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In phylogenetic study, trees are used for describing evolutionary histories. In particular, a species tree presents population divergences, and a gene tree indicates the times that genes start to differentiate within populations. Even though speciation is driven by gene mutations, using a single gene tree to infer the species tree is not ideal. Often, the inconsistency between gene trees and species trees makes describing species relationships very difficult. Common causes of the conflict include gene duplication, horizontal gene transfer, incomplete lineage sorting, and hybridization. If speciation events occur closely, it is likely that some gene copies remain the same after species divergence. This inconsistency between gene trees and species tree is referred
as incomplete lineage sorting.
Hybridization refers to interbreeding between species. Offspring who carry gene from both parental species then reproduce, and form a new species. For closely related species, however,
