Data and Code for Publication "Testing the Utility of Dental Morphological Trait Combinations for Inferring Human Neutral Genetic Variation"
2020-03-17

&lt;p&gt;Data and code for publication: H. Rathmann, H. Reyes-Centeno, Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation. &lt;em&gt;Proc. Natl. Acad. Sci. U.S.A.&lt;/em&gt; 117, 10769-10777 (2020). DOI: 10.1073/pnas.1914330117&lt;/p&gt; &lt;p&gt;The repository contains:&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&ldquo;R-code.txt&rdquo;: R code for an exhaustive search algorithm testing the utility of dental morphological traits and trait combinations for inferring human neutral genetic variation.&lt;/li&gt; &lt;li&gt;&ldquo;dental trait frequencies.csv&rdquo;: 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. Martin&oacute;n-Torres, &lt;em&gt;The Anthropology of Modern Human Teeth&lt;/em&gt; (Cambridge University Press, 2018). DOI: 10.1017/ 9781316795859&lt;/li&gt; &lt;li&gt;&ldquo;microsatellite loci mean sizes.csv&rdquo;: 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. &lt;em&gt;G3: Genes Genom. Genet.&lt;/em&gt; 3, 891&ndash;907 (2013). DOI: 10.1534/g3.113.005728&lt;/li&gt; &lt;li&gt;&ldquo;utility estimates for 134217727 trait combinations.txt&rdquo;: A large table with utility estimates for 27 dental morphological traits and all 134,217,700 possible trait combinations.&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Abbreviations for the 20 population names (rows) in &ldquo;dental trait frequencies.csv&rdquo; and &ldquo;microsatellite loci mean sizes.csv&rdquo; as follows:&lt;/p&gt; &lt;ul&gt; &lt;li&gt;AUS = Australia&lt;/li&gt; &lt;li&gt;CAS = Central Asia&lt;/li&gt; &lt;li&gt;EAF = Eastern Africa&lt;/li&gt; &lt;li&gt;EAS = East Asia&lt;/li&gt; &lt;li&gt;EEU = Eastern Europe&lt;/li&gt; &lt;li&gt;IND = India&lt;/li&gt; &lt;li&gt;MAM = Mesoamerica&lt;/li&gt; &lt;li&gt;MEL = Melanesia&lt;/li&gt; &lt;li&gt;MIC = Micronesia&lt;/li&gt; &lt;li&gt;NAF = North Africa&lt;/li&gt; &lt;li&gt;NAM = North America&lt;/li&gt; &lt;li&gt;NESI = Northeast Siberia&lt;/li&gt; &lt;li&gt;NGU = New Guinea&lt;/li&gt; &lt;li&gt;NWAM = Na-Dene&lt;/li&gt; &lt;li&gt;POL = Polynesia&lt;/li&gt; &lt;li&gt;SAM = South America&lt;/li&gt; &lt;li&gt;SAN = San&lt;/li&gt; &lt;li&gt;SEAS = Southeast Asia&lt;/li&gt; &lt;li&gt;WEU = Western Europe&lt;/li&gt; &lt;li&gt;WSAF = Sub-Saharan Africa&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Abbreviations for the 27 dental morphological trait names (columns) in &ldquo;dental trait frequencies.csv&rdquo; as follows:&lt;/p&gt; &lt;ul&gt; &lt;li&gt;T1 = Winging (UI1)&lt;/li&gt; &lt;li&gt;T2 = Shoveling (UI1)&lt;/li&gt; &lt;li&gt;T3 = Double-Shoveling (UI1)&lt;/li&gt; &lt;li&gt;T4 = Interruption Grooves (UI2)&lt;/li&gt; &lt;li&gt;T5 = Tuberculum Dentale (UI2)&lt;/li&gt; &lt;li&gt;T6 = Mesial Ridge (UC)&lt;/li&gt; &lt;li&gt;T7 = Distal Accessory Ridge (UC)&lt;/li&gt; &lt;li&gt;T8 = Hypocone (UM2)&lt;/li&gt; &lt;li&gt;T9 = Carabelli Trait (UM1)&lt;/li&gt; &lt;li&gt;T10 = Cusp 5 (UM1)&lt;/li&gt; &lt;li&gt;T11 = Enamel Extensions (UM1)&lt;/li&gt; &lt;li&gt;T12 = Peg-Reduced-Missing (UM3)&lt;/li&gt; &lt;li&gt;T13 = Lingual Cusp Number (LP2)&lt;/li&gt; &lt;li&gt;T14 = Groove Pattern (LM2)&lt;/li&gt; &lt;li&gt;T15 = Cusp 6 (LM1)&lt;/li&gt; &lt;li&gt;T16 = Cusp Number (LM2)&lt;/li&gt; &lt;li&gt;T17 = Deflecting Wrinkle (LM1)&lt;/li&gt; &lt;li&gt;T18 = Distal Trigonid Crest (LM1)&lt;/li&gt; &lt;li&gt;T19 = Protostylid (LM1)&lt;/li&gt; &lt;li&gt;T20 = Cusp 7 (LM1)&lt;/li&gt; &lt;li&gt;T21 = Odontomes (UP-LP)&lt;/li&gt; &lt;li&gt;T22 = Root Number (UP1)&lt;/li&gt; &lt;li&gt;T23 = Root Number (UM2)&lt;/li&gt; &lt;li&gt;T24 = Root Number (LC)&lt;/li&gt; &lt;li&gt;T25 = Tomes&rsquo; Root (LP1)&lt;/li&gt; &lt;li&gt;T26 = Root Number (LM1)&lt;/li&gt; &lt;li&gt;T27 = Root Number (LM2)&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Abbreviations for the 645 microsatellite allele locus names (columns) in &ldquo;microsatellite loci mean sizes.csv&rdquo; as in T. J. Pemberton, M. DeGiorgio, N. A. Rosenberg, Population structure in a comprehensive genomic data set on human microsatellite variation. &lt;em&gt;G3: Genes Genom. Genet.&lt;/em&gt; 3, 891&ndash;907 (2013). DOI: 10.1534/g3.113.005728&lt;/p&gt;