Figure 1.
The processes of discord. Three biological processes can generate gene trees that differ from the species tree. (A) The combined action of gene duplication and loss, (B) horizontal gene transfer, and (C) deep coalescence, where polymorphic alleles can remain present in a population for a time than spans two speciations (black squares show the alleles that coexist for this period). In each of these examples, the genes from species C and D are closest relatives, although species C is more closely related to species B (adapted from Maddison 1997).
