The mtDNA haplotypes of the plant pathogen Phytophthora infestans present in dried potato and tomato leaves from herbarium specimens collected during the Irish potato famine and later in the 19th and early 20th century were identified. A 100 bp fragment of ribosomal DNA (rDNA) specific for P. infestans was amplified from 90% of the specimens (n=186), confirming infection by P. infestans. Primers were designed that distinguish the extant mtDNA haplotypes. 86% percent of the herbarium specimens from historic epidemics were infected with the Ia mtDNA haplotype. Two mid-20th century potato leaves from Ecuador (1967) and Bolivia (1944) were infected with the Ib mtDNA haplotype of the pathogen. Both the Ia and IIb haplotypes were found in specimens collected in Nicaragua in the 1950s. The data suggest that the Ia haplotype of P. infestans was responsible for the historic epidemics during the 19th century in the UK, Europe, and the USA. The Ib mtDNA haplotype of the pathogen was dispersed later in the early 20th century from Bolivia and Ecuador. Multiple haplotypes were present outside Mexico in the 1940s–60s, indicating that pathogen diversity was greater than previously believed.

DNA was extracted from soil collected from the upper 15 cm of the profile at three sclerophyll forest sites in New South Wales three days before, and 14 d after prescribed burning events. rDNA internal transcribed spacer (ITS) regions were amplified by PCR using fungus-specific primers, and ITS products cloned. Restriction fragment length polymorphism (RFLP) analysis was conducted on the ITS clones using the endonucleases HaeIII, HinfI, MboI and AluI. Cloned ITS products from the three sites were thus separated into 120 RFLP types and the ITS product for each RFLP type was sequenced. Comparison of sequences with those available in the GenBank nucleotide database allowed putative assignment of ITS clones to the following functional groups: ectomycorrhizal (ECM), arbuscular mycorrhizal (AM), ericoid mycorrhizal (ERM), decomposer basidiomycetes (DEC), other soil fungi (OSF). While abundant ECM-like clones were amplified from pre-fire soils at the North Rocks and South Maroota sites, they were largely absent in the post-fire soils at these sites, being replaced mainly by microfungi. In contrast, no decrease in ECM-like ITS clones was observed at the Ridgecrop site following fire. The data indicate that, while the abundance of extraradical ECM fungal propagules in the upper soil profile may be reduced by prescribed burning, the effect is site-specific.

Differences in morphology, ITS, IGS, mtSSU and β-tubulin sequences and UP–PCR hybridization were compared between morphologically identified F. avenaceum, F. arthrosporioides, F. anguioides, F. tricinctum, F. graminum and F. acuminatum strains. According to the combined β-tubulin, IGS and ITS tree, the strains of the Fusarium avenaceum/F. arthrosporioides/F. tricinctum species complex species can be divided into seven clusters supported by bootstrap values higher than 50%. The two main groups of European F. avenaceum, which cannot be distinguished by morphology, were separated in the tree based on β-tubulin sequences and less clearly in trees based on IGS and ITS sequences. MtSSU sequences were identical in all F. avenaceum and F. tricinctum strains studied. The European F. avenaceum strains of main group II had identical β-tubulin sequences with one American F. avenaceum strain and four European F. arthrosporioides strains, while F. avenaceum strains of main group I were closely related to two European F. arthrosporioides strains and to one Japanese F. anguioides strain. According to the combined β-tubulin/IGS/ITS sequence tree, European F. arthrosporioides strains were divided into four groups; F. tricinctum strains formed a well-supported cluster, in which two European clusters were separated from one African isolate. In the IGS sequence tree two European F. acuminatum strains together with one American F. acuminatum strain formed a cluster, which was separate from another American F. acuminatum strain. The F. acuminatum cluster was nested within the large F. tricinctum cluster together with one F. reticulatum strain in the combined IGS/β-tubulin tree. Several strains may be intermediates between the F. avenaceum/F. arthrosporioides/F. anguioides and F. tricinctum clusters and represent their own species. These results are partially supported by the results of UP–PCR hybridization analysis. Thus the molecular results may be helpful in future revision in the taxonomy of these species.

