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To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five  Phytophthora  pathogens, including  P. infestans , the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among  P. infestans ,  P. andina , and  P. ipomoeae . The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that  P. andina  is a hybrid species, with  P. infestans  representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to  P. ipomoeae . While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.

Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives