three of five DFA equations outperformed LogR under the B index, while all five LogR equations outperformed the DFA equations under the Q index. Both methods saw an improvement in overall accuracy (DFA: 86.74–95.79%; LogR: 86.74–95.76%) when individuals with a classification probability lower than 0.80 were excluded. Additionally, we propose a method for calculating additional cutoff points (PMarks) based on posterior probability values. In conclusion, we recommend using LogR over DFA due to the increased flexibility, robusticity, and benefits for future users of the statistical models; however, if DFA is preferred, use of the proposed PMarks facilitates future analysis while avoiding unnecessary dichotomization.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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
μ
m) 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%CI0.463, 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%CI0.0618, 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
μ
m 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.
The main aim of this study is to present a novel method of nonadult (ca. 1–19 years) age‐at‐death estimation using the dental wear of deciduous, mixed deciduous‐permanent, and permanent dentitions, ...including the incisors, canines, premolars, and first and second molars. The stage‐based method is derived from degrees of dental wear in known‐age (n = 39) and estimated‐age (n = 11) nonadults containing 951 teeth from the predominately 19th century cemetery of Middenbeemster, The Netherlands. The need for such a method is warranted in cases where dental development and/or eruption cannot be assessed for age‐at‐death estimation. As well, by establishing a baseline for normal age‐related nonadult tooth wear, users may better document wear that could be due to extramasticatory behaviours. The regression analysis reveals a strong quadratic correlation—F(2, 47) = 555.1, p < .001, R2 = .95, standard error of the estimate = 1.14, residual sum of squares (RSS) = 68.89, predicted residual error sum of squares (PRESS) = 77.67—between age and wear and multivariate adaptive regression splines (R2 = .95, generalised cross validation = 1.67, RSS = 67.68, PRESS = 89.34), which are used to develop an R‐package that users may employ to estimate age‐at‐death from dental wear. The accuracy of this method (78–98%) is evaluated using leave‐one‐out cross‐validation. Analyses of males versus females, deciduous versus permanent, upper versus lower, and anterior versus posterior teeth revealed no apparent reason to warrant separate methods for these groups of separated dentitions. This method fills a disciplinary gap in the understudied area of deciduous and nonadult dental wear and hopes to stimulate much future research. With the R‐package, we also provide the foundation and framework for the development of additional reference populations across different spatiotemporal contexts, to make the method more widely applicable.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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 ...domestic canids 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 from Lake 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 be of interest for determining the origin of the One Gun phase. Le chien portait un rôle significatif au mode de vie dans le Nord des Grandes Plaines jusqu'à la réintroduction du cheval qui suivi le contact européen. Peu de recherches ont été effectuées au sujet de la variabilité des canidés domestiques dans les Prairies ni sur le potentiel de cette variabilité en tant que substitut qui servirait à identifier des relations entre différentes entités culture-historiques. Différencier des canidés sympatriques en utilisant des caractéristiques morphologiques peut être difficile lorsque les spécimens dégénérés, qui ont une grande variabilité intraspécifique, ou quand des hybrides loup-chien, qui peuvent montrer une morphologie de transition, sont analysés. Ici, nous présentons des données d'ADN fossile préalable, venant de canidés en contexte archéologique, recueillie de FM Ranch (EfPk-1) et Cluny (EePf-1) en Alberta, ainsi que de Lake Midden (EfNg-1) en Saskatchewan. En utilisant la région de contrôle mitochondriale, nous pouvons reclassifier les restes zooarchéologiques de façon taxonomique, prouver la présence de chiens Européens dans composant qui correspondant à la période de protocontact en plus de montrer des indications préalables pour la distinction d'une population de chiens dissemblables sur le site de Cluny, qui pourrait être d'intérêt pour définir l'origine de la phase One Gun.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.org) 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 rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.
Results
AncientMetagenomeDir was extended to include standardised metadata of over 6000 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 reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.
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.
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