Current classifications of the Lyophylleae and the importance of siderophilous granulation in the basidia for the classification of agaricoid fungi were evaluated using parsimony analyses of sequence data from the nuclear ribosomal large subunit gene (nLSU), the internal transcribed spacer region of the nuclear ribosomal array (ITS), and the mitochondrial ribosomal small subunit gene (mtSSU). These three different data partitions were phylogenetically congruent on the basis of the Mickevich–Farris statistical test, but not from the ILD and the Templeton tests. Bootstrap supports for nodes in phylogenetic trees generated from combined nLSU, ITS, and mtSSU sequence data were generally higher than those in trees generated from individual data sets. This suggests a lack of major conflict in the phylogenetic signal among the different data sets. We conclude that the Mickevich–Farris test is more appropriate for estimating congruence and combinability between different sources of molecular data than the more widely used ILD and Templeton tests, at least when the different data sets have their respective resolution power at different depths in the phylogeny. Results of the combined analyses show that the Entolomataceae are a sister group to a clade composed of the Lyophylleae, Termitomyceteae, and Tricholomateae p.p. This implies that presence of siderophilous granulation in the basidia of agaric fungi has probably a single origin, and would have been lost in the Tricholomateae. Inclusion of the Termitomyceteae within the Lyophylleae suggests homology of the macro type granulation. Because the exact placement of Tricholomateae pro parte remains uncertain, it remains unclear whether the Lyophylleae (including Termitomyceteae) are monophyletic or paraphyletic. Within the Lyophylleae, genera Lyophyllum and Calocybe are shown to be artificial, as are Lyophyllum sections Lyophyllum, Difformia, and Tephrophana. Four main natural groups of Lyophylleae have been identified that should serve as a basis for developing a more natural classification system for these fungi.

Arbuscular mycorrhizal fungi (AMF) show significant potential for biocontrol of Phytophthora spp., but there is little evidence for the mechanisms involved in the process. This study establishes that microorganism free exudates from roots colonised by AMF result in significantly less sporulation of P. fragariae than those from uncolonised plants. Experiments in vitro showed that after 48 h in the presence of exudates from strawberry roots colonised by Glomus etunicatum and G. monosporum, sporulation of P. fragariae was reduced by ca 67% and 64% relative to sporulation in the presence of uncolonised roots. After 72 h sporulation was reduced by 83% and 89% respectively. These data were then confirmed in an in vivo system in which Phytophthora fragariae was inoculated into the mycorrhizosphere of either uncolonised strawberry plants or those colonised by G. etunicatum. A similar trend was observed, with a 69% reduction in sporulation of P. fragariae after 72 h in the mycorrhizosphere of colonised plants relative to sporulation in the mycorrhizosphere of uncolonised plants.

Fusarium graminearum and F. pseudograminearum are important plant pathogens in New Zealand and around the world. Headblight and crown rot diseases of cereals caused by these species are responsible for large economic losses due to reduction in seed quality and contamination of grain with tricothecene mycotoxins. In the current study we have used two different molecular phylogenetic approaches, AFLPs and gene genealogies, to gain insight into the evolutionary relationships between F. graminearum, and F. pseudograminearum in New Zealand. The worldwide genetic diversity of F. graminearum clade is represented by at least eight biogeographically distinct species (previously designated as lineages of F. graminearum). Our analysis demonstrated that this clade is represented by F. graminearum (=F. graminearum Lineage 7) and F. cortaderiae (=F. graminearum Lineage 8) in New Zealand. Through our analysis we also confirm the presence of F. pseudograminearum in New Zealand as a first record for this organism. Information on species is necessary for preventing the inadvertent intercontinental introduction of genetically unique foreign pathogens associated with world trade. The ability to place species information into a worldwide context enabled postulation that the New Zealand representatives of F. graminearum clade originated from at least two regions, and probably on at least two hosts. Correlation of species descriptions with biogeographical and host information revealed evidence for co-localisation of F. graminearum clade species with potential for genetic outcrossing in the field. Mycotoxin analysis showed F. graminearum (=lineage 7) isolates produce either nivalenol (NIV) or deoxnivalenol (DON). In contrast, F. cortaderiae isolates produced only NIV. These findings support earlier observations that mycotoxin production in the F. graminearum clade is not species specific, but suggest maintenance of chemotype diversity through speciation may have been restricted to a subset of species.

