The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

AgroBioInstitute Agricultural Academy 8 Dragan Tsankov blvd 1164 Sofia Bulgaria

Department of Crop and Forest Sciences Agrotecnio Center CERCA University of Lleida Alcalde Rovira Roure 191 25198 Lleida Spain

Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Box 7026 750 07 Uppsala Sweden

Flanders Research Institute for Agriculture Fisheries and Food Plant Sciences Unit Burg Van Gansberghelaan 96 9820 Merelbeke Belgium

Julius Kühn Institute Messeweg 11 12 38104 Braunschweig Germany

Laboratory of Molecular Biotechnology and Phytopathology Centre for Mediterranean Bioresources and Food University of Algarve 8005 130 Faro Portugal

Life Sciences Department Walloon Agricultural Research Centre Rue de Liroux 4 5030 Gembloux Belgium

Ministère de l'agriculture et de l'alimentation Direction générale de l'alimentation Département de la Santé des Forêts 75015 Paris France

Phytophthora Research Centre Mendel University 613 00 Brno Czech Republic

Université de Lorraine Institut National de la Recherche Agronomique 54000 Nancy France

Wageningen University and Research Business Unit Biointeractions and Plant Health PO BOX 16 6700 AA Wageningen the Netherlands

Westerdijk Fungal Biodiversity Institute P O Box 85167 3508 AD Utrecht the Netherlands

Zobrazit více v PubMed

Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Boughman J, Brelsford A, Buerkle CA, Buggs R, Butlin RK, Dieckmann U, Eroukhmanoff F, Grill A, Cahan SH, Hermansen JS, Hewitt G, Hudson AG, Jiggins C, Jones J, Keller B, Marczewski T, Mallet J, Martinez-Rodriguez P, Möst M, Mullen S, Nichols R, Nolte AW, Parisod C, Pfennig K, Rice AM, Ritchie MG, Seifert B, Smadja CM, Stelkens R, Szymura JM, Väinölä R, Wolf JBW, Zinner D. Hybridization and speciation. J Evol Biol. 2013;26(2):229–246. doi: 10.1111/j.1420-9101.2012.02599.x. PubMed DOI

Alexander DH, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics. 2011;12(1):246. doi: 10.1186/1471-2105-12-246. PubMed DOI PMC

Alix K, Gérard PR, Schwarzacher T, Pat Heslop-Harrison JS. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann Bot. 2017;120(2):183–194. doi: 10.1093/aob/mcx079. PubMed DOI PMC

Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. Source verification of mis-identified Arabidopsis thaliana accessions. Plant J. 2011;67(3):554–566. doi: 10.1111/j.1365-313X.2011.04606.x. PubMed DOI

Anderson BM, Thiele KR, Krauss SL, Barrett MD. Genotyping-by-sequencing in a species complex of Australian hummock grasses (Triodia): methodological insights and phylogenetic resolution. PLoS One. 2017;12:e0171053. doi: 10.1371/journal.pone.0171053. PubMed DOI PMC

Arbizu CI, Ellison SL, Senalik D, et al. Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae) BMC Evol Biol. 2016;16:234. doi: 10.1186/s12862-016-0806-x. PubMed DOI PMC

Baum DA. Species as ranked taxa. Syst Biol. 2009;58(1):74–86. doi: 10.1093/sysbio/syp011. PubMed DOI

Beakes GW, Glockling SL, Sekimoto S. The evolutionary phylogeny of the oomycete “fungi”. Protoplasma. 2012;249(1):3–19. doi: 10.1007/s00709-011-0269-2. PubMed DOI

Beckerman J, Goodwin S, Gibson K (2014) The threat of hybrid Phytophthoras. USDA Forest Service Proceedings RMRS-P-72 12–17

Bennett MD. Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) using flow cytometry show genome size in Arabidopsis to be 157 Mb and thus 25% larger than the Arabidopsis genome initiative estimate of 125 Mb. Ann Bot. 2003;91(5):547–557. doi: 10.1093/aob/mcg057. PubMed DOI PMC

Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D. A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants. Plant Cell. 2016;28(3):606–609. doi: 10.1105/tpc.15.00502. PubMed DOI PMC

