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Bongsoo Park
Bongsoo Park

2008 Phytophthora Workshop in Italy

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How many Phytophthora species? Clive Brasier Forest Research Agency Farnham UK
Many new Phytophthora species are being discovered. This prompted me to take a look at the theoretical question: How many Phytophthoras species are there? What might the answer mean for Phytophthora taxonomy and phylogeny? .. and for the plant health risk to forests and natural ecosystems? (cf. P. alni, P. ramorum etc) Going to explore these issues. It seems best to begin with a brief history of Phytophthora species over time.
Phytophthora species over time 1876 Anton De Bary 1 species ~ up to 1920 ~ generic confusion 1931 C M Tucker ca 20 species 1963 G M Waterhouse ca 41 species 1976 Newhook, Waterhouse, Stamps ca 50 species 1996 Erwin, Ribeiro ca 54 species
Phytophthora species over time 1996 Erwin & Ribeiro ca 54 species
Phytophthora species described Pre 2000 In Erwin & Ribeiro 1996 P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina 1999 P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 54 + 1
Phytophthora species over time 1876 Anton De Bary 1 species ~ up to 1920 ~ generic confusion 1931 C M Tucker ca 20 species 1963 G M Waterhouse ca 41 species 1976 Newhook, Waterhouse, Stamps ca 50 species 1996 Erwin, Ribeiro ca 54 species 1999 + P. quercina ca 55 species Round off (part described taxa etc) ~ 60 species pre 2000
How many Phytophthoras? Take as the baseline ca 60 species known pre 2000 Hawksworth (2001) estimated only 10% of fungi were known to science. Crous & Groenwald (2005) estimated only 7% known Take 10% as the estimate of unknowns Then there may be ~ 600 Phytophthora species in total, of which only ~ 60 species were accounted for by 2000 Leaving ~ 540 still unknown in 1999!
How many Phytophthoras? Instead of 600, take a much more conservative estimate: 200-600 extant Phytophthora species Then there may have been anything from 140 - 540 unknown species in ca 2000 An average of 340 ± 200 species still unknown How many of these 140 - 540 unknown species might damage forests or natural ecosystems if they become invasives?
Phytophthora species described Pre 2000 P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 55
Phytophthora species described Pre 2000 Damaging to nursery trees, forests and natural ecosystems P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 11 / 55 = 20%
How many Phytophthoras? So information prior to 2000 suggests ~20% of Phytophthoras were damaging to forests or natural ecosystems Take as a more conservative estimate ~ 10%. Then on this basis, in 2000 there may still have been between 14 - 54 ie average 34 ± 20 unknown Phytophthora species potentially damaging to forests or natural ecosystems
And since 2000? ...
Phytophthora species Pre 2000 P. arecae P. japonica P. boehmeriae P. katsurae P. botryosa P. lateralis P. cactorum P. macrochlamydospora P. cajani P. meadii P. cambivora P. medicaginis P. capsici P. megakarya P. cinnamomi P. megasperma P. citricola P. melonis P. citrophthora P. mexicana P. clandestina P. mirabilis P. colocasiae P. multivesiculata P. cryptogea P. nicotianae P. drechsleri P. palmivora P. erythroseptica P. phaseoli P. fragariae var frag. P. porri P. fragariae var rubi P. primulae P. gonapodyides P. pseudotsugae P. heveae P. quercina P. hibernalis P. quininea P. humicola P. richardiae P. idaei P. sinensis P. ilicis P. sojae P. infestans P. syringae P. inflata P. tentaculata P. insolita P. trifolii P. iranica P. vignae P.italica 55
Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida P. botryosa P. lateralis P. asparagi P. austrocedrae P. cactorum P. macrochlamydospora P. bisheria P. lagoariana P. cajani P. meadii P. brassicae P. cuyabensis P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum P. cinnamomi P. megasperma P. fallax P. sulawesiensis P. citricola P. melonis P. gallica P. siskiyouensis P. citrophthora P. mexicana P. glovera P. uliginosa P. clandestina P. mirabilis P. hedraiandra P. colocasiae P. multivesiculata P. inundata P. taxon salixsoil P. cryptogea P. nicotianae P. ipomoeae P. taxon pgchlamydo P. drechsleri P. palmivora P. kelmania P. taxon riversoil P. erythroseptica P. phaseoli P. kernoviae P. taxon oaksoil P. fragariae var frag. P. porri P. nemorosa P. parvasperma P. fragariae var rubi P. primulae P. niederhauserii P .hungarica P. gonapodyides P. pseudotsugae P. pistaciae P. sylvatica P. heveae P. quercina P. polonica P. parsiana P. hibernalis P. quininea P. pseudosyringae P. quercetorum P. humicola P. richardiae P. psychrophila P. taxon meadii-like P. idaei P. sinensis P. ramorum P. taxon Acer P. ilicis P. sojae P. sansomea P. taxon Agathis P. infestans P. syringae P. taxon. Banksia P. taxon orphan P. inflata P. tentaculata P. taxon. Chicory P. insolita P. trifolii P. cact x nic P. iranica P. vignae P. tropicalis P.italica 55 50+
Phytophthora species Post 2000 Species described or under construction P. alni (x 3) P. kernoviae P. frigida P. taxon salixsoil P. andina P. nemorosa P. austrocedrae P. tax. pgchlamydo P. asparagi P. niederhauserii P. lagoariana P. taxon riversoil P. bisheria P. pistaciae P. cuyabensis P. taxon oaksoil P. brassicae P. polonica P. cact x hedr P. parvasperma P. captiosa P. pseudosyringae P. foliorum P .hungarica P. europaea P. psychrophila P. sulawesiensis P. sylvatica P. fallax P. ramorum P. siskiyouensis P. parsiana P. gallica P. sansomea P. uliginosa P. quercetorum P. glovera P. taxon Banksia P. pinifolia P. tax. meadii-like P. hedraiandra P. taxon. chicory P. taxon Acer P. inundata P. cact x nic P. taxon Agathis P. ipomoeae P. tropicalis P. taxon orphan P. kelmania P. alticola 51 – (54)
Phytophthora species / taxa Post 2000 Associated with research on nursery trees, forests and natural ecosystems P. alni (x 3) P. kernoviae P. frigida P. taxon salixsoil P. andina P. nemorosa P. austrocedrae P. tax. pgchlamydo P. asparagi P. niederhauserii P. lagoariana P. taxon riversoil P. bisheria P. pistaciae P. cuyabensis P. taxon oaksoil P. brassicae P. polonica P. cact x hedr P. parvasperma P. captiosa P. pseudosyringae P. foliorum P .hungarica P. europaea P. psychrophila P. sulawesiensis P. sylvatica P. fallax P. ramorum P. siskiyouensis P. parsiana P. gallica P. sansomea P. uliginosa P. quercetorum P. glovera P. taxon Banksia P. pinifolia P. tax. meadii-like P. hedraiandra P. taxon. chicory P. taxon Acer P. inundata P. cact x nic P. taxon Agathis P. ipomoeae P. tropicalis P. taxon orphan P. kelmania P. alticola 31+ /51 = ~60 % Estimate for the 55 pre- 2000 species was only 20% ...