Random amplification of polymorphic DNA (RAPD), using both fingerprinting (M13, [GTG]5, [GACA]4) and random [V5] primers, has been used to analyse 145 isolates characteristic of Trichoderma sect. Longibrachiatum and Hypocrea species with anamorphs referable to that section, and to identify strains with named species of sect. Longibrachiatum. To this end, ex-type strains of T. longibrachiatum, T. pseudokoningii, T. citrinoviride, T. parceramosum and T. reesei were analysed, and the similarity coefficients of RAPD characters used as a criterion for the alignment of strains to individual species. The ex-type strains of T. saturnisporum and T. ghanense exhibited the same interspecific similarity index as the other ex-type strains of Trichoderma sect. Longibrachiatum, and clustered well within it and were therefore included into this section. 103 isolates were identified as members of Trichoderma sect. Longibrachiatum and further investigated. Most of the anamorphic isolates could be aligned with T. citrinoviride or T. longibrachiatum, whereas only a few strains of T. saturnisporum and T. parceramosum were found. No naturally occurring anamorphs with homology to the ex-type strains of T. reesei and T. pseudokoningii were found. While T. longibrachiatum and T. citrinoviride overlapped through much of their geographic ranges, the former was present in Africa and India but not in southeast Asia, while the reverse was true of the latter. The African strains of T. longibrachiatum were equally distant from the ex-type strains of T. longibrachiatum, T. parceramosum and T. saturnisporum. The type strain of T. ghanense was identified as belonging to this group. T. pseudokoningii, the anamorph of Hypocrea schweinitzii, was found exclusively in eastern Australia and New Zealand. Attempts to identify potential teleomorphs of the other anamorphs revealed another subgroup of H. schweinitzii, occurring in temperate climates in Europe and U.S.A., as homologous to T. citrinoviride. No Hypocrea strains could be identified as teleomorphs of T. longibrachiatum, T. parceramosum or T. saturnisporum.

Seed samples of maize (Zea mays ssp. mays) from Mexico and of teosintes (Zea spp.), the nearest wild relatives of maize, from Mexico, Guatemala, and Nicaragua were assessed for infection with Fusarium species. Strains similar in morphology to Fusarium moniliforme and F. subglutinans were the most frequent isolates from maize and from teosinte species including Z. diploperennis, Z. luxurians, Z. mays ssp. mexicana, and Z. mays ssp. parviglumis. Analysis of fertility, vegetative compatibility and mycotoxin production identified 63% of the 70 F. moniliforme strains from teosinte as genetically diverse members of Gibberella fujikuroi mating population A, a common pathogen of maize. The F. subglutinans strains from maize and teosinte were similarly genetically diverse, but were not fertile with standard testers of G. fujikuroi mating populations B and E, common pathogens of Poaceae, or of mating population H, which causes pitch canker disease of pine. Fifty-four percent of the 80 F. subglutinans strains were fertile when crossed with female tester strains from teosinte and maize collected in a field at Netzahualcoyotyl in the state of Mexico. These strains from Mexico and Central America may comprise a new and distinct G. fujikuroi mating population, but a strain from the Netzahualcoyotyl field site was fertile with a strain of G. fujikuroi mating population H from California. Thus, F. subglutinans from teosinte and maize may have a close relationship to mating population H from pine.