Bertier L, Leus L, D’hondt L, de Cock AWAM, Höfte M. Host adaptation and speciation through hybridization and polyploidy in Phytophthora. PLoS One. 2013;8(12):e85385. doi: 10.1371/journal.pone.0085385. PubMed DOI PMC

Blair JE, Coffey MD, Park S-Y, Geiser DM, Kang S. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol. 2008;45(3):266–277. doi: 10.1016/J.FGB.2007.10.010. PubMed DOI

Bonants P, Edema M, Robert V. Q-bank, a database with information for identification of plant quarantine plant pest and diseases. EPPO Bull. 2013;43(2):211–215. doi: 10.1111/epp.12030. DOI

Boyer F, Mercier C, Bonin A, et al. OBITOOLS: a UNIX-inspired software package for DNA metabarcoding. Mol Ecol Resour. 2016;16:176–182. doi: 10.1111/1755-0998.12428. PubMed DOI

Brasier CM. Rapid evolution of introduced plant pathogens via interspecific hybridization. BioScience. 2001;51(2):123–133. doi: 10.1641/0006-3568(2001)051[0123:REOIPP]2.0.CO;2. DOI

Brasier CM, Cooke DE, Duncan JM. Origin of a new Phytophthora pathogen through interspecific hybridization. Proc Natl Acad Sci U S A. 1999;96:5878–5883. doi: 10.1073/PNAS.96.10.5878. PubMed DOI PMC

Brasier CM, Cooke DEL, Duncan JM, Hansen EM. Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile. Mycol Res. 2003;107(3):277–290. doi: 10.1017/S095375620300738X. PubMed DOI

Brasier CM, Franceschini S, Vettraino AM, Hansen EM, Green S, Robin C, Webber JF, Vannini A. Four phenotypically and phylogenetically distinct lineages in Phytophthora lateralis. Fungal Biol. 2012;116(12):1232–1249. doi: 10.1016/J.FUNBIO.2012.10.002. PubMed DOI

Brasier CM, Hansen EM. Evolutionary biology of Phytophthora part II: phylogeny, speciation, and population structure. Annu Rev Phytopathol. 1992;30:173–200. doi: 10.1146/annurev.py.30.090192.001133. DOI

Brasier CM, Kirk SA, Delcan J, Cooke DEL, Jung T, Man in’t Veld WA. Phytophthora alni sp. nov. and its variants: designation of emerging heteroploid hybrid pathogens spreading on Alnus trees. Mycol Res. 2004;108(10):1172–1184. doi: 10.1017/S0953756204001005. PubMed DOI

Burgess TI. Molecular characterization of natural hybrids formed between five related indigenous clade 6 Phytophthora species. PLoS One. 2015;10(8):1–23. doi: 10.1371/journal.pone.0134225. PubMed DOI PMC

Burgess TI, Scott JK, Mcdougall KL, Stukely MJC, Crane C, Dunstan WA, Brigg F, Andjic V, White D, Rudman T, Arentz F, Ota N, Hardy GESJ. Current and projected global distribution of Phytophthora cinnamomi, one of the world’s worst plant pathogens. Glob Chang Biol. 2017;23(4):1661–1674. doi: 10.1111/gcb.13492. PubMed DOI

Callaghan S, Guest D. Globalisation, the founder effect, hybrid Phytophthora species and rapid evolution: new headaches for biosecurity. Australas Plant Pathol. 2015;44:255–262. doi: 10.1007/s13313-015-0348-5. DOI

Catal M, King L, Tumbalam P, Wiriyajitsomboon P, Kirk WW, Adams GC. Heterokaryotic nuclear conditions and a heterogeneous nuclear population are observed by flow cytometry in Phytophthora infestans. Cytometry A. 2010;77(8):769–775. doi: 10.1002/cyto.a.20888. PubMed DOI

Chapman MA, Burke JM. Genetic divergence and hybrid speciation. Evolution. 2007;61:1773–1780. doi: 10.1111/j.1558-5646.2007.00134.x. PubMed DOI

Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics. 2015;16(Suppl 10):S2. doi: 10.1186/1471-2164-16-S10-S2. PubMed DOI PMC

Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evol Appl. 2015;8(1):23–46. doi: 10.1111/eva.12234. PubMed DOI PMC

