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We examined the evolutionary history ofPhytophthora infestansand its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates ofPhytophthoraspecies in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis. We consistently identified distinct and later divergence of the two MexicanPhytophthoraspecies,P.mirabilisandP.ipomoeae, fromP.infestansand other 1c clade species.Phytophthora infestansexhibited more recent divergence from other 1c clade species ofPhytophthorafrom South America,P.andinaandP.betacei. Speciation in the 1c clade and evolution ofP.infestansoccurred in the Andes.P.andina–P.betacei–P.infestansformed a species complex with indistinct species boundaries, hybridizations between the species, and short times to common ancestry. Furthermore, the distinction between modern Mexican and South AmericanP.infestansproved less discrete, suggesting gene flow between populations over time. Admixture analysis indicated a complex relationship among these populations, hinting at potential gene flow across these regions. HistoricP.infestans, collected from 1845–1889, were the first to diverge from all otherP.infestanspopulations. Modern South American populations diverged next followed by Mexican populations which showed later ancestry. Both populations were derived from historicP.infestans. Based on the time of divergence ofP.infestansfrom its closest relatives,P.andinaandP.betaceiin the Andean region, we consider the Andes to be the center of origin ofP.infestans, with modern globalization contributing to admixture betweenP.infestanspopulations today from Mexico, the Andes and Europe. 

Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P . infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.