DOI: 10.5061/dryad.41ns1rngw
title: Phylogenetic data for: High diversity of new and known Phytophthora species from phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the Americas

description: During extensive surveys of Phytophthora diversity, 14 new species were
 detected in natural ecosystems in Chile, Louisiana, Sweden, Ukraine,
 Vietnam and Indonesia. Multigene phylogeny based on the nuclear LSU,
 rpl10, ITS, ßtub, enl, hsp90, tef-1α, ras-ypt1 and tigA and the
 mitochondrial cox1, nadh1 and rps10 gene sequences demonstrated that they
 belong to phylogenetic Clade 10 which is structured into three subclades.
 Subclades 10a and 10b comprise soil- and waterborne species with
 nonpapillate sporangia and variable breeding systems, including the known
 P. afrocarpa, P. gallica and P. intercalaris and the new P. ludoviciana,
 P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P.
 tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in
 Subclade 10c are airborne with papillate sporangia and homothallic
 breeding system, including the known P. boehmeriae, P. kernoviae and P.
 morindae and the new P. celebensis, P. chilensis, P. javanensis, P.
 multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new species
 differed from each other and from related species by a unique combination
 of morphological characters, the breeding system, cardinal temperatures
 and growth rates. The biogeography and evolutionary history of Clade 10
 are discussed and the hypothesis put forward that the extant subclades
 originate from early divergences of pre-Gondwanan ancestors (&gt;175
 Mya) into water-/soilborne and airborne lineages which during their global
 spread experienced multiple allopatric and sympatric radiations.
description: For phylogenetic analyses, the sequences
 obtained in this study were complemented with publicly available sequences
 of isolates from <em>Phytophthora</em> Clade10 sourced from
 the GenBank Nucleotide Collection and GenBank Whole-Genome Shotgun
 contigs. For the informally designated Clade 10 taxa
 <em>P.</em> sp. canthium and <em>P.</em> sp.
 Maryland 6 and several isolates of <em>P. boehmeriae </em>and
 <em>P. gallica,</em> only sequences from the ITS and partly a
 few other gene regions were available at GenBank, so they could not be
 included in the multigene phylogenetic analyses of this study. To assess
 the phylogenetic positions of <em>P.</em> sp. canthium and
 <em>P.</em> sp. Maryland 6 within Clade 10 and to confirm the
 identity of a geographically representative range of isolates designated
 at GenBank as <em>P. boehmeriae</em> and <em>P.
 gallica</em>, respectively, a 892-character ITS-dataset was
 analysed. It included 74 isolates of the 14 new
 <em>Phytophthora</em> species, 53 isolates belonging to the
 seven described species and three informally designated taxa of Clade 10,
 and two isolates of the Clade 9 species <em>P. constricta</em>
 (CBS 125801) and <em>P. fallax</em> (CBS 119109) as outgroup
 taxa. The relative phylogenetic positions of the 14
 new and eight described or informally designated
 <em>Phytophthora</em> species from Clade 10 were assessed with
 a 12-partition (LSU, ITS, <em>β</em><em>tub</em>, <em>hsp90</em>,
 <em>tigA</em>, <em>rpl10</em>,
 <em>tef-1α</em>, <em>enl</em>,
 <em>ras-ypt1</em>, <em>cox1</em>,
 <em>nadh1</em>, <em>rps10</em>) dataset (11,259
 characters), which included 88 Clade 10 isolates representative of genetic
 variation and geographic distribution and <em>P.
 constricta</em> (CBS 125801) and <em>P. fallax</em> as
 outgroup taxa. For <em>P. fallax</em>, sequences from two
 isolates (CBS 119109 and ICMP 17563) were combined since for neither of
 them all 12 loci were available at GenBank (the two isolates shared an
 identical <em>cox1</em> sequence). The 90-isolates datasets of
 the 12 loci were also analysed separately. Briefly, the sequences of all loci used in the
 analyses were aligned using the MAFFT v. 7. Bayesian
 Inference (BI) analyses were performed using BEAST 2 and
 Maximum-Likelihood (ML) analyses were carried out using IQ-TREE. Detailed
 methodology can be found on the official publication "High diversity
 of new and known <em>Phytophthora</em> species from
 phylogenetic Clade 10 in natural ecosystems of Asia, Europe and the
 Americas".
description: Data
 supplied: Table for identification of species, isolates
 and sequences used on the phylogenetic analyses;
 MAFFT sequence alignments
 (fasta files, used as input files in BEAST 2 and
 IQ-TREE). Trees obtained from BI and ML analyses (50%
 majority-rule consensus trees).