Cooke DE, Drenth A, Duncan JM, et al. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Biol. 2000;30(1):17–32. doi: 10.1006/fgbi.2000.1202. PubMed DOI

DaCosta JM, Sorenson MD. ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: analyses of two avian genera with contrasting histories. Mol Phylogenet Evol. 2016;94(Pt A):122–135. doi: 10.1016/J.YMPEV.2015.07.026. PubMed DOI

Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9:772–772. doi: 10.1038/nmeth.2109. PubMed DOI PMC

Dice LR. Measures of the amount of ecologic association between species. Ecology. 1945;26(3):297–302. doi: 10.2307/1932409. DOI

Doležel J, Greilhuber J. Nuclear genome size: are we getting closer? Cytometry A. 2010;77(7):635–642. doi: 10.1002/cyto.a.20915. PubMed DOI

Doležel J, Sgorbati S, Lucretti S. Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiol Plant. 1992;85(4):625–631. doi: 10.1111/j.1399-3054.1992.tb04764.x. DOI

Dowle M, Srinivasan A (2018) Data.Table: extension of “data.Frame”. R package version 1.11.2. https://cran.r-project.org/package=data.table

Dupuis JR, Brunet BMT, Bird HM, Lumley LM, Fagua G, Boyle B, Levesque R, Cusson M, Powell JA, Sperling FAH. Genome-wide SNPs resolve phylogenetic relationships in the north American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol. 2017;111:158–168. doi: 10.1016/j.ympev.2017.04.001. PubMed DOI

Ellstrand NC, Schierenbeck KA. Hybridization as a stimulus for the evolution of invasiveness in plants? Proc Natl Acad Sci U S A. 2000;97(13):7043–7050. doi: 10.1073/PNAS.97.13.7043. PubMed DOI PMC

Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379. doi: 10.1371/journal.pone.0019379. PubMed DOI PMC

Érsek T. Creation of species hybrids of Phytophthora with modified host ranges by zoospore fusion. Phytopathology. 1995;85(11):1343. doi: 10.1094/Phyto-85-1343. DOI

Érsek T, Nagy ZÁ. Species hybrids in the genus Phytophthora with emphasis on the alder pathogen Phytophthora alni: a review. Eur J Plant Pathol. 2008;122(1):31–39. doi: 10.1007/s10658-008-9296-z. DOI

Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. American Phytopathological Society (APS Press), St. Paul

Escudero M, Eaton DAR, Hahn M, Hipp AL. Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: a case study in Carex (Cyperaceae) Mol Phylogenet Evol. 2014;79:359–367. doi: 10.1016/j.ympev.2014.06.026. PubMed DOI

Fang H, Gough J. SupraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. Biochem Biophys Res Commun. 2014;443(1):285–289. doi: 10.1016/j.bbrc.2013.11.103. PubMed DOI PMC

Fernández-Mazuecos M, Mellers G, Vigalondo B, Sáez L, Vargas P, Glover BJ. Resolving recent plant radiations: power and robustness of genotyping-by-sequencing. Syst Biol. 2018;67(2):250–268. doi: 10.1093/sysbio/syx062. PubMed DOI

Fry W. Phytophthora infestans: the plant (and R gene) destroyer. Mol Plant Pathol. 2008;9(3):385–402. doi: 10.1111/j.1364-3703.2007.00465.x. PubMed DOI PMC

Giraud T, Villaréal LMMA, Austerlitz F, et al. Importance of the life cycle in sympatric host race formation and speciation of pathogens. Phytopathology. 2006;96:280–287. doi: 10.1094/PHYTO-96-0280. PubMed DOI

Goss EM, Cardenas ME, Myers K, et al. The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans. PLoS ONE. 2011;6:e24543. doi: 10.1371/journal.pone.0024543. PubMed DOI PMC

Goss EM, Larsen M, Vercauteren A, Werres S, Heungens K, Grünwald NJ. Phytophthora ramorum in Canada: evidence for migration within North America and from Europe. Phytopathology. 2011;101(1):166–171. doi: 10.1094/PHYTO-05-10-0133. PubMed DOI

