Fig 1.
Number of species in the Phytophthora genus.
Line graph showing the number of Phytophthora species included in different phylogenies from 2000 to the current study.
Fig 2.
Phylogeny of the Phytophthora genus.
Radial phylogeny of the genus Phytophthora inferred with maximum likelihood and 1,000 bootstrap replicates for an alignment of 8 concatenated nuclear genes. Coloring on the inner ring indicates clade. Colors on the middle ring indicate substrate. Colors on the outer ring indicate host range (broad, specific, or no host reported). The branches in the tree are drawn to scale and the scale bar represents 0.06 substitutions per site.
Fig 3.
Phylogeny of major Phytophthora clades.
Collapsed phylogenetic tree of the genus Phytophthora showing the relationships between the clades, outgroups, and species that do not fit into the conventional clade system. Clade 12 is highlighted in pink. Phylogeny is inferred using maximum likelihood and 1,000 bootstrap replicates for an alignment of 8 concatenated nuclear loci. Bootstrap values (in percent) are shown above each branch. The branches in the tree are drawn to scale and the scale bar represents 0.06 substitutions per site.
Table 1.
Recently described Phytophthora taxa in TBAS phylogeny along with a summary of their associated metadata and species description paper.
Fig 4.
Phylogeny of clades 1, 3 4, 5, and 12.
Collapsed phylogeny of the genus Phytophthora showing clades 1 (red), 3 (yellow), 4 (green), 5 (beige), and 12 (pink) in detail. Subclade values are shown as variations in color hue. Phylogeny is inferred using maximum likelihood and 1,000 bootstrap replicates for an alignment of 8 concatenated nuclear loci. Bootstrap values (in percent) are shown above each branch. The branches in the tree are drawn to scale and the scale bar represents 0.06 substitutions per site (0.003 substitutions per site in the inset).
Fig 5.
(A) Histogram of Phytophthora species in each lifestyle category over time. Histogram showing the number of Phytophthora species in each lifestyle category in major phylogenies published since 2000. (B) Histogram of Phytophthora species sorted by host ranges over time. Histogram showing the number of Phytophthora species in each host range category in major phylogenies published since 2000. Host specificity was characterized as “broad” or “specific”. Species with reported hosts in three or more plant families were characterized as "broad”, while species with reported hosts in two or fewer plant families were described as "specific”.
Fig 6.
Phylogeny of Phytophthora clades 6, 7, and 9.
Collapsed phylogeny of the genus Phytophthora showing 6 (green), 7 (teal), and 9 (blue) in detail. Subclade values are shown as variations in color hue. Phylogeny is inferred using maximum likelihood and 1,000 bootstrap replicates for an alignment of 8 concatenated nuclear loci. Bootstrap values (in percent) are shown for each branch. The branches in the tree are drawn to scale and the scale bar represents 0.06 substitutions per site.