title: Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach.
abstract: Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants.
authors.affiliation: Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany. Electronic address: mycochoi@gmail.com.
authors.forename: Young-Joon
authors.initials: YJ
authors.lastname: Choi
authors.affiliation: USDA-ARS, 1636 E. Alisal St, Salinas, CA, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Klosterman
authors.affiliation: University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 1, D-14469 Potsdam, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Kummer
authors.affiliation: BOKU-University of Natural Resources and Life Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, Peter Jordan-Straße 82, 1190 Vienna, Austria; University of Vienna, Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Wien, Austria.
authors.forename: Hermann
authors.initials: H
authors.lastname: Voglmayr
authors.affiliation: Korea University, Division of Environmental Science and Ecological Engineering, Seoul 136-701, Republic of Korea.
authors.forename: Hyeon-Dong
authors.initials: HD
authors.lastname: Shin
authors.affiliation: Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Thines
mesh_terms: D001499:Bayes Theorem; D027461:Beta vulgaris / Q000382:microbiology; D004271:DNA, Fungal / Q000235:genetics; D049810:Genetic Speciation; D016013:Likelihood Functions; D008957:Models, Genetic; D044742:Peronospora / Q000145:classification*; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA; D018724:Spinacia oleracea / Q000382:microbiology
chemical_list: D004271:DNA, Fungal
keywords: Cospeciation; Host shift; Multi-locus phylogeny; Oomycetes; Peronospora farinosa; Species tree