Griffin PC, Robin C, Hoffmann AA. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol. 2011;9(1):19. doi: 10.1186/1741-7007-9-19. PubMed DOI PMC

Grünwald NJ, Garbelotto M, Goss EM, Heungens K, Prospero S. Emergence of the sudden oak death pathogen Phytophthora ramorum. Trends Microbiol. 2012;20(3):131–138. doi: 10.1016/J.TIM.2011.12.006. PubMed DOI

Gu Y-H, Ko W-H. Creation of hybrid vigor through nuclear transplantation in Phytophthora. Can J Microbiol. 2001;47(7):662–666. doi: 10.1139/w01-074. PubMed DOI

Hantula J, Lilja A, Nuorteva H. Pathogenicity, morphology and genetic variation of Phytophthora cactorum from strawberry, apple, rhododendron, and silver birch. Mycol Res. 2000;104(9):1062–1068. doi: 10.1017/S0953756200002999. DOI

Hantula J, Lilja A, Parikka P. Genetic variation and host specificity of Phytophthora cactorum isolated in Europe. Mycol Res. 1997;101(5):565–572. doi: 10.1017/S0953756296002900. DOI

Hapke A, Thiele D. GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome. Mol Ecol Resour. 2016;16(4):979–990. doi: 10.1111/1755-0998.12510. PubMed DOI

Hardham AR. Phytophthora cinnamomi. Mol Plant Pathol. 2005;6(6):589–604. doi: 10.1111/J.1364-3703.2005.00308.X. PubMed DOI

Herten K, Hestand MS, Vermeesch JR, Van Houdt JK. GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. BMC Bioinformatics. 2015;16(1):73. doi: 10.1186/s12859-015-0514-3. PubMed DOI PMC

Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol. 2013;22(11):3002–3013. doi: 10.1111/mec.12239. PubMed DOI PMC

Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding missing data biases in phylogenomic inference: an empirical study in the Landfowl (Aves: Galliformes) Mol Biol Evol. 2016;33(4):1110–1125. doi: 10.1093/molbev/msv347. PubMed DOI

Hou Y, Nowak MD, Mirré V, Bjorå CS, Brochmann C, Popp M. Thousands of RAD-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus Diapensia (Diapensiaceae) PLoS One. 2015;10(10):e0140175. doi: 10.1371/journal.pone.0140175. PubMed DOI PMC

Husson C, Aguayo J, Revellin C, Frey P, Ioos R, Marçais B. Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex. Fungal Genet Biol. 2015;77:12–21. doi: 10.1016/j.fgb.2015.02.013. PubMed DOI

Ioos R, Andrieux A, Marçais B, Frey P. Genetic characterization of the natural hybrid species Phytophthora alni as inferred from nuclear and mitochondrial DNA analyses. Fungal Genet Biol. 2006;43(7):511–529. doi: 10.1016/J.FGB.2006.02.006. PubMed DOI

Jafari F, Mostowfizadeh-Ghalamfarsa R, Safaiefarahani B, Burgess TI. Potential host range of four Phytophthora interspecific hybrids from clade 8a. Plant Pathol. 2020;69(7):1281–1290. doi: 10.1111/ppa.13205. DOI

Joly S, Starr JR, Lewis WH, Bruneau A. Polyploid and hybrid evolution in roses east of the Rocky Mountains. Am J Bot. 2006;93(3):412–425. doi: 10.3732/ajb.93.3.412. PubMed DOI

Jones JC, Fan S, Franchini P, Schartl M, Meyer A. The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol. 2013;22(11):2986–3001. doi: 10.1111/mec.12269. PubMed DOI

Jung T, Chang TT, Bakonyi J, Seress D, Pérez-Sierra A, Yang X, Hong C, Scanu B, Fu CH, Hsueh KL, Maia C, Abad-Campos P, Léon M, Horta Jung M. Diversity of Phytophthora species in natural ecosystems of Taiwan and association with disease symptoms. Plant Pathol. 2017;66(2):194–211. doi: 10.1111/ppa.12564. DOI

