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Abstract ObjectivesMost research in human dental age estimation has focused on point estimates of age, and most research on dental development theories has focused on morphology or eruption. Correlations between developing teeth using ordinal staging have received less attention. The effect of demographic variables on these correlations is unknown. I tested the effect of reference sample demographic variables on the residual correlation matrix using the lens of cooperative genetic interaction (CGI). Materials and MethodsThe sample consisted of Moorrees et al.,Journal of Dental Research, 1963, 42, 1490–1502, scores of left mandibular permanent teeth from panoramic radiographs of 880 London children 3–22.99 years of age stratified by year of age, sex, and Bangladeshi or European ancestry. A multivariate cumulative probit model was fit to each sex/ancestry group (n = 220), each sex or ancestry (n = 440), and all individuals (n = 880). Residual correlation matrices from nine reference sample configurations were compared using Bartlett's tests of between‐sample difference matrices against the identity matrix, hierarchical cluster analysis, and dendrogram cophenetic correlations. ResultsBartlett's test results were inconclusive. Cluster analysis showed clustering by tooth class, position within class, and developmental timing. Clustering patterns and dendrogram correlations showed similarity by sex but not ancestry. DiscussionExpectations of CGI were supported for developmental staging. This supports using CGI as a model for explaining patterns of variation within the dentition. Sex was found to produce consistent patterns of dental correlations, whereas ancestry did not. Clustering by timing of development supports phenotypic plasticity in the dentition and suggests shared environment over genetic ancestry to explain population differences.
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AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software
Abstract SummaryAdmixture is a fundamental process that has shaped levels and patterns of genetic variation in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to identify the genetic ancestries in admixed populations. However, this software does not have a built-in method to visually summarize the results of analyses. Here, we introduce the AncestryGrapher toolkit, which converts the numerical output of RFMIX2 into graphical representations of global and local ancestry (i.e. the per-individual ancestry components and the genetic ancestry along chromosomes, respectively). ResultsTo demonstrate the utility of our methods, we applied the AncestryGrapher toolkit to visualize the global and local ancestry of individuals in the North African Mozabite Berber population from the Human Genome Diversity Panel. Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). We also found that the population origin of ancestry varied considerably along chromosomes (local ancestry). For example, we observed variance in local ancestry in the genomic region on Chromosome 2 containing the regulatory sequence in the MCM6 gene associated with lactase persistence, a human trait tied to the cultural development of adult milk consumption. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations. Availability and implementationThe AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot.
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- Award ID(s):
- 2221920
- PAR ID:
- 10635103
- Editor(s):
- Kendziorski, Christina
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- Volume:
- 40
- Issue:
- 11
- ISSN:
- 1367-4811
- Page Range / eLocation ID:
- btae616
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/bioinformatics/btae616
