Exploring Directional and Fluctuating Asymmetry in the human palate during growth (dataset and R scripts)

DESCRIPTION

The present digital archive is the outcome of the paper: Oxilia, G., Menghi Sartorio JC., Bortolini, E. et al. Exploring Directional and Fluctuating Asymmetry in the human palate during growth. The american Journal of Physical Anthropology.

The dataset included in this repository provides a collection of palatal arches of 183 individuals from two Italian identified human skeletal collections (Bologna and Florence) aged from 1 to 72 years. The individuals from the Bologna collection (n=87), housed at the Museum of Anthropology of the University of Bologna, are from the Certosa cemetery (Bologna). The collection includes a total of 425 individuals of known sex, name and age at death (range 0-91 years), most of whom belonged to the less-advantaged urban classes of late 19th and early 20th Century (Belcastro et al. 2017). The sample from the Florence collection (n=96), hosted in the Natural History Museum (Anthropology and Ethnology section), University of Florence, belongs to unclaimed indigents from the Florence hospital and comprises lower-class citizens of known sex, name and age at death (range 1-57 years), who lived in the town of Florence in the 19th century (industrialized only after 1890). Paleopathological information of the Bologna individuals was sourced from archival data, which indicated that most of the individuals died following infections diseases (Belcastro et al. 2017) while the Florence individuals health profiles indicated a tendency to breastfeed children until 12-18 months of age and an unbalanced dietary intake induced by poor living conditions (Moggi-Cecchi et al., 1994). Both these findings were consistent with pre- and post-unification Italy in Bologna and pre-industrialised Florence.

For the study, male and female individuals from Bologna and Florence were separated into six groups (Table 1) based on direct observation of skeletal remains. Age groups were subdivided considering mixed dentition until permanent dentition based on the time of eruption/occlusion of the molars. The groups have been divided based on eruption of the dm2 (Group I; 1, 3-1.7 years old – yo), permanent first molar (Group II; 2-6 yo), permanent second molar (Group III; 7-12 yo) and third molar (Groups IV; 13-18 y.o) in occlusion (Groups V; 19-35 y.o) and showing worn crown (Group VI; 36-72 yo). Individuals with damaged maxillae or presenting pathological conditions such as abscesses and extended alveolar bone absorption were excluded to avoid any spurious measurement of asymmetry.

We are grateful to the Natural History Museum (Anthropology and Ethnology section), University of Florence (Dr. Monica Zavattaro), and to the Museum of Anthropology of the University of Bologna for granting access to the collections.

CONTENTS

Main folder “Oxilia_etal_2021_DataAndCodes”

  • Commented R Script providing all codes to reproduce all analyses and figures contained in the paper (Oxilia_etal_2021_Log.R)

Folder “Oxilia_etal_2021_dataSource”

  • R Script for calculating pairwise Procrustes distances to be used in statistical analysis (pwisedist.R)

  • A series of 6 .txt files providing coordinates (X, Y, Z) extracted from Viewbox for each landmark and semilandmark used in the study for all age groups I-VI (ClassI-VI.txt)

  • A .txt file providing the list of landmarks and semilandmarks on curve used to compute Generalised Procrustes Analysis (curveslide.txt)

  • A .txt file provifing the list of sliding semilandmarks used for Generalised Procrustes Analysis (surfslide.txt)

  • A .txt file providing pairs of left-right landmarks and semilandmarks used to generate RR copies and to perform downstream analyses (landpairs.txt)

  • A .txt file providing the output of codes for calculating DA values to be used for the final statistical analysis (Dunn test) (DA_tot.txt)

Licences

Dataset: CC-BY (http://creativecommons.org/licenses/by/4.0/)

Code: MIT (https://choosealicense.com/licenses/mit/ year: 2021, copyright holder: Jessica Cristina Menghi Sartorio, Eugenio Bortolini, and Gregorio Oxilia.

Dependencies

R version 4.0.3 (2020-10-10)

Packages * geomorph (v.3.2.1) * Morpho (v. 2.8) * shapes (v. 1.2.5) * abind (v. 1.4.5) * pegas (v. 0.13) * RColorBrewer (v. 1.1.2) * plotrix (v. 3.7.8) * vegetarian (v. 1.2) * vegan (v. 2.5.6) * FSA (v. 0.8.32)