Jung T, Durán A, Sanfuentes von Stowasser E, Schena L, Mosca S, Fajardo S, González M, Navarro Ortega AD, Bakonyi J, Seress D, Tomšovský M, Cravador A, Maia C, Horta Jung M. Diversity of Phytophthora species in Valdivian rainforests and association with severe dieback symptoms. For Pathol. 2018;48(5):e12443. doi: 10.1111/efp.12443. DOI

Jung T, Jung MH, Cacciola SO, et al. Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal. IMA Fungus. 2017;8:219–244. doi: 10.5598/imafungus.2017.08.02.02. PubMed DOI PMC

Jung T, Jung MH, Scanu B, Seress D, Kovács GM, Maia C, Pérez-Sierra A, Chang TT, Chandelier A, Heungens K, van Poucke K, Abad-Campos P, Léon M, Cacciola SO, Bakonyi J. Six new Phytophthora species from ITS clade 7a including two sexually functional heterothallic hybrid species detected in natural ecosystems in Taiwan. Persoonia. 2017;38(1):100–135. doi: 10.3767/003158517X693615. PubMed DOI PMC

Jung T, Nechwatal J. Phytophthora gallica sp. nov., a new species from rhizosphere soil of declining oak and reed stands in France and Germany. Mycol Res. 2008;112(10):1195–1205. doi: 10.1016/J.MYCRES.2008.04.007. PubMed DOI

Jung T, Orlikowski L, Henricot B, Abad-Campos P, Aday AG, Aguín Casal O, Bakonyi J, Cacciola SO, Cech T, Chavarriaga D, Corcobado T, Cravador A, Decourcelle T, Denton G, Diamandis S, Doğmuş-Lehtijärvi HT, Franceschini A, Ginetti B, Green S, Glavendekić M, Hantula J, Hartmann G, Herrero M, Ivic D, Horta Jung M, Lilja A, Keca N, Kramarets V, Lyubenova A, Machado H, Magnano di San Lio G, Mansilla Vázquez PJ, Marçais B, Matsiakh I, Milenkovic I, Moricca S, Nagy ZÁ, Nechwatal J, Olsson C, Oszako T, Pane A, Paplomatas EJ, Pintos Varela C, Prospero S, Rial Martínez C, Rigling D, Robin C, Rytkönen A, Sánchez ME, Sanz Ros AV, Scanu B, Schlenzig A, Schumacher J, Slavov S, Solla A, Sousa E, Stenlid J, Talgø V, Tomic Z, Tsopelas P, Vannini A, Vettraino AM, Wenneker M, Woodward S, Peréz-Sierra A. Widespread Phytophthora infestations in European nurseries put forest, semi-natural and horticultural ecosystems at high risk of Phytophthora diseases. For Pathol. 2016;46(2):134–163. doi: 10.1111/efp.12239. DOI

Jung T, Pérez-Sierra A, Durán A, Jung MH, Balci Y, Scanu B. Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands. Persoonia. 2018;40(1):182–220. doi: 10.3767/persoonia.2018.40.08. PubMed DOI PMC

Kamoun S. Molecular genetics of pathogenic oomycetes. Eukaryot Cell. 2003;2(2):191–199. doi: 10.1128/ec.2.2.191-199.2003. PubMed DOI PMC

Kamoun S, Furzer O, Jones JDG, Judelson HS, Ali GS, Dalio RJD, Roy SG, Schena L, Zambounis A, Panabières F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grünwald NJ, Mukhtar MS, Tomé DFA, Tör M, van den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJG, Petre B, Ristaino J, Yoshida K, Birch PRJ, Govers F. The top 10 oomycete pathogens in molecular plant pathology. Mol Plant Pathol. 2015;16(4):413–434. doi: 10.1111/mpp.12190. PubMed DOI PMC

Keriö S, Daniels HA, Gómez-Gallego M, et al. From genomes to forest management – tackling invasive Phytophthora species in the era of genomics. Can J Plant Pathol. 2019;42:1–29. doi: 10.1080/07060661.2019.1626910. DOI

Kroon LPNM, Bakker FT, van den Bosch GBM, et al. Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genet Biol. 2004;41:766–782. doi: 10.1016/J.FGB.2004.03.007. PubMed DOI

Leaché AD, Chavez AS, Jones LN, Grummer JA, Gottscho AD, Linkem CW. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol Evol. 2015;7(3):706–719. doi: 10.1093/gbe/evv026. PubMed DOI PMC

