Evolutionary Relationships and a T-BAS Interactive Phylogeny of Emerging Lineages of the Plant Pathogen <i>Phytophthora ramorum</i>

The spread of <i>Phytophthora ramorum</i>, the causal agent of Sudden Oak Death and Sudden Larch Death, has resulted in a destructive loss of trees, woody shrubs, and ornamentals in nurseries and forests in the US, Canada, and Europe since the late 1990s. Twelve lineages of <i>P. ramorum</i> are described that vary in global distribution and virulence. Herein, we present a maximum likelihood phylogeny for <i>P. ramorum</i> inferred using IQ-TREE and Tree-Based Alignment Selector Toolkit (T-BAS). The phylogeny was generated based on six loci (<i>avh120, avh121, btub,</i> gweuk.30.30.1, <i>hsp90,</i> and <i>trp1</i>). This phylogeny of <i>P. ramorum</i> improves on previous phylogenies since it is dynamic and interactive and incorporates a diverse set of all known global lineages from the US, Europe (NA1, NA2, EU1, and EU2), and ancestral lineages from the putative native range in East Asia. The phylogenetic relationships inferred in the T-BAS tree support lineages NP1 and NP2 of <i>P. ramorum</i> as ancestral to NA1 and NA2 lineages found in North America. In addition, East Asian IC1, IC2, IC3, and IC4 lineages are ancestral to EU1 and EU2 lineages found in Europe. We used sequence data generated from isolates of <i>P. ramorum</i> collected from Ireland and Northern Ireland and placed them accurately in the tree. The <i>P. ramorum</i> phylogeny is available through T-BAS within the DeCIFR platform. This "interactive phylogeny" can be used by the research community to rapidly update and better reflect the evolutionary relationships of new lineages of <i>P. ramorum</i>.