Data and Code for Publication "Inferring human neutral genetic variation from craniodental phenotypes"

Data and code for publication: H. Rathmann et al., Inferring human neutral genetic variation from craniodental phenotypes. PNAS Nexus.

The repository contains:

“R code for DP-DG analysis.txt”: R code for testing levels of neutral evolutionary signals preserved in five craniodental data types: cranial metrics, dental metrics, cranial non-metric traits, dental non-metric traits, and craniodental metrics and non-metric traits combined.

“Cranial metric data.csv”: Dataset consisting of 37 cranial metric variables for 26 worldwide modern populations, provided in a comma-separated values file format. The data were collected by T. Hanihara and originally presented in the publication titled: T. Hanihara, Comparison of craniofacial features of major human groups. Am. J. Phys. Anthropol. 99, 389–412 (1996) (https://doi.org/10.1002/(SICI)1096-8644(199603)99:3<389::AID-AJPA3>3.0.CO;2-S).

“Dental metric data.csv”: Dataset comprising 28 dental metric variables for 26 worldwide modern populations, provided in a comma-separated values file format. The data were collected by T. Hanihara and originally presented in the publication titled: T. Hanihara, H. Ishida, Metric dental variation of major human populations. Am. J. Phys. Anthropol. 128, 287–298 (2005) (https://doi.org/10.1002/ajpa.20080).

“Cranial non-metric trait data.csv”: Dataset consisting of 24 cranial non-metric trait variables for 26 worldwide modern populations, provided in a comma-separated values file format. The data were collected for the most part by T. Hanihara and presented in the publication titled: T. Hanihara, H. Ishida, Y. Dodo, Characterization of biological diversity through analysis of discrete cranial traits. Am. J. Phys. Anthropol. 121, 241–251 (2003) (https://doi.org/10.1002/ajpa.10233).

“Dental non-metric trait data.csv”: Dataset comprising 25 dental non-metric trait variables for 26 worldwide modern populations, provided in a comma-separated values file format. The data were collected by C. G. Turner II, G. R. Scott, and J. D. Irish. This individual-level dataset was artificially created from population-level trait frequency information presented in the publications: G. R. Scott, J. D. Irish, Human Tooth Crown and Root Morphology (Cambridge University Press, 2017) (https://doi.org/10.1017/9781316156629); and: J. D. Irish, A. Morez, L. Girdland Flink, E. L. W. Phillips, G. R. Scott, Do dental nonmetric traits actually work as proxies for neutral genomic data? Some answers from continental- and global-level analyses. Am. J. Phys. Anthropol. 172, 347–375 (2020) (https://doi.org/10.1002/ajpa.24052).

“SNP data.txt”: Dataset comprising 8,821 SNP markers for 26 worldwide modern populations, provided in a genepop file format. The data were obtained from various published sources: I. Lazaridis et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014) (https://doi.org/10.1038/nature13673); P. Qin, M. Stoneking, Denisovan ancestry in east Eurasian and native American populations. Mol. Biol. Evol. 32, 2665–2674 (2015) (https://doi.org/10.1093/molbev/msv141); P. Skoglund et al., Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016) (https://doi.org/10.1038/nature19844); M. R. Nelson et al., The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am. J. Hum. Genet. 83, 347–358 (2008) (https://doi.org/10.1016/j.ajhg.2008.08.005); J. K. Pickrell, J. K. Pritchard, Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012) (https://doi.org/10.1371/journal.pgen.1002967); A. Bergström et al., Insights into human genetic variation and population history from 929 diverse genomes. Science 367 (2020) (https://doi.org/10.1126/science.aay5012); B. M. Henn et al., Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, e1002397 (2012) (https://doi.org/10.1371/journal.pgen.1002397); S. Mallick et al., The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016) (https://doi.org/10.1038/nature18964); Lao et al., Correlation between genetic and geographic structure in Europe. Curr. Biol. 18, 1241–1248 (2008) (https://doi.org/10.1016/j.cub.2008.07.049); and M. Lipson et al., Population Turnover in Remote Oceania Shortly after Initial Settlement. Curr. Biol. 28, 1157-1165.e7 (2018) (https://doi.org/10.1016/j.cub.2018.02.051).

For population and variable names and abbreviations, see Supplementary Information in: H. Rathmann et al., Inferring human neutral genetic variation from craniodental phenotypes. PNAS Nexus.