Li Y, Shen H, Zhou Q, Qian K, van der Lee T, Huang S. Changing ploidy as a strategy: the Irish potato famine pathogen shifts ploidy in relation to its sexuality. Mol Plant-Microbe Interact. 2017;30(1):45–52. doi: 10.1094/MPMI-08-16-0156-R. PubMed DOI

Liebhold AM, Brockerhoff EG, Garrett LJ, Parke JL, Britton KO. Live plant imports: the major pathway for forest insect and pathogen invasions of the US. Front Ecol Environ. 2012;10(3):135–143. doi: 10.1890/110198. DOI

Lorsch JR, Collins FS, Lippincott-Schwartz J. Fixing problems with cell lines. Science. 2014;346(6216):1452–1453. doi: 10.1126/science.1259110. PubMed DOI PMC

Mallet J. Hybrid speciation. Nature. 2007;446:279–283. doi: 10.1038/nature05706. PubMed DOI

Man in ‘t Veld WA, De Cock AWAM, Summerbell RC. Natural hybrids of resident and introduced Phytophthora species proliferating on multiple new hosts. Eur J Plant Pathol. 2007;117(1):25–33. doi: 10.1007/s10658-006-9065-9. DOI

Man in ‘t Veld WA, Rosendahl KCHM, Hong C. Phytophthora ×serendipita sp. nov. and P. ×pelgrandis, two destructive pathogens generated by natural hybridization. Mycologia. 2012;104(6):1390–1396. doi: 10.3852/11-272. PubMed DOI

Martens C, Van de Peer Y. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics. 2010;11(1):353. doi: 10.1186/1471-2164-11-353. PubMed DOI PMC

Martin FN, Blair JE, Coffey MD. A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora. Fungal Genet Biol. 2014;66:19–32. doi: 10.1016/J.FGB.2014.02.006. PubMed DOI

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17(1):10. doi: 10.14806/ej.17.1.200. DOI

McCarthy CGP, Fitzpatrick DA. Phylogenomic reconstruction of the oomycete phylogeny derived from 37 genomes. mSphere. 2017;2(2):e00095–e00017. doi: 10.1128/mSphere.00095-17. PubMed DOI PMC

McDade LA. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. Evolution. 1992;46(5):1329–1346. doi: 10.1111/j.1558-5646.1992.tb01127.x. PubMed DOI

Mchau GRA, Coffey MD. Isozyme diversity in Phytophthora palmivora: evidence for a southeast Asian Centre of origin. Mycol Res. 1994;98(9):1035–1043. doi: 10.1016/S0953-7562(09)80430-9. DOI

Mideros MF, Turissini DA, Guayazán N, Ibarra-Avila H, Danies G, Cárdenas M, Myers K, Tabima J, Goss EM, Bernal A, Lagos LE, Grajales A, Gonzalez LN, Cooke DEL, Fry WE, Grünwald N, Matute DR, Restrepo S. Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia. Persoonia. 2018;41(1):39–55. doi: 10.3767/persoonia.2018.41.03. PubMed DOI PMC

Nagel JH, Gryzenhout M, Slippers B, Wingfield MJ, Hardy GESJ, Stukely MJC, Burgess TI. Characterization of Phytophthora hybrids from ITS clade 6 associated with riparian ecosystems in South Africa and Australia. Fungal Biol. 2013;117(5):329–347. doi: 10.1016/J.FUNBIO.2013.03.004. PubMed DOI

Nelson SC, Abad GZ. Phytophthora morindae, a new species causing black flag disease on noni (Morinda citrifolia L) in Hawaii. Mycologia. 2010;102(1):122–134. doi: 10.3852/08-209. PubMed DOI

Nute M, Chou J, Molloy EK, Warnow T. The performance of coalescent-based species tree estimation methods under models of missing data. BMC Genomics. 2018;19(S5):286. doi: 10.1186/s12864-018-4619-8. PubMed DOI PMC

Oudemans P, Coffey MD. A revised systematics of twelve papillate Phytophthora species based on isozyme analysis. Mycol Res. 1991;95:1025–1046. doi: 10.1016/S0953-7562(09)80543-1. DOI