A Phytophthora pathogen of trees and shrubs previously designated Phytophthora sp. O-group is formally named as P. inundata sp. nov. P. inundata falls within the P. gonapodyides-P. megasperma major ITS Clade 6, its present nearest known relative being P. humicola. It has non-papillate sporangia, fairly large oogonia (average ca 40 μm) with thick walled oospores, amphigynous antheridia, a distinctive colony type, a high optimum temperature for growth of 28–30°C, fast growth at the optimum, and a high upper temperature limit for growth of ca 35–37°. A study of the breeding system of eight P. inundata isolates showed them to be classically heterothallic with A1 and A2 compatibility types. However some P. inundata A1×A2 combinations failed to mate even though the same isolates mated successfully with P. drechsleri testers. Others were ‘silent’ A1s or A2s, unable to produce their own gametangia but able to induce gametangial formation in the opposite sexual compatibility type of another species. This indicates a partial breakdown of the sexual mechanism in the species. Two isolates (one A1 and one A2) were unpredictably and chimaerically self-fertile, suggesting A1+A2 chromosomal heteroploidy. The association of P. inundata with ponds and rivers and with root and collar rots of trees and shrubs after flooding is discussed.

Chlorophenols have been commonly used as disinfectants and preservatives but their recalcitrant nature, persistence and toxicities make them priority pollutants for treatment. The ability of various fungi (Armillaria gallica, A. mellea, Ganoderma lucidum, Lentinula edodes, Phanerochaete chrysosporium, Pleurotus pulmonarius, a Polyporus sp., Coprinus cinereus and Volvariella volvacea), and the spent mushroom substrate of P. pulmonarius (SMS) to remove pentachlorophenol (PCP) was compared using a batch cultivation system. The PCP content was monitored by reversed phase HPLC, and the breakdown products were determined by GC-MS. Possession of ligninolytic ability was determined by ability to decolourize the dye Poly-R478 at two N levels. Not all the fungi tested decolourized the dye, and for those that did, not all showed N-modulation response on dye decolourization. All these fungi showed active breakdown in addition to biosorption as their PCP removal mechanisms. The tolerance level of the fungus towards PCP did not correlate with its degradative capacity, nor to its ability to decolourize Poly-R478. The A. mellea strain showed the highest degradative capacity (13 mg PCP g−1 mycelium; D.W.) while the Polyporus possessed the greatest biosorption capacity (31 mg PCP−1 mycelium, d.w.). In comparison, Pleurotus SMS harbouring both bacteria and fungi functioned over a wide range of initial PCP concentrations and reached a higher degradative capacity (19 mg PCP g−1) in only 3 d. GC-MS chromatograms revealed only residual PCP peaks in SMS extracts, a contrast with the mycelial incubations in which a variety of breakdown products were detectable. Use of SMS for bioremediation of biocide-contaminated sites seems promising.

The present investigation deals with the main factors involved in early infection of nematode eggs by fungal parasites. We studied the effect of hydrophobicity on appressorium formation by germlings of Pochonia rubescens (syn. Verticillium suchlasporium), P. chlamydosporia (syn. V. chlamydosporium) and Lecanicillium lecanii (syn. V. lecanii). Appressoria were frequently formed on hydrophobic surfaces such as polyvinyl chloride or polystyrene and were infrequently formed on hydrophilic materials such as glass or aluminium. Infected eggs probed with the FITC-labelled lectin Concanavalin-A showed intense labelling corresponding to appressoria formed by fungal parasites on the eggshell surface. Proteolytic activity was found in extracts from conidia and germlings of fungal parasites (especially P. chlamydosporia) in the absence of nematode eggs. Addition of the serine proteinase inhibitors phenylmetylsulphonyl fluoride (PMSF) or diisopropyl fluorophosphonate (DFP) to the extracts reduced their proteolytic activity. PMSF was the most effective inhibitor. Zymography also revealed proteolytic activity in extracts from the three fungi tested. This activity mostly corresponded to bands of Rf's of substrate degradation similar to that of purified main protease (P32) from P. rubescens. Other bands with molecular weight higher than P32 (low Rf) were found especially for P. chlamydosporia extracts. For L. lecanii only bands of low Rf were found. Serum anti-P32 partially inhibited proteolytic activity of extracts from conidia and germlings. Application of PMSF and DFP to the inoculum, reduced egg penetration for the three species studied. PMSF caused the highest reduction in eggs infected by L. lecanii, while DFP significantly reduced egg infection by both P. chlamydosporia and L. lecanii. Our results therefore show hydrophobicity, appresorium formation and protease production as factors involved in early parasitism of nematode eggs.

