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In the last twenty years, there has been a complete overhaul of <i>Fusarium</i> systematics at the species level, as molecular phylogenetic approaches have facilitated the recognition of species boundaries using evolutionary criteria. While genealogical concordance principles have provided excellent guidance for recognizing species boundaries, in cases such as the <i>F. oxysporum</i> complex and <i>F. solani</i> species complex, non-concordance of gene genealogies due to possible unorthodox evolutionary patterns have been confounding factors. In addition, complete genome sequences of members of these groups and associated experimental results have led to hypotheses that large portions of their genomes have origins outside <i>Fusarium</i>, and support the potential for horizontal gene transfer. Can genealogical concordance principles be utilized to recognize species boundaries in a high background of interspecific gene exchange? Can signatures of speciation events be identified from complete genome sequences in such a background? In this talk, I will develop a framework for addressing these basic questions, and propose some approaches that may allow species recognition in groups that show dynamic genome evolutionary patterns.<p><p>Keywords: