Evolutionary trees and admixture: phylogenetic inference when some populations are hybridized

Maximum likelihood estimation of admixture parameters and divergence times for an evolutionary tree in which some populations may be hybridized is developed. A test of treeness against the alternative of hybridization using a hierarchy of admixture models is proposed as an adjunct to the goodness-of-fit test suggested by Cavalli-Sforza & Piazza (1975). The method is illustrated by an application to gene frequency data from Makiritare Indian villages in southern Venezuela.