Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred

Urban environments provide opportunities for early detections of Phytophthora invasions

An early version of this paper was presented at a workshop on ‘Non-native species in urban environments’ hosted and funded by the DST-NRF Centre of Excellence for Invasion Biology (C⋅I⋅B) in Stellenbosch, South Africa, in November 2016.Globalization has increased the frequency of inadvertent introductions of plant pathogens. Many catastrophic invasions of both natural and agricultural systems have been initiated through anthropogenic dissemination pathways. Phytophthora species are a group of invasive plant pathogens causing many of the most important plant disease epidemics. A review of Phytophthora species descriptions published following the publication of the first DNA-based Phytophthora phylogeny was conducted to highlight patterns of recent introductions and to provide insights for early pathogen detection initiatives. Seventy-two publications from 2001 to 2016 describing 98 Phytophthora species were evaluated. Of the 91 species with data on geographic location isolation, 22% were described from type specimens isolated from urban environments, 33% from agricultural environments and 45% from natural environments. Within the urban environment, ornamental plant trading nurseries were the most important sources. Specifically, for Phytophthora ramorum, a species causing multiple epidemics globally, the largest proportion of first report publications were from urban environments, including nurseries. We therefore suggest that detection programs for invasive plant pathogens within the urban environment would be valuable. In this regard, specialized monitoring and citizen science projects that target urban areas where live plant-trading industries are concentrated would be particularly effective to both promote early detection and to facilitate a rapid response to new species invasions.The Department of Science and Technology (DST)-National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB; http://www.fabinet.up.ac.za/research-groups/dst-nrf-centre-of-excellence-in-tree-health-biotechnology) and also from support contributed to the crowd-funding campaign “Discovering Plant Destroyers in South Africa with Citizen Science” (doi: 10.18258/2066).http://link.springer.com/journal/105302018-12-23hj2018Forestry and Agricultural Biotechnology Institute (FABI

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper