Phylogenetic Incongruence: Window into Genome History and Molecular Evolution

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

“…Observations of our phylogenies show that incongruence are primarily deep ones that affect the topological positions of major clades, not positions of species within clades. Such discordances between phylogenies based on nuclear and chloroplast markers are generally caused by convergent evolution, lineage sorting, or ancient hybridization and introgression (Rieseberg and Soltis, 1991;Mason-Gamer et al, 1995;Rieseberg et al, 1996;Wendel and Doyle, 1998;Sang and Zhong, 2000;Comes and Abbott, 2001;Linder and Rieseberg, 2004). Among these, hybridization and incomplete lineage sorting have gained considerable attention and are known to confound phylogenetic analyses (Sang and Zhong, 2000;Maddison and Knowles, 2006;Joly et al, 2009).…”

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

“…majalis S1 Fig. 3 (continued) and horizontal gene transfer) can cause these phylogenetic inconsistencies (Cronn and Wendel, 2004;Linder and Rieseberg, 2004;Maddison, 1997;Rieseberg and Soltis, 1991;Wendel and Doyle, 1998;Zou and Ge, 2008). Among these causes, introgression and incomplete lineage sorting have been frequently discussed as the prominent factors of phylogenetic incongruence at lower taxonomic levels (Cronn and Wendel, 2004;Joly et al, 2009;Maddison and Knowles, 2006).…”

Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

“…Possible evolutionary processes that lead to incongruence between gene trees and species trees or among gene trees include the processes of rapid diversification, genetic introgression following hybridization, incomplete lineage sorting, and horizontal gene transfer (Rieseberg and Soltis, 1991;Maddison, 1997;Wendel and Doyle, 1998). In many studies, phylogenetic analyses based on chloroplast data failed to agree with morphology-based taxonomy, which were supported by nuclear markers, because the chloroplasts of these taxa are acquired from other taxa (Okuyama et al, 2005;Gehrke et al, 2008).…”

“…Also, when the level of divergence among closely related species is low, it is often difficult to distinguish these two processes from each other in phylogenetic analysis (Wendel and Doyle, 1998). On the other hand, these two processes predict different spatial patterns and thus a biogeographic analysis can be used to differentiate them (Goodman et al, 1999).…”