Phylotypes or ‘virtual taxa’ Molecular technology, especially PCR, has provided opportunity to probe the environment for known or unknown taxa based solely on DNA sequence profiles. Especially used in bacteriology where soil profiles revealing remarkable numbers of prokaryote organisms. Since the product is a DNA sequence to fit to a phylogenetic tree and no culture is available the resulting ‘taxa’ are commonly referred to as phylotypes. For Phytophthora, I have personally tended to think of them as ‘virtual taxa’ to underline the lack of hard information.
Virtual taxa or phylotypes Arcate, Karp & Nelson (2006) recently applied these methods to search for Oomycetes in tomato and other rhizosphere soils in NY State. They found - Many Pythiums! (and a couple of Phytopthoras) Greater diversity than by direct baiting methods They were able to the sample the dormant oospore flora as well as active propagules.
Virtual taxa or phylotypes At least two other research groups have begun to apply these methods to screen for Phytophthoras in forests and natural ecosystems, so far mainly in water environments (streams): • Everett Hansen’s group at Corvallis • David Cooke’s group at SCRI Dundee
Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction Phylotypes or virtual taxa P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida SW Oregon streams Hansen / Reeser / Sutton P. botryosa P. lateralis P. asparagi P. austrocedrae Combined SSCP of ITS, Cox P. cactorum P. macrochlamydospora P. bisheria P. lagoariana 30 species P. cajani P. meadii P. brassicae P. cuyabensis 10 unknown / new taxa ? P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum Central Oregon stream (Oak Creek) P. cinnamomi P. megasperma P. fallax P. sulawesiensis Remigi / sutton / Reeser / Hansen P. citricola P. melonis P. gallica Combined SSCP of ITS, Cox P. siskiyouensis 11 specie s P. citrophthora P. mexicana P. glovera P. uliginosa 5 unknown / new taxa ? P. clandestina P. mirabilis P. hedraiandra P. pinifolia P. colocasiae P. multivesiculata P. inundata West Australian bush P. cryptogea P. nicotianae P. ipomoeae P. taxon salixsoil Burgess / Hardy P. drechsleri P. palmivora P. kelmania P. taxon pgchlamydo ITS sequence P. erythroseptica P. phaseoli P. kernoviae P. taxon riversoil 9 unknown / new taxa ? P. fragariae var frag. P. porri P. nemorosa P. taxon oaksoil P. fragariae var rubi P. primulae P. niederhauserii P. parvasperma West Scotland streams P. gonapodyides P. pseudotsugae P. pistaciae P .hungarica Scibetta / Cooke / Cacciola P. heveae P. quercina P. polonica P. sylvatica ITS1 nested PCR P. hibernalis P. quininea P. pseudosyringae P. carica 17 species 3 unknown / new taxa ? P. humicola P. richardiae P. psychrophila P. quercetorum P. idaei P. sinensis P. ramorum P. taxon meadii-like P. ilicis P. sojae P. sansomea Ecuador streams P. taxon Acer Scibetta / Cooke P. infestans P. syringae P. taxon. Banksia P. taxon Agathis ITS1 nested PCR P. inflata P. tentaculata P. taxon. Chicory P. taxon orphan 10 species P. insolita P. trifolii P. cact x nic 4 unknown / new taxa ? P. iranica P. vignae P. tropicalis 51 + P.italica 55
Phytophthora species post 2000 Phylotypes or virtual taxa West Scotland streams Scibetta / Cooke / Cacciola SW Oregon streams ITS1 nested PCR Hansen / Reeser / Sutton 17 species Combined SSCP of ITS, Cox 3 unknown / new taxa ? 30 species 10 unknown / new taxa ? Ecuador streams Scibetta / Cooke ITS1 nested PCR Central Oregon stream (Oak Creek) 10 Phy species (+ 3 Per spp) Remigi / Sutton / Reeser / Hansen 4 unknown / new taxa ? Combined SSCP of ITS, Cox 11 species West Australian bush 5 unknown / new taxa ? Burgess / Hardy ITS sequence 9 unknown / new taxa ?
Electropherogram for ITS1 products generated by GeneScan P. cambivora P. ilicis P. gonapodyides P. ramorum P. lateralis P. citricola Hansen group Slide courtesy Hansen et al
Electrophoretic Mobility ITS 4500 4600 4700 4800 4900 5000 5100 5200 5300 5400 5500 WA55.1-041904 WA1-051704 33-2-3.2-1102 PO WA1-030403 Hansen group WA32-040504 P. citricola 18EX2-17-SOIL-0804 18EX3-3-SOIL-0804 C-ITS B1 P. citrophthora P. hibernalis ITS B2 WA5-030804 Isolate C-ITS G1 P. ramorum P. lateralis COX B1 P. psychrophila COX G1 SSCP FINGERPRINTING P. ilicis P. pseudosyringae WA55-051704 WA33-032204 WA42.2-051704 WA50.2-051704 WA24.1-030804 Phytophthora diversity in streams and soil - P. nemorosa ITS1 and COX spacer peaks for some unknown isolates 5600 5650 5700 5750 5800 5850 5900 5950 Slide courtesy Hansen et al Electrophoretic Mobility COX spacer
South west Oregon streams Hansen / Reeser / Sutton Combined SSCP of ITS, Cox 30 Phytophthora species ~ 10 unknown / new taxa ?