The importance of pneumocandin B0 as the fermentation-derived starting material for the antifungal drug candidate, MK-991, along with the identification of our production strain as Z. arboricola (ATCC 20868) as CBS prompted a search for other strains of Z. arboricola or Zalerion species with improved titres or that might produce natural pneumocandin analogues. Analysis of morphology, secondary metabolites profiles, and DNA fingerprinting demonstrated that ATCC 20868 was not congeneric with Z. arboricola. Ribosomal DNA sequences were compared among Zalerion species and pneumocandin-producing fungi and with rDNA sequences in GenBank. No good matches with sequences in GenBank were obtained for Z. arboricola or Z. maritimum, but for Z. varium, P. carpinea and ATCC 20868, relevant similarities were observed with ITS1 sequences from fungi of Leotiales. ATCC 20868 was phylogenetically more akin to P. carpinea, another pneumocandin producer, than initially suspected. The closest relative of ATCC 20868 seemed to be Hymenoscyphus monotropae. We conclude that the genus Zalerion is artificial; its species bear no phylogenetic relation among themselves. ATCC 20868 and Z. varium were related to fungi of the Leotiales. We propose a new anamorph genus and species, Glarea lozoyensis, to accommodate ATCC 20868.

Phylogenetic analysis of the ITS rDNA region was carried out with two economically important downy mildews, Pseudoperonospora cubensis, which infects species of Cucumis, Cucurbita, and Citrullus belonging to Cucurbitaceae, and P. humuli, which infects plants of the genus Humulus belonging to Cannabaceae. Two closely related species, P. cannabina and P. celtidis, were also included to reveal taxonomic relationships with the first two mildews. All four species formed a well-resolved clade when compared with the ITS sequences of other downy mildew genera, using Bayesian inference and maximum parsimony. The P. cubensis isolates obtained from different hosts and (or) geographical origins in Korea, exhibited no intraspecific variability in the ITS sequences. The phylogenetic analyses of P. cubensis and P. humuli showed that they share a high level of sequence homology; the morphology of the sporangiophores, sporangia, and dehiscence apparatus confirmed the similarity of the two species. We therefore reduce P. humuli to the status of a taxonomic synonym of P. cubensis.

Potato dry rot, caused by Fusarium sambucinum, is a major postharvest disease of economic significance worldwide. Postharvest application of thiabendazole to control dry rot is becoming less effective since many strains of F. sambucinum have become resistant to this fungicide. Thus, alternative control strategies are needed. In vitro studies showed that several salts (0.2 M) inhibited completely mycelial growth and spore germination of F. sambucinum. Among these salts, sodium benzoate, sodium metabisulfite, potassium sorbate, trisodium phosphate and aluminium salts were fungitoxic. In vivo studies showed that aluminium chloride in curative application and sodium metabisulfite, sodium carbonate and sodium bicarbonate in preventive application significantly reduced the development of dry rot in potato tuber. Results from this study demonstrate that selected salts can be used to control potato dry rot.

