Phylogenetic and population genetic analyses reveal patterns of divergence among isolates in the Ceratocystis manginecans complex

The taxonomic boundaries within the Ceratocystis manginecans complex have remained contentious due to limited morphological variation, interfertility in laboratory mating studies, and the application of different species concepts. However, recent studies have highlighted significant differences among isolates, such as host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity, and population structure of isolates treated broadly in the Ceratocystis manginecans complex, specifically those treated as C. eucalypticola and C. manginecans in various studies. This study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Detailed morphological comparisons for representative isolates residing in discrete clades were conducted. Phylogenetic analyses of sequence data for seven gene regions, supported by multilocus genotyping of 16 SSR loci, identified two genetically distinct groups that broadly separated isolates having distinct ecological characteristics, the most relevant of which are infections primarily of roots or above ground tree parts. Morphological comparisons also provided support for the two groupings. Although the results supported the existence of two groups in the C. manginecans complex, there was also evidence of hybridization between isolates in the respective groups suggesting incomplete reproductive isolation, leading to taxonomic ambiguity. Isolates in the two groups are, therefore, treated as distinct lineages within the C. manginecans complex, recognizing their divergence while maintaining a conservative taxonomic approach.