ABSTRACT
Phylogenetics began with the concept of a single branching tree representing ancestral relationships among its taxa. Reality is not always so straightforward. Non-treelike phylogenetic signal can arise in several ways. While it can be mimicked by error obscuring an underlying treelike phylogeny, it can also represent genuine reticulations in the ancestry relationships: cases in which a single taxon or sequence has multiple ancestors. Reticulations can arise within populations via recombinational mechanisms including crossing over, gene conversion, and chromosome segregation, and between populations or species by ancestral polymorphism (incomplete lineage sorting), hybridization, or horizontal gene transfer. For example, when a patient is infected with two strains of HIV-1, recombination can produce a hybrid molecule with two distinct ancestors, each contributing one or more segments of the viral chromosome. Such a sequence cannot be correctly placed on a normal phylogenetic tree, because it did not arise by a treelike process.