Central Oregon stream (Oak Creek) Remigi / Sutton / Reeser / Hansen Combined SSCP of ITS, Cox 11 Phytophthora species ~ 5 unknown / new taxa ?
Monitoring Phytophthora using molecular methods Silvia Scibetta, David Cooke & Santina Cacciola 18Ph2F 18S ITS1 5.8 ITS2 28S Inverpolly * 5.8S-2R *Beinn Eighe ITS6 Loch Lomond 1st round product ~ 490bp * * ITS1 Clyde Valley * Invergowrie 5.8S-1R ITS1 Nested product ~ 260bp No cross reaction with Pythium Nature reserves sampled (water and soil) • DNA extraction • PCR • Cloning • Sequencing 10 litre samples of standing or flowing water filtered
Phytophthora phylotypes found in 2006 Scottish Survey WATER 12 11 P. t hedraiandra-like Soil 10 Number of samples P. hedraiandra Water P. taxon Oaksoil 8 6 P.niederhausierii 6 P. taxon Pgchlamydo 6 P.hibernalis 4 4 WATER 4 3 P.cinnamomi P. hedraiandra- 2 1 like P. hedraiandra 0 P. taxon Oaksoil 0 1 0 P.drechsleri P.niederhausierii 2 0 P. taxon 3 Pgchlamydo 4 P.hibernalis 5 P.cambivora* P.gonapodyides* Number of species P.cinnamomi P.alni subsp. P.drechsleri P.gonapodyides multiformis* P.cambivora* P.alni subsp. P.pseudosyringae multiformis* P.syringae P.pseudosyringae Fewer samples from soil but P.syringae up to 5 species detected in a P.europaea P.europaea P.inundata P. taxon Salixsoil P. taxon Salixsoil single water sample P.inundata P.taxon Raspberry P. taxon Raspberry 17 different Phytophthora sp. in water samples cf. only 5 in soil samples
West Scotland streams Scibetta / Cooke / Cacciola ITS 1 nested PCR 17 Phytophthora species ~ 3 unknown / new taxa ?
Ecuador streams 2 - 3000 m. asl. Scibetta / Cooke Combined SSCP of ITS, Cox 10 Phytophthora species (+ 3 Peronospora spp) ~ 3 unknown / new taxa ?
West Australian Bush - unidentified isolates Stukely/ Burgess / Hardy Screening of the VHS culture collection - ITS sequence data and blast search ~ 7-9 unknown / new taxa ? NB. Not phylotaxa, because cultures are available
Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction Virtual taxa or phylotypes P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida SW Oregon streams Hansen / Reeser / Sutton P. botryosa P. lateralis P. asparagi P. austrocedrae Combined SSCP of ITS, Cox P. cactorum P. macrochlamydospora P. bisheria P. lagoariana 30 species P. cajani P. meadii P. brassicae P. cuyabensis 10 unknown / new taxa ? P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum Central Oregon stream (Oak Creek) P. cinnamomi P. megasperma P. fallax P. sulawesiensis Remigi / sutton / Reeser / Hansen P. citricola P. melonis P. gallica P. siskiyouensis Combined SSCP of ITS, Cox P. citrophthora P. mexicana P. glovera P. uliginosa 11 specie s P. clandestina P. mirabilis P. hedraiandra P. pinifolia 5 unknown / new taxa ? P. colocasiae P. multivesiculata P. inundata P. cryptogea P. nicotianae P. ipomoeae P. taxon salixsoil West Australian bush P. drechsleri P. palmivora P. kelmania P. taxon pgchlamydo Burgess / Hardy P. erythroseptica P. phaseoli P. kernoviae P. taxon riversoil ITS sequence P. fragariae var frag. P. porri P. nemorosa P. taxon oaksoil 9 unknown / new taxa ? P. fragariae var rubi P. primulae P. niederhauserii P. parvasperma P. gonapodyides P. pseudotsugae P. pistaciae P .hungarica West Scotland streams P. heveae P. quercina P. polonica P. sylvatica Scibetta / Cooke / Cacciola P. hibernalis P. quininea P. pseudosyringae P. carica ITS1 nested PCR P. humicola P. richardiae P. psychrophila P. quercetorum 17 species P. idaei P. sinensis P. ramorum P. taxon meadii-like 3 unknown / new taxa ? P. ilicis P. sojae P. sansomea P. taxon Acer P. infestans P. syringae P. taxon. Banksia P. taxon Agathis Ecuador streams P. inflata P. tentaculata P. taxon. Chicory P. taxon orphan Scibetta / Cooke P. insolita P. trifolii P. cact x nic ITS1 nested PCR 10 species P. iranica P. vignae P. tropicalis 51+ P.italica 55 4 unknown / new taxa ?
Described Phytophthora species over time 140 130 120 110 Turin 2008 100 Described species 90 80 70 60 Erwin & Ribeiro 50 Waterhouse1963 1996 40 30 Tucker 1931 20 10 DeBary 1876 0 1860 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 Year
Described Phytophthora species over time Period of evolutionary and genomic exploration 140 and 130 uncertainty ? 120 Period of 110 Period of discovery Turin 100 biological morphology pathology 2008 consolidation Described species 90 80 and ‘certainty’ 70 60 Erwin & 50 Waterhouse Ribeiro 1996 1963 key summary 40 30 Tucker 1931 20 synthesis 10 DeBary 1876 0 1860 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 Year Pandoras box?
Why such an increase in species since 2000? The emergence of more holistic, population- based species concepts since the 1980s The rapid application of molecular tools for defining evolutionary units in fung Increasing international trade in rooted plants Increased environmental screening for Phytophthora species – sample surveys
Growing number of described Phytophthora species: significance for Phylogeny? ca 50 Phytophthora species Cooke et al 2000 Oomycete ITS tree
Hansen group Water filtering method in use (Yunnan)
Growing number of described Phytophthora species: significance for Phylogeny? Since 2000 seeing marked increase in species in Clades 9 and 10 (only about 3 species known in 2000) Cooke et al 2000 Oomycete ITS tree
Blair et al 2006 seven locus consensus tree Today already ca 10 ‘new’ species in these clades….
