Illustration of an embedded quartet in a gene tree. In each 11-taxon unrooted gene tree (shown in gray thin lines), we look at the relationship of any four taxa at a time (shown in thick black lines is an example of an embedded tree for taxa 1, 4, 9, and 10), which we call an embedded quartet. In one gene tree, an embedded quartet can support only one of three possible phylogenetic relationships among the four taxa. However, in other gene trees, an alternative phylogenetic relationship for this quartet can be observed. In each 11-taxon gene tree, all possible (4 11) four-taxon trees embedded within the gene tree are examined.