Ericoid mycorrhizal fungi can alleviate heavy metal toxicity to their host plant, but the mechanisms that lie behind this increased tolerance are unknown. As a first step in the characterisation of two isolates of Oidiodendron maius from mycorrhizal roots of Vaccinium myrtillus growing in heavily contaminated soils, we investigated their taxonomic position, their mycorrhizal capabilities and their ability to grow in the presence of heavy metals. When growth was compared with isolates from non-polluted soils, a better performance was observed in the presence of increasing concentrations of zinc salts, especially at higher ion concentrations. The mechanisms of tolerance may include the production of mucilage and extracellular pigments.

Monilinia fructigena isolates from Japan were compared with isolates from Europe. General colony characteristics, stroma formation, growth rate and conidial dimensions were determined for six isolates each from both groups, as well as sporulation intensity on potato dextrose agar (PDA) and germ tube features. Potential differences in pathogenicity were tested on the pear cultivars ‘Conference’ and ‘Doyenné du Comice’, and on the apple cultivar ‘Cox's Orange Pippin’. A marked difference in stroma formation occurred, the area of stromatal plates ranged from 4·1 to 5·2 cm2 in the Japanese group, and from 0 to 0·9 cm2 in the European. The mean growth rate was significantly higher for Japanese isolates (t-test, P = 0·01). Length and width of conidia were significantly greater in European isolates (t-test, P = 0·01). Conidia measured on average 19×11·5 μm in European isolates, and 16×10 μm in Japanese ones when grown on cherry agar. On fruits, the difference in conidium size was even more pronounced. Sporulation intensity on PDA and germ tube features did not differ between both groups. No differences were found in latency period, lesion growth rate or sporulation intensity on apple and pear fruits between both groups. Together with previously published differences in the ITS region of ribosomal DNA, our results show that the Japanese isolates belong to a distinct species, Monilia polystroma sp. nov. A description of the anamorph is given, as well as a table summarising key features for all four brown rot associated Monilia species.

The phylogeny of the nuclear large ribosomal subunit (LSU) rDNA from Peronosporomycetes (Oomycota) was studied. Five orders Rhipidiales, Leptomitales, Saprolegniales, Pythiales and Peronosporales were included in the study in order to reveal phylogenetic relationships within the group. Based on maximum parsimony, neighbour-joining and maximum-likelihood the Peronosporomycetes seem to have evolved as two major lineages. One lineage includes members of the Rhipidiales, Leptomitales and Saprolegniales and the other includes the members of Pythiales and Peronosporales. However, the inclusion of Rhipidiales in Saprolegniomycetidae was not well supported. Leptomitales were placed basal to the Saprolegniales in the LSU rDNA based tree. In the Saprolegniaceae sensu lato the primary zoospore seems to have been lost several times in the evolution of this family. Species of Aphanomyces were placed on the most basal branch in this family. The obligate parasite, Albugo, was placed on the most basal branch within the Peronosporomycetidae. Phytophthora showed a closer relationship to Peronospora and Peronophythora than to Pythium suggesting that this genus should be removed from Pythiales to Peronosporales.

The interaction between Puccinia recondita f. sp. tritici (now widely referred to as P. triticina) and endophytic fungi in wheat was examined in laboratory experiments to determine whether the presence of fungal endophytes suppresses leaf rust disease caused by this fungus. Endophytes and cell-free washings from culture plates of the endophytes reduced the density and size of pustules in a susceptible cultivar when inoculated 3, 7 and 14 d prior to the pathogen. Disease at 12 d was reduced when the endophytes were inoculated simultaneously up to 50 mm from the fungus. Interactions between endophytes and this Puccinia are most probably mediated by defence mechanisms induced in the host plant.