Cooke et al 2000 ITS tree Clades 1-8 only ca 47 species In Clades 1-8:
Since 2000 - a rapid increase in species in Clades1-8 e.g. 3 new species associated with the previously remote P. lateralis subclade in Clade 8 Cooke et al 2000 ITS tree Clades 1-8 ca 47 species
Blair et al 2008 seven locus consensus tree P. lateralis now joined by P.hibernalis, P.ramorum, P.foliorum
Since 2000 a dramatic increase in Clade 6 species 5 species in 2000 Cooke et al 2000 ITS tree Clades 1-8 ca 47 species
15 taxa in Clade 6 by 2004: Strill growing: would now need to add P. hungarica sp.nov; P. taxon orphan: P. pinifolia ... Brasier et al 2004 ITS tree Clade 6
99 Phytophthora inundata Five new 74 100 99 P.sp. 6 : P.sp. 10 100 Clade 6 taxa 100 100 P.sp. 7 Clade 6 Phytophthora megasperma 100 in the WA 67 61 97 P.sp. 3 93 100P.sp. 8 VHS 78 97 Phytophthora gonapodyides 82 Phytophthora citricola collection … Phytophthora 85 inflata 100P.sp. 4 100 ITS sequence tree Clade 2 Phytophthora capsici 100 courtesy Burgess, 100 Phytophthora multivesiculata 94 100 Stukely, Hardy 98 Phytophthora alticola 99 100 P.sp. 2 100 100 Phytophthora nicotianae Clade 1 100 73 Phytophthora cactorum 100 Phytophthora arecae Clade 4 100 100 100 Phytophthora frigida 98 P.sp. 1 100 100 Phytophthora cinnamomi Clade 7 Phytophthora ramorum 100 100 Phytophthora drechsleri 94 Phytophthora cryptogea 100 95 P.sp. 5 Clade 8 87 100 95 Phytophthora captiosa 91 Phytophthora fallax 100 100 P.sp. 9 Clades 9, 10 100 100 Phytophthora kernoviae 100 Phytophthora boehmeriae 10 changes
South west Oregon streams Hansen / Reeser / Sutton Combined SSCP of ITS, Cox 30 Phytophthora species ~ 10 unknown / new taxa ? Majority probably in Clade 6
So how many species in Clade 6? Take the 2007 data: ca 17 of the 105 known Phytophthora species are in Clade 6 = 16% - ‘biggest’ Clade of all? Taking the estimate of 200 - 600 total Phytophthora species This gives an estimate of 32-96 species in Clade 6
(Clade 6 by 2004) Brasier et al 2004 ITS tree Clade 6
‘Enlarge’ hypothetically to ca 32 spp:
If many of these 32 (- 96) ‘new’ species are also aquatic, sterile or inbreeding, high temperature species like Pg, P t pgchlamydo etc – – we may even have to rethink our species concept for this subclade
So we now have new and rapidly expanding molecular phylogenetic trees : But what do these trees mean in terms of how we understand Phytophthoras?
Obviously the trees are a major step forward from the Waterhouse 1963 morphological Groups 1-6 - The former were identification aids and were necessarily artificial constructs - - Whereas our molecular trees are closer to ‘natural relationships’ Noneless I suggest we treat them with a degree of caution:
1. Much data is missing because of extinctions! 2. Much data is missing because we still have to add the ~100 – 500 extant species!
3. Much evidence of past reticulation events is missing … …the footprints of hybridisation and genetic introgression will have been lost over time …
What is important is not so much that we can show that species X and species Y are related… eg that P. ramorum and P. lateralis are related So what? In Darwinian terms, what is more important is to understand the processes and events that gave rise to their divergence… The Darwinian meaning is all in the nodes …
Why did ancestral species W give rise to three species X, Y and Z...? W XYZ Why did Clade 1 ancestral species A give A rise to two Clade 2 clades 1 and 2? and so on...
Concluding comments ... This dip into Phytophthora numerical biodiversity and phylogenetic uncertainties has put me in mind of just how little we know about the origins of the genus. Indeed, it seems reasonable to suggest that the construction of a phylogenetic tree is simply the point at which the real evolutionary challenges begin.
So, given that there are probably 200-600 species of Phytophthora out there - - I see two key challenges for the future: 1. Understanding why there are so many Phytophthoras. ie. What environmental processes and events (geographic, climatic, biotic) drove their evolution? Why did eg P. ramorum diverge from P. lateralis? - the job of the evolutionary biologist 2. Understanding at the genetic level how eg P. ramorum behaves so differently from P. lateralis? - the job of the genomicist
Fortunately, these how and why challenges are not mutually exclusive, and answers obtained for one will enormously benefit the understanding in the other. I suggest, therefore, that we are in for an exciting time over the next decade! Thank you
A written version of this talk will be published shortly: Brasier C. M (2008). Phytophthora biodiversity: How many Phytophthora species are there? In Proceedings of the 4th IUFRO Workshop on Phytophthoras in Forests and Natural Ecosystems (E. Goheen ed). in press USDA Forest Service.

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O1 Brasier

  • 1. How many Phytophthora species? Clive Brasier Forest Research Agency Farnham UK
  • 2. Many new Phytophthora species are being discovered. This prompted me to take a look at the theoretical question: How many Phytophthoras species are there? What might the answer mean for Phytophthora taxonomy and phylogeny? .. and for the plant health risk to forests and natural ecosystems? (cf. P. alni, P. ramorum etc) Going to explore these issues. It seems best to begin with a brief history of Phytophthora species over time.
