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, and can potentially infect a wider host range and display enhanced vigour. Consequently, Phytophthora hybrids pose a serious threat to agriculture as well as 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 positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we combined Genotyping-by-Sequencing (GBS) and genome size estimation on a genus-wide collection of 657 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 nine previously described hybrid species and discover 16 new hybrids. Our method was also valuable for species identification, at an unprecedented resolution, and allowed to correct 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 linked to their progenitors in this phylogenetic tree via bi- or trifurcate links. This repository contains all scripts which were developed during this project. Our study paves the way for relatively low cost but high resolution identification of hybrids and their phylogenetic relations in many other phyla.
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