A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

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In 2013 a survey of Phytophthora diversity was performed in 25 natural and semi-natural forest stands and 25 rivers in temperate montane and subtropical lowland regions of Taiwan. Using baiting assays, ten described species and 17 previously unknown taxa of Phytophthora were isolated from 71.5% of the 144 rhizosphere soil samples from 33 of 40 tree species sampled in 24 forest stands ,and from 19 rivers: P. capensis, P. citrophthora, P. plurivora, P. tropicalis, P.citricola VII, P. sp. x botryosa-like, P. sp. x meadii-like and P. sp. occultans-like from Clade 2; P. palmivora from Clade 4; P. castaneae and P. heveae from Clade 5; P. chlamydospora and P. sp.forestsoil-like from Clade 6; P. cinnamomi (Pc), P. parvispora, P. attenuata nom. prov., P. flexuosa nom. prov., P. formosa nom. prov., P. intricata nom. prov., P. x incrassata nom. prov. and P. x heterohybrida nom. prov. from Clade 7; P. sp. palustris and five new hybrid species from Clade 9.The A1 mating type of Pc was widespread in both montane and lowland forests and rarely associated with disease, whereas the A2 mating type was limited to lowland forests and in some cases causing severe dieback. Most other Phytophthora species were not associated with obvious disease symptoms. It is concluded that (1) Taiwan is within the center of origin of most Phytophthora taxa found, (2) PcA2 is an introduced invasive pathogen, and (3) interspecific hybridisations play a major role in speciation and species radiations in diverse natural ecosystems.