  • 3. Phytophthora species over time 1876 Anton De Bary 1 species ~ up to 1920 ~ generic confusion 1931 C M Tucker ca 20 species 1963 G M Waterhouse ca 41 species 1976 Newhook, Waterhouse, Stamps ca 50 species 1996 Erwin, Ribeiro ca 54 species
  • 4. Phytophthora species over time 1996 Erwin & Ribeiro ca 54 species
  • 5. Phytophthora species described Pre 2000 In Erwin & Ribeiro 1996 P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina 1999 P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 54 + 1
  • 6. Phytophthora species over time 1876 Anton De Bary 1 species ~ up to 1920 ~ generic confusion 1931 C M Tucker ca 20 species 1963 G M Waterhouse ca 41 species 1976 Newhook, Waterhouse, Stamps ca 50 species 1996 Erwin, Ribeiro ca 54 species 1999 + P. quercina ca 55 species Round off (part described taxa etc) ~ 60 species pre 2000
  • 7. How many Phytophthoras? Take as the baseline ca 60 species known pre 2000 Hawksworth (2001) estimated only 10% of fungi were known to science. Crous & Groenwald (2005) estimated only 7% known Take 10% as the estimate of unknowns Then there may be ~ 600 Phytophthora species in total, of which only ~ 60 species were accounted for by 2000 Leaving ~ 540 still unknown in 1999!
  • 8. How many Phytophthoras? Instead of 600, take a much more conservative estimate: 200-600 extant Phytophthora species Then there may have been anything from 140 - 540 unknown species in ca 2000 An average of 340 ± 200 species still unknown How many of these 140 - 540 unknown species might damage forests or natural ecosystems if they become invasives?
  • 9. Phytophthora species described Pre 2000 P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 55
  • 10. Phytophthora species described Pre 2000 Damaging to nursery trees, forests and natural ecosystems P. arecae P. erythroseptica P. japonica P. phaseoli P. boehmeriae P. fragariae frag. P. katsurae P. porri P. botryosa P. fragariae rubi P. lateralis P. primulae P. cactorum P. gonapodyides P. macrochlamy. P. pseudotsugae P. cajani P. heveae P. meadii P. quercina P. cambivora P. hibernalis P. medicaginis P. quininea P. capsici P. humicola P. megakarya P. richardiae P. cinnamomi P. idaei P. megasperma P. sinensis P. citricola P. ilicis P. melonis P. sojae P. citrophthora P. infestans P. mexicana P. syringae P. clandestina P. inflata P. mirabilis P. tentaculata P. colocasiae P. insolita P. multivesiculata P. trifolii P. cryptogea P. iranica P. nicotianae P. vignae P. drechsleri P. italica P. palmivora 11 / 55 = 20%
  • 11. How many Phytophthoras? So information prior to 2000 suggests ~20% of Phytophthoras were damaging to forests or natural ecosystems Take as a more conservative estimate ~ 10%. Then on this basis, in 2000 there may still have been between 14 - 54 ie average 34 ± 20 unknown Phytophthora species potentially damaging to forests or natural ecosystems
  • 13. Phytophthora species Pre 2000 P. arecae P. japonica P. boehmeriae P. katsurae P. botryosa P. lateralis P. cactorum P. macrochlamydospora P. cajani P. meadii P. cambivora P. medicaginis P. capsici P. megakarya P. cinnamomi P. megasperma P. citricola P. melonis P. citrophthora P. mexicana P. clandestina P. mirabilis P. colocasiae P. multivesiculata P. cryptogea P. nicotianae P. drechsleri P. palmivora P. erythroseptica P. phaseoli P. fragariae var frag. P. porri P. fragariae var rubi P. primulae P. gonapodyides P. pseudotsugae P. heveae P. quercina P. hibernalis P. quininea P. humicola P. richardiae P. idaei P. sinensis P. ilicis P. sojae P. infestans P. syringae P. inflata P. tentaculata P. insolita P. trifolii P. iranica P. vignae P.italica 55
  • 14. Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida P. botryosa P. lateralis P. asparagi P. austrocedrae P. cactorum P. macrochlamydospora P. bisheria P. lagoariana P. cajani P. meadii P. brassicae P. cuyabensis P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum P. cinnamomi P. megasperma P. fallax P. sulawesiensis P. citricola P. melonis P. gallica P. siskiyouensis P. citrophthora P. mexicana P. glovera P. uliginosa P. clandestina P. mirabilis P. hedraiandra P. colocasiae P. multivesiculata P. inundata P. taxon salixsoil P. cryptogea P. nicotianae P. ipomoeae P. taxon pgchlamydo P. drechsleri P. palmivora P. kelmania P. taxon riversoil P. erythroseptica P. phaseoli P. kernoviae P. taxon oaksoil P. fragariae var frag. P. porri P. nemorosa P. parvasperma P. fragariae var rubi P. primulae P. niederhauserii P .hungarica P. gonapodyides P. pseudotsugae P. pistaciae P. sylvatica P. heveae P. quercina P. polonica P. parsiana P. hibernalis P. quininea P. pseudosyringae P. quercetorum P. humicola P. richardiae P. psychrophila P. taxon meadii-like P. idaei P. sinensis P. ramorum P. taxon Acer P. ilicis P. sojae P. sansomea P. taxon Agathis P. infestans P. syringae P. taxon. Banksia P. taxon orphan P. inflata P. tentaculata P. taxon. Chicory P. insolita P. trifolii P. cact x nic P. iranica P. vignae P. tropicalis P.italica 55 50+
  • 15. Phytophthora species Post 2000 Species described or under construction P. alni (x 3) P. kernoviae P. frigida P. taxon salixsoil P. andina P. nemorosa P. austrocedrae P. tax. pgchlamydo P. asparagi P. niederhauserii P. lagoariana P. taxon riversoil P. bisheria P. pistaciae P. cuyabensis P. taxon oaksoil P. brassicae P. polonica P. cact x hedr P. parvasperma P. captiosa P. pseudosyringae P. foliorum P .hungarica P. europaea P. psychrophila P. sulawesiensis P. sylvatica P. fallax P. ramorum P. siskiyouensis P. parsiana P. gallica P. sansomea P. uliginosa P. quercetorum P. glovera P. taxon Banksia P. pinifolia P. tax. meadii-like P. hedraiandra P. taxon. chicory P. taxon Acer P. inundata P. cact x nic P. taxon Agathis P. ipomoeae P. tropicalis P. taxon orphan P. kelmania P. alticola 51 – (54)
  • 16. Phytophthora species / taxa Post 2000 Associated with research on nursery trees, forests and natural ecosystems P. alni (x 3) P. kernoviae P. frigida P. taxon salixsoil P. andina P. nemorosa P. austrocedrae P. tax. pgchlamydo P. asparagi P. niederhauserii P. lagoariana P. taxon riversoil P. bisheria P. pistaciae P. cuyabensis P. taxon oaksoil P. brassicae P. polonica P. cact x hedr P. parvasperma P. captiosa P. pseudosyringae P. foliorum P .hungarica P. europaea P. psychrophila P. sulawesiensis P. sylvatica P. fallax P. ramorum P. siskiyouensis P. parsiana P. gallica P. sansomea P. uliginosa P. quercetorum P. glovera P. taxon Banksia P. pinifolia P. tax. meadii-like P. hedraiandra P. taxon. chicory P. taxon Acer P. inundata P. cact x nic P. taxon Agathis P. ipomoeae P. tropicalis P. taxon orphan P. kelmania P. alticola 31+ /51 = ~60 % Estimate for the 55 pre- 2000 species was only 20% ...
