Evolutionary Relationships and a Tree-Based Alignment Selector Interactive Phylogeny of the Emerging Lineages of the...

The spread of Phytophthora ramorum, 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 United States, Canada, and Europe since the late 1990s. Twelve lineages of P. ramorum are described that vary in global distribution and virulence. Herein, we present a maximum likelihood phylogeny for P. ramorum inferred using IQ-TREE and the Tree-Based Alignment Selector (T-BAS) toolkit. The phylogeny was generated based on six loci (avh120, avh121, btub, gweuk.30.30.1, hsp90, and trp1). This phylogeny of P. ramorum improves on previous phylogenies because it is dynamic and interactive and incorporates a diverse set of all known global lineages from the United States and 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 P. ramorum 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 P. ramorum collected from Ireland and Northern Ireland and placed them accurately in the tree. The P. ramorum 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 P. ramorum.