Pandit MK, Pocock MJO, Kunin WE. Ploidy influences rarity and invasiveness in plants. J Ecol. 2011;99(5):1108–1115. doi: 10.1111/j.1365-2745.2011.01838.x. DOI

Pánek M, Fér T, Mrácek J, Tomsovský M. Evolutionary relationships within the Phytophthora cactorum species complex in Europe. Fungal Biol. 2016;120:836–851. doi: 10.1016/j.funbio.2016.03.006. PubMed DOI

Pisupati R, Reichardt I, Seren Ü, Korte P, Nizhynska V, Kerdaffrec E, Uzunova K, Rabanal FA, Filiault DL, Nordborg M. Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples. Sci Data. 2017;4(1):170184. doi: 10.1038/sdata.2017.184. PubMed DOI PMC

Poland JA, Brown PJ, Sorrells ME, Jannink J-L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One. 2012;7(2):e32253. doi: 10.1371/journal.pone.0032253. PubMed DOI PMC

Rambaut A. FigTree. 2018.

Redondo MA, Boberg J, Olsson CHB, Oliva J. Winter conditions correlate with Phytophthora alni subspecies distribution in Southern Sweden. Phytopathology. 2015;105(9):1191–1197. doi: 10.1094/PHYTO-01-15-0020-R. PubMed DOI

Redondo MA, Boberg J, Stenlid J, Oliva J. Functional traits associated with the establishment of introduced Phytophthora spp. in Swedish forests. J Appl Ecol. 2018;55(3):1538–1552. doi: 10.1111/1365-2664.13068. DOI

Redondo MA, Boberg J, Stenlid J, Oliva J. Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits. ISME J. 2018;12(12):2967–2980. doi: 10.1038/s41396-018-0229-3. PubMed DOI PMC

Robideau GP, De Cock AWAM, Coffey MD, et al. DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour. 2011;11(6):1002–1011. doi: 10.1111/j.1755-0998.2011.03041.x. PubMed DOI PMC

Roch S, Warnow T. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst Biol. 2015;64(4):663–676. doi: 10.1093/sysbio/syv016. PubMed DOI

Safaiefarahani B, Mostowfizadeh-Ghalamfarsa R, Hardy GESJ, Burgess TI. Re-evaluation of the Phytophthora cryptogea species complex and the description of a new species, Phytophthora pseudocryptogea sp. nov. Mycol Prog. 2015;14:108. doi: 10.1007/s11557-015-1129-9. DOI

Safaiefarahani B, Mostowfizadeh-Ghalamfarsa R, Hardy GESJ, Burgess TI. Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize. Fungal Biol. 2016;120:975–987. doi: 10.1016/j.funbio.2016.05.002. PubMed DOI

Sansome E, Brasier CM, Hamm PB. Phytophthora meadii may be a species hybrid. Mycol Res. 1991;95(3):273–277. doi: 10.1016/S0953-7562(09)81232-X. DOI

Santini A, Ghelardini L, De Pace C, et al. Biogeographical patterns and determinants of invasion by forest pathogens in Europe. New Phytol. 2013;197(1):238–250. doi: 10.1111/j.1469-8137.2012.04364.x. PubMed DOI

Sayyari E, Mirarab S. Fast coalescent-based computation of local branch support from quartet frequencies. Mol Biol Evol. 2016;33(7):1654–1668. doi: 10.1093/molbev/msw079. PubMed DOI PMC

Schardl CL, Craven KD. Interspecific hybridization in plant-associated fungi and oomycetes: a review. Mol Ecol. 2003;12(11):2861–2873. doi: 10.1046/j.1365-294X.2003.01965.x. PubMed DOI

Schierenbeck KA, Ellstrand NC. Hybridization and the evolution of invasiveness in plants and other organisms. Biol Invasions. 2009;11(5):1093–1105. doi: 10.1007/s10530-008-9388-x. DOI

Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27(6):863–864. doi: 10.1093/bioinformatics/btr026. PubMed DOI PMC

Simamora AV, Stukely MJC, Hardy GES, Burgess TI. Phytophthora boodjera sp. nov., a damping-off pathogen in production nurseries and from urban and natural landscapes, with an update on the status of P. alticola. IMA Fungus. 2015;6:319–335. doi: 10.5598/imafungus.2015.06.02.04. PubMed DOI PMC