  • 17. Phylotypes or ‘virtual taxa’ Molecular technology, especially PCR, has provided opportunity to probe the environment for known or unknown taxa based solely on DNA sequence profiles. Especially used in bacteriology where soil profiles revealing remarkable numbers of prokaryote organisms. Since the product is a DNA sequence to fit to a phylogenetic tree and no culture is available the resulting ‘taxa’ are commonly referred to as phylotypes. For Phytophthora, I have personally tended to think of them as ‘virtual taxa’ to underline the lack of hard information.
  • 18. Virtual taxa or phylotypes Arcate, Karp & Nelson (2006) recently applied these methods to search for Oomycetes in tomato and other rhizosphere soils in NY State. They found - Many Pythiums! (and a couple of Phytopthoras) Greater diversity than by direct baiting methods They were able to the sample the dormant oospore flora as well as active propagules.
  • 19. Virtual taxa or phylotypes At least two other research groups have begun to apply these methods to screen for Phytophthoras in forests and natural ecosystems, so far mainly in water environments (streams): • Everett Hansen’s group at Corvallis • David Cooke’s group at SCRI Dundee
  • 20. Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction Phylotypes or virtual taxa P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida SW Oregon streams Hansen / Reeser / Sutton P. botryosa P. lateralis P. asparagi P. austrocedrae Combined SSCP of ITS, Cox P. cactorum P. macrochlamydospora P. bisheria P. lagoariana 30 species P. cajani P. meadii P. brassicae P. cuyabensis 10 unknown / new taxa ? P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum Central Oregon stream (Oak Creek) P. cinnamomi P. megasperma P. fallax P. sulawesiensis Remigi / sutton / Reeser / Hansen P. citricola P. melonis P. gallica Combined SSCP of ITS, Cox P. siskiyouensis 11 specie s P. citrophthora P. mexicana P. glovera P. uliginosa 5 unknown / new taxa ? P. clandestina P. mirabilis P. hedraiandra P. pinifolia P. colocasiae P. multivesiculata P. inundata West Australian bush P. cryptogea P. nicotianae P. ipomoeae P. taxon salixsoil Burgess / Hardy P. drechsleri P. palmivora P. kelmania P. taxon pgchlamydo ITS sequence P. erythroseptica P. phaseoli P. kernoviae P. taxon riversoil 9 unknown / new taxa ? P. fragariae var frag. P. porri P. nemorosa P. taxon oaksoil P. fragariae var rubi P. primulae P. niederhauserii P. parvasperma West Scotland streams P. gonapodyides P. pseudotsugae P. pistaciae P .hungarica Scibetta / Cooke / Cacciola P. heveae P. quercina P. polonica P. sylvatica ITS1 nested PCR P. hibernalis P. quininea P. pseudosyringae P. carica 17 species 3 unknown / new taxa ? P. humicola P. richardiae P. psychrophila P. quercetorum P. idaei P. sinensis P. ramorum P. taxon meadii-like P. ilicis P. sojae P. sansomea Ecuador streams P. taxon Acer Scibetta / Cooke P. infestans P. syringae P. taxon. Banksia P. taxon Agathis ITS1 nested PCR P. inflata P. tentaculata P. taxon. Chicory P. taxon orphan 10 species P. insolita P. trifolii P. cact x nic 4 unknown / new taxa ? P. iranica P. vignae P. tropicalis 51 + P.italica 55
  • 21. Phytophthora species post 2000 Phylotypes or virtual taxa West Scotland streams Scibetta / Cooke / Cacciola SW Oregon streams ITS1 nested PCR Hansen / Reeser / Sutton 17 species Combined SSCP of ITS, Cox 3 unknown / new taxa ? 30 species 10 unknown / new taxa ? Ecuador streams Scibetta / Cooke ITS1 nested PCR Central Oregon stream (Oak Creek) 10 Phy species (+ 3 Per spp) Remigi / Sutton / Reeser / Hansen 4 unknown / new taxa ? Combined SSCP of ITS, Cox 11 species West Australian bush 5 unknown / new taxa ? Burgess / Hardy ITS sequence 9 unknown / new taxa ?
  • 22. Electropherogram for ITS1 products generated by GeneScan P. cambivora P. ilicis P. gonapodyides P. ramorum P. lateralis P. citricola Hansen group Slide courtesy Hansen et al
  • 23. Electrophoretic Mobility ITS 4500 4600 4700 4800 4900 5000 5100 5200 5300 5400 5500 WA55.1-041904 WA1-051704 33-2-3.2-1102 PO WA1-030403 Hansen group WA32-040504 P. citricola 18EX2-17-SOIL-0804 18EX3-3-SOIL-0804 C-ITS B1 P. citrophthora P. hibernalis ITS B2 WA5-030804 Isolate C-ITS G1 P. ramorum P. lateralis COX B1 P. psychrophila COX G1 SSCP FINGERPRINTING P. ilicis P. pseudosyringae WA55-051704 WA33-032204 WA42.2-051704 WA50.2-051704 WA24.1-030804 Phytophthora diversity in streams and soil - P. nemorosa ITS1 and COX spacer peaks for some unknown isolates 5600 5650 5700 5750 5800 5850 5900 5950 Slide courtesy Hansen et al Electrophoretic Mobility COX spacer
  • 24. South west Oregon streams Hansen / Reeser / Sutton Combined SSCP of ITS, Cox 30 Phytophthora species ~ 10 unknown / new taxa ?
