Data and Code for Publication "Testing the Utility of Dental Morphological Trait Combinations for Inferring Human Neutral Genetic Variation"

Data and code for publication: H. Rathmann, H. Reyes-Centeno, Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation. Proc. Natl. Acad. Sci. U.S.A. 117, 10769-10777 (2020). DOI: 10.1073/pnas.1914330117

The repository contains:

• “R-code.txt”: R code for an exhaustive search algorithm testing the utility of dental morphological traits and trait combinations for inferring human neutral genetic variation.
• “dental trait frequencies.csv”: Data set with 27 dental morphological trait frequencies for 20 modern human populations worldwide used for analysis. Data from G. R. Scott, C. G. Turner, G. C. Townsend, M. Martinón-Torres, The Anthropology of Modern Human Teeth (Cambridge University Press, 2018). DOI: 10.1017/ 9781316795859
• “microsatellite loci mean sizes.csv”: Data set with 645 microsatellite mean allele sizes for 20 modern human populations worldwide used for analysis. Data from T. J. Pemberton, M. DeGiorgio, N. A. Rosenberg, Population structure in a comprehensive genomic data set on human microsatellite variation. G3: Genes Genom. Genet. 3, 891–907 (2013). DOI: 10.1534/g3.113.005728
• “utility estimates for 134217727 trait combinations.txt”: A large table with utility estimates for 27 dental morphological traits and all 134,217,700 possible trait combinations.

Abbreviations for the 20 population names (rows) in “dental trait frequencies.csv” and “microsatellite loci mean sizes.csv” as follows:

• AUS = Australia
• CAS = Central Asia
• EAF = Eastern Africa
• EAS = East Asia
• EEU = Eastern Europe
• IND = India
• MAM = Mesoamerica
• MEL = Melanesia
• MIC = Micronesia
• NAF = North Africa
• NAM = North America
• NESI = Northeast Siberia
• NGU = New Guinea
• NWAM = Na-Dene
• POL = Polynesia
• SAM = South America
• SAN = San
• SEAS = Southeast Asia
• WEU = Western Europe
• WSAF = Sub-Saharan Africa

Abbreviations for the 27 dental morphological trait names (columns) in “dental trait frequencies.csv” as follows:

• T1 = Winging (UI1)
• T2 = Shoveling (UI1)
• T3 = Double-Shoveling (UI1)
• T4 = Interruption Grooves (UI2)
• T5 = Tuberculum Dentale (UI2)
• T6 = Mesial Ridge (UC)
• T7 = Distal Accessory Ridge (UC)
• T8 = Hypocone (UM2)
• T9 = Carabelli Trait (UM1)
• T10 = Cusp 5 (UM1)
• T11 = Enamel Extensions (UM1)
• T12 = Peg-Reduced-Missing (UM3)
• T13 = Lingual Cusp Number (LP2)
• T14 = Groove Pattern (LM2)
• T15 = Cusp 6 (LM1)
• T16 = Cusp Number (LM2)
• T17 = Deflecting Wrinkle (LM1)
• T18 = Distal Trigonid Crest (LM1)
• T19 = Protostylid (LM1)
• T20 = Cusp 7 (LM1)
• T21 = Odontomes (UP-LP)
• T22 = Root Number (UP1)
• T23 = Root Number (UM2)
• T24 = Root Number (LC)
• T25 = Tomes’ Root (LP1)
• T26 = Root Number (LM1)
• T27 = Root Number (LM2)

Abbreviations for the 645 microsatellite allele locus names (columns) in “microsatellite loci mean sizes.csv” as in T. J. Pemberton, M. DeGiorgio, N. A. Rosenberg, Population structure in a comprehensive genomic data set on human microsatellite variation. G3: Genes Genom. Genet. 3, 891–907 (2013). DOI: 10.1534/g3.113.005728