Soltis PS. Hybridization, speciation and novelty. J Evol Biol. 2013;26(2):291–293. doi: 10.1111/jeb.12095. PubMed DOI

Soltis PS, Soltis DE. The role of hybridization in plant speciation. Annu Rev Plant Biol. 2009;60(1):561–588. doi: 10.1146/annurev.arplant.043008.092039. PubMed DOI

Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313. doi: 10.1093/bioinformatics/btu033. PubMed DOI PMC

Stetter MG, Schmid KJ. Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Mol Phylogenet Evol. 2017;109:80–92. doi: 10.1016/J.YMPEV.2016.12.029. PubMed DOI

Stukenbrock EH, McDonald BA. The origins of plant pathogens in agro-ecosystems. Annu Rev Phytopathol. 2008;46(1):75–100. doi: 10.1146/annurev.phyto.010708.154114. PubMed DOI

Tange O (2018) GNU Parallel 2018. Zenodo

te Beest M, Le Roux JJ, Richardson DM, et al. The more the better? The role of polyploidy in facilitating plant invasions. Ann Bot. 2012;109(1):19–45. doi: 10.1093/aob/mcr277. PubMed DOI PMC

Than C, Ruths D, Nakhleh L. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics. 2008;9(1):322. doi: 10.1186/1471-2105-9-322. PubMed DOI PMC

Tyler BM. Phytophthora sojae: root rot pathogen of soybean and model oomycete. Mol Plant Pathol. 2007;8(1):1–8. doi: 10.1111/j.1364-3703.2006.00373.x. PubMed DOI

Vachaspati P, Warnow T. SVDquest: improving SVDquartets species tree estimation using exact optimization within a constrained search space. Mol Phylogenet Evol. 2018;124:122–136. doi: 10.1016/J.YMPEV.2018.03.006. PubMed DOI

Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017;18(7):411–424. doi: 10.1038/nrg.2017.26. PubMed DOI

Vettraino AM, Brasier CM, Brown AV, Vannini A. Phytophthora himalsilva sp. nov. an unusually phenotypically variable species from a remote forest in Nepal. Fungal Biol. 2011;115(3):275–287. doi: 10.1016/j.funbio.2010.12.013. PubMed DOI

Werres S, Marwitz R, Man WA, et al. Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and Viburnum. Mycol Res. 2001;105(10):1155–1165. doi: 10.1016/S0953-7562(08)61986-3. DOI

Wickham H (2016) ggplot2: elegant graphics for data analysis, 2nd edn. Springer International Publishing

Yang X, Hong C (2018) Differential usefulness of nine commonly used genetic markers for identifying Phytophthora species. Front Microbiol 9:2334. 10.3389/fmicb.2018.02334 PubMed PMC

Yang X, Richardson PA, Hong C. Phytophthora ×stagnum nothosp. Nov., a new hybrid from irrigation reservoirs at ornamental plant nurseries in Virginia. PLoS One. 2014;9(7):e103450. doi: 10.1371/journal.pone.0103450. PubMed DOI PMC

Yang X, Tyler BM, Hong C. An expanded phylogeny for the genus Phytophthora. IMA Fungus. 2017;8(2):355–384. doi: 10.5598/imafungus.2017.08.02.09. PubMed DOI PMC

Yoshida K, Schuenemann VJ, Cano LM, et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife. 2013;2:e00731. doi: 10.7554/eLife.00731. PubMed DOI PMC

Zentmyer GA (1980) Phytophthora cinnamomi and the diseases it causes. American Phytopathological Society

Zhang C, Rabiee M, Sayyari E, Mirarab S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018;19(S6):153. doi: 10.1186/s12859-018-2129-y. PubMed DOI PMC

Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics. 2014;30(5):614–620. doi: 10.1093/bioinformatics/btt593. PubMed DOI PMC

Zimmer EA, Wen J. Using nuclear gene data for plant phylogenetics: progress and prospects II. Next-gen approaches. J Syst Evol. 2015;53(5):371–379. doi: 10.1111/jse.12174. DOI

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