  • 25. Central Oregon stream (Oak Creek) Remigi / Sutton / Reeser / Hansen Combined SSCP of ITS, Cox 11 Phytophthora species ~ 5 unknown / new taxa ?
  • 26. Monitoring Phytophthora using molecular methods Silvia Scibetta, David Cooke & Santina Cacciola 18Ph2F 18S ITS1 5.8 ITS2 28S Inverpolly * 5.8S-2R *Beinn Eighe ITS6 Loch Lomond 1st round product ~ 490bp * * ITS1 Clyde Valley * Invergowrie 5.8S-1R ITS1 Nested product ~ 260bp No cross reaction with Pythium Nature reserves sampled (water and soil) • DNA extraction • PCR • Cloning • Sequencing 10 litre samples of standing or flowing water filtered
  • 27. Phytophthora phylotypes found in 2006 Scottish Survey WATER 12 11 P. t hedraiandra-like Soil 10 Number of samples P. hedraiandra Water P. taxon Oaksoil 8 6 P.niederhausierii 6 P. taxon Pgchlamydo 6 P.hibernalis 4 4 WATER 4 3 P.cinnamomi P. hedraiandra- 2 1 like P. hedraiandra 0 P. taxon Oaksoil 0 1 0 P.drechsleri P.niederhausierii 2 0 P. taxon 3 Pgchlamydo 4 P.hibernalis 5 P.cambivora* P.gonapodyides* Number of species P.cinnamomi P.alni subsp. P.drechsleri P.gonapodyides multiformis* P.cambivora* P.alni subsp. P.pseudosyringae multiformis* P.syringae P.pseudosyringae Fewer samples from soil but P.syringae up to 5 species detected in a P.europaea P.europaea P.inundata P. taxon Salixsoil P. taxon Salixsoil single water sample P.inundata P.taxon Raspberry P. taxon Raspberry 17 different Phytophthora sp. in water samples cf. only 5 in soil samples
  • 28. West Scotland streams Scibetta / Cooke / Cacciola ITS 1 nested PCR 17 Phytophthora species ~ 3 unknown / new taxa ?
  • 29. Ecuador streams 2 - 3000 m. asl. Scibetta / Cooke Combined SSCP of ITS, Cox 10 Phytophthora species (+ 3 Peronospora spp) ~ 3 unknown / new taxa ?
  • 30. West Australian Bush - unidentified isolates Stukely/ Burgess / Hardy Screening of the VHS culture collection - ITS sequence data and blast search ~ 7-9 unknown / new taxa ? NB. Not phylotaxa, because cultures are available
  • 31. Phytophthora species Phytophthora species Post 2000 Pre 2000 Described or under construction Virtual taxa or phylotypes P. arecae P. japonica P. alni (x3) P. alticola P. boehmeriae P. katsurae P. andina P. frigida SW Oregon streams Hansen / Reeser / Sutton P. botryosa P. lateralis P. asparagi P. austrocedrae Combined SSCP of ITS, Cox P. cactorum P. macrochlamydospora P. bisheria P. lagoariana 30 species P. cajani P. meadii P. brassicae P. cuyabensis 10 unknown / new taxa ? P. cambivora P. medicaginis P. captiosa P. cact x hed P. capsici P. megakarya P. europaea P. foliorum Central Oregon stream (Oak Creek) P. cinnamomi P. megasperma P. fallax P. sulawesiensis Remigi / sutton / Reeser / Hansen P. citricola P. melonis P. gallica P. siskiyouensis Combined SSCP of ITS, Cox P. citrophthora P. mexicana P. glovera P. uliginosa 11 specie s P. clandestina P. mirabilis P. hedraiandra P. pinifolia 5 unknown / new taxa ? P. colocasiae P. multivesiculata P. inundata P. cryptogea P. nicotianae P. ipomoeae P. taxon salixsoil West Australian bush P. drechsleri P. palmivora P. kelmania P. taxon pgchlamydo Burgess / Hardy P. erythroseptica P. phaseoli P. kernoviae P. taxon riversoil ITS sequence P. fragariae var frag. P. porri P. nemorosa P. taxon oaksoil 9 unknown / new taxa ? P. fragariae var rubi P. primulae P. niederhauserii P. parvasperma P. gonapodyides P. pseudotsugae P. pistaciae P .hungarica West Scotland streams P. heveae P. quercina P. polonica P. sylvatica Scibetta / Cooke / Cacciola P. hibernalis P. quininea P. pseudosyringae P. carica ITS1 nested PCR P. humicola P. richardiae P. psychrophila P. quercetorum 17 species P. idaei P. sinensis P. ramorum P. taxon meadii-like 3 unknown / new taxa ? P. ilicis P. sojae P. sansomea P. taxon Acer P. infestans P. syringae P. taxon. Banksia P. taxon Agathis Ecuador streams P. inflata P. tentaculata P. taxon. Chicory P. taxon orphan Scibetta / Cooke P. insolita P. trifolii P. cact x nic ITS1 nested PCR 10 species P. iranica P. vignae P. tropicalis 51+ P.italica 55 4 unknown / new taxa ?
  • 32. Described Phytophthora species over time 140 130 120 110 Turin 2008 100 Described species 90 80 70 60 Erwin & Ribeiro 50 Waterhouse1963 1996 40 30 Tucker 1931 20 10 DeBary 1876 0 1860 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 Year
  • 33. Described Phytophthora species over time Period of evolutionary and genomic exploration 140 and 130 uncertainty ? 120 Period of 110 Period of discovery Turin 100 biological morphology pathology 2008 consolidation Described species 90 80 and ‘certainty’ 70 60 Erwin & 50 Waterhouse Ribeiro 1996 1963 key summary 40 30 Tucker 1931 20 synthesis 10 DeBary 1876 0 1860 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 Year Pandoras box?
