M. Liu, S. Hambleton, Y. Anikster, And J. Kolmer 2019. Gene flow as a character in polyphasic classification of phytopathogenic fungi: a case study in wheat leaf rust species complex

The combination of phylogenetics and molecular technologies has dramatically increased the resolution of fungal classification over the past 30 years. Numerous species defined by morphology turn out to be complexes. Along with the achievements of more refined species recognition, a commonly encountered dilemma and debate is whether paraphyletic species should be recognized. Topology based species recognition considers that species must be supported by evidence of monophyly. A study of four host-associated forms of P. triticina Erikss. by Liu et al 2013 showed that tree topologies varied when different loci and analytical methods were used. The combined ITS and EF1-α analyses grouped all four forms as one clade whereas phylogenetic analysis of 239 SNPs from 15 loci resolved two strongly supported monophyletic groups and coalescence-based analysis (BEAST) resolved three monophyletic groups. In this case, 1, 2 or 3 species could be recognized based on various tree topologies. The form on Aegilops speltoides Tausch was previously recognized as a forma speciales based on infection experiments by Anikster et al 2005, which showed that A. speltoides was resistant to P. triticina isolated from wheat. Gene flow analysis (IMa2) indicated that there was no detectable gene flow between the Aegilops form and any other forms while constant gene flow was detected among other forms. We consider the lack of gene flow as strong evidence of genetic separation and propose to recognize Aegilops form as a separate species: Puccinia speltoides sp. nov., while other forms belong to one species.