A data set with 1551 fungal sequences of the small subunit ribosomal RNA has been analysed phylogenetically. Four animal sequences were used to root the tree. The parsimony ratchet algorithm in combination with tree fusion was used to find most parsimonious trees and the parsimony jackknifing method was used to establish support frequencies. The full-length consensus tree, of the most parsimonious trees, is published and jackknife frequencies above 50% are plotted on the consensus tree at supported nodes. Until recently attempts to find the most parsimonious trees for large data sets were impractical, given current computational limitations. The parsimony ratchet in combination with tree fusion was found to be a very efficient method of rapid parsimony analysis of this large data set. Parsimony jackknifing is a very fast and efficient method for establishing group support. The results show that the Glomeromycota are the sister group to a monophyletic Dikaryomycota. The majority of the species in the Glomeromycota/Dikaryomycota group have a symbiotic lifestyle – a possible synapomorphy for a group ‘Symbiomycota’. This would suggest that symbiosis between fungi and green plants evolved prior to the colonization of land by plants and not as a result of the colonization process. The Basidiomycotina and the Ascomycotina are both supported as monophyletic. The Urediniomycetes is the sister group to the rest of the Basidiomycotina successively followed in a grade by Ustilaginomycetes, Tremellomycetes, Dacrymycetales, Ceratobasidiales and Homobasidiomycetes each supported as monophyletic except the Homobasidiomycetes which are left unsupported. The ascomycete node begins with a polytomy consisting of the Pneumocystidomycetes, Schizosaccharomycetes, unsupported group with the Taphrinomycetes and Neolectales, and finally an unnamed, monophyletic and supported group including the Saccharomycetes and Euascomycetes. Within the Euascomycetes the inoperculate euascomycetes (Inoperculata) are supported as monophyletic excluding the Orbiliomycetes which are included in an unsupported operculate, pezizalean sister group together with Helvellaceae, Morchellaceae, Tuberaceae and others. Geoglossum is the sister group to the rest of the inoperculate euascomycetes. The Sordariomycetes, Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes are each highly supported as monophyletic. The Leotiomycetes and the Lecanoromycetes both appear in the consensus of the most parsimonious trees but neither taxon receives any jackknife support.

Sudden oak death has been an emerging disease problem in coastal California and has caused significant losses in forest ecosystems in some regions of the state. The causal agent of this disease has been described as Phytophthora ramorum with two other less aggressive species, P. nemorosa and P. pseudosyringae, recovered from some symptomatic plants. The phylogenetic relationship of these species with other members of the genus was examined by sequence alignment of 667 bp of the mitochondrially-encoded cytochrome oxidase II gene and the nuclear encoded rDNA internal transcribed spacer region. P. ramorum was most closely related to P. hibernalis and P. lateralis in trees from both regions, although the specific relationship among species differed depending on the tree. In the cox II tree these species were on a single clade with P. lateralis basal to a group containing P. ramorum and P. hibernalis. On the maximum parsimony ITS tree P. ramorum was most closely affiliated with P. lateralis and in the same clade as P. hibernalis, but with maximum likelihood analysis P. ramorum was basal to a grouping of P. hibernalis and P. lateralis. While bootstrap support was strong for the grouping of these species together, it was not for determining the relationship among them. In contrast to the cox II tree, the clade containing these three species grouped with P. cryptogea, P. drechsleri, P. erythroseptica, and P. syringae in the ITS tree. Since the same isolates of these species were used for both the cox II and ITS sequence analysis, this difference in species grouping suggests either a differential rate of evolutionary divergence for these two regions, incorrect assumptions about alignment of ITS sequences, or different evolutionary histories of the regions under study. Analysis of combined cox II and ITS data sets gave trees where the relationships among these species were the same as for the ITS tree alone, although the results of the partition homogeneity test (P=0.072) suggest caution should be used in interpretation of this data. All analyses supported a close relationship between P. ilicis, P. nemorosa and P. pseudosyringae, although the analysis did not clarify the evolutionary relationships among these three species. Interestingly, these three species had a unique 6 bp deletion in the cox II gene just before the termination codon. While there was some similarity in phylogenetic grouping of these species and morphological characteristics, this was not consistent across all comparisons in the genus. Data would suggest that P. ramorum, P. nemorosa and P. pseudosyringae are phylogenetically distinct new species and not the result of interspecific hybridization.