The data on the distribution and frequencies of private polymorphisms in the tribal populations of Central and South America are used to address the question of the extent to which such data can be used to address questions of phylogenetic history. It is shown that due to the great increases in population number that accompanied agricultural development, most private polymorphisms have arisen since population settlement and tribal differentiation. Conversely, the absence of Amerindian variants of wide distribution confirms the small size of the hemispheric population until relatively recent times. Patterns of recent population decline and recovery that accompanied European contact since 1492 have also had a strong impact on the age distribution of extant variants, eliminating many that were relatively young in 1492. The majority of surviving variants that have achieved polymorphic frequencies in a tribe or group of tribes are from 100 to 400 generations old (2500 to 10,000 years). Such genetic variants thus characterize tribes, or groups of closely related tribes, but do not provide a greater time depth of phylogenetic history.