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The value of phylogenetic comparisons between populations based on tooth morphology as an indicator of genetic differences between them is evaluated by considering populations at various stages of differentiation (e.g., local differentiation at village and village-cluster level, tribal level, racial level). By a partition of total variability of dental morphologic variation into its between and within population components we observe some departure from a similar genetic analysis. This departure may be due to differences at the level of evolutionary rates of divergence for monogenic and polygenic traits. However, by a dendrogram analysis it is shown that at a relatively broad level of differentiation (e.g., tribal level) some general features of tooth morphology make them useful indicators of biological distance.