Approaches to the Detection of Hybridization Events and Genetic Introgression upon Phylogenetic Incongruence

Introgressive hybridization is a widespread phenomenon in the evolution of plants and animals. The conclusion of interspecific gene flow is often made in the detection of discordance among gene trees. However, the found phylogenetic incongruence can also be caused by other evolutionary processes, such as incomplete lineage sorting. In this case, the detection and quantitative characterization of introgression is a very difficult task. This review briefly characterizes the main processes (hybridization and introgression, incomplete lineage sorting) that are responsible for the incongruence between gene tree topologies. Data on classical phylogenetic and analytical methods that make it possible to detect and distinguish hybridization and introgression from incomplete lineage sorting in the comparison of phylogenetic trees built based on individual genetic markers are summarized. Approaches developed not only for the detection of introgression patterns in the presence of incomplete lineage sorting but also for the quantification of the detected introgression (proportion of admixture, direction, time) are considered; the advantages and methodological limitations of each of them are briefly considered. The methods of phylogenetic networks, which seem to be an indispensable tool for the reconstruction of complex evolutionary histories in the presence of reticulate events (hybridization, introgression, and others), are also considered.