  • 34. Why such an increase in species since 2000? The emergence of more holistic, population- based species concepts since the 1980s The rapid application of molecular tools for defining evolutionary units in fung Increasing international trade in rooted plants Increased environmental screening for Phytophthora species – sample surveys
  • 35. Growing number of described Phytophthora species: significance for Phylogeny? ca 50 Phytophthora species Cooke et al 2000 Oomycete ITS tree
  • 36. Hansen group Water filtering method in use (Yunnan)
  • 37. Growing number of described Phytophthora species: significance for Phylogeny? Since 2000 seeing marked increase in species in Clades 9 and 10 (only about 3 species known in 2000) Cooke et al 2000 Oomycete ITS tree
  • 38. Blair et al 2006 seven locus consensus tree Today already ca 10 ‘new’ species in these clades….
  • 39. Cooke et al 2000 ITS tree Clades 1-8 only ca 47 species In Clades 1-8:
  • 40. Since 2000 - a rapid increase in species in Clades1-8 e.g. 3 new species associated with the previously remote P. lateralis subclade in Clade 8 Cooke et al 2000 ITS tree Clades 1-8 ca 47 species
  • 41. Blair et al 2008 seven locus consensus tree P. lateralis now joined by P.hibernalis, P.ramorum, P.foliorum
  • 42. Since 2000 a dramatic increase in Clade 6 species 5 species in 2000 Cooke et al 2000 ITS tree Clades 1-8 ca 47 species
  • 43. 15 taxa in Clade 6 by 2004: Strill growing: would now need to add P. hungarica sp.nov; P. taxon orphan: P. pinifolia ... Brasier et al 2004 ITS tree Clade 6
  • 44. 99 Phytophthora inundata Five new 74 100 99 P.sp. 6 : P.sp. 10 100 Clade 6 taxa 100 100 P.sp. 7 Clade 6 Phytophthora megasperma 100 in the WA 67 61 97 P.sp. 3 93 100P.sp. 8 VHS 78 97 Phytophthora gonapodyides 82 Phytophthora citricola collection … Phytophthora 85 inflata 100P.sp. 4 100 ITS sequence tree Clade 2 Phytophthora capsici 100 courtesy Burgess, 100 Phytophthora multivesiculata 94 100 Stukely, Hardy 98 Phytophthora alticola 99 100 P.sp. 2 100 100 Phytophthora nicotianae Clade 1 100 73 Phytophthora cactorum 100 Phytophthora arecae Clade 4 100 100 100 Phytophthora frigida 98 P.sp. 1 100 100 Phytophthora cinnamomi Clade 7 Phytophthora ramorum 100 100 Phytophthora drechsleri 94 Phytophthora cryptogea 100 95 P.sp. 5 Clade 8 87 100 95 Phytophthora captiosa 91 Phytophthora fallax 100 100 P.sp. 9 Clades 9, 10 100 100 Phytophthora kernoviae 100 Phytophthora boehmeriae 10 changes
  • 45. South west Oregon streams Hansen / Reeser / Sutton Combined SSCP of ITS, Cox 30 Phytophthora species ~ 10 unknown / new taxa ? Majority probably in Clade 6
  • 46. So how many species in Clade 6? Take the 2007 data: ca 17 of the 105 known Phytophthora species are in Clade 6 = 16% - ‘biggest’ Clade of all? Taking the estimate of 200 - 600 total Phytophthora species This gives an estimate of 32-96 species in Clade 6
  • 47. (Clade 6 by 2004) Brasier et al 2004 ITS tree Clade 6
  • 49. If many of these 32 (- 96) ‘new’ species are also aquatic, sterile or inbreeding, high temperature species like Pg, P t pgchlamydo etc – – we may even have to rethink our species concept for this subclade
  • 50. So we now have new and rapidly expanding molecular phylogenetic trees : But what do these trees mean in terms of how we understand Phytophthoras?
  • 51. Obviously the trees are a major step forward from the Waterhouse 1963 morphological Groups 1-6 - The former were identification aids and were necessarily artificial constructs - - Whereas our molecular trees are closer to ‘natural relationships’ Noneless I suggest we treat them with a degree of caution:
  • 52. 1. Much data is missing because of extinctions! 2. Much data is missing because we still have to add the ~100 – 500 extant species!
  • 53. 3. Much evidence of past reticulation events is missing … …the footprints of hybridisation and genetic introgression will have been lost over time …
  • 54. What is important is not so much that we can show that species X and species Y are related… eg that P. ramorum and P. lateralis are related So what? In Darwinian terms, what is more important is to understand the processes and events that gave rise to their divergence… The Darwinian meaning is all in the nodes …
  • 55. Why did ancestral species W give rise to three species X, Y and Z...? W XYZ Why did Clade 1 ancestral species A give A rise to two Clade 2 clades 1 and 2? and so on...
  • 56. Concluding comments ... This dip into Phytophthora numerical biodiversity and phylogenetic uncertainties has put me in mind of just how little we know about the origins of the genus. Indeed, it seems reasonable to suggest that the construction of a phylogenetic tree is simply the point at which the real evolutionary challenges begin.
  • 57. So, given that there are probably 200-600 species of Phytophthora out there - - I see two key challenges for the future: 1. Understanding why there are so many Phytophthoras. ie. What environmental processes and events (geographic, climatic, biotic) drove their evolution? Why did eg P. ramorum diverge from P. lateralis? - the job of the evolutionary biologist 2. Understanding at the genetic level how eg P. ramorum behaves so differently from P. lateralis? - the job of the genomicist
  • 58. Fortunately, these how and why challenges are not mutually exclusive, and answers obtained for one will enormously benefit the understanding in the other. I suggest, therefore, that we are in for an exciting time over the next decade! Thank you
  • 59. A written version of this talk will be published shortly: Brasier C. M (2008). Phytophthora biodiversity: How many Phytophthora species are there? In Proceedings of the 4th IUFRO Workshop on Phytophthoras in Forests and Natural Ecosystems (E. Goheen ed). in press USDA Forest Service.