Phylogenetic and Population Genetic Analyses Reveal Patterns of Divergence Among Isolates of Ceratocystis manginecans

The taxonomic boundaries of Ceratocystis species related to C. manginecans 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 species recently reduced to synonymy with C. manginecans , including host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity and population structure of isolates considered broadly as Ceratocystis manginecans , specifically those treated as C. eucalypticola and C. manginecans in various previous studies. The study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Multi‐locus phylogenetic analyses, supported by genotyping at 16 SSR loci, resolved two genetically distinct lineages: Lineage 1 (previously treated as C. eucalypticola ) and Lineage 2 (previously treated as C. manginecans ). These lineages showed structured genetic differentiation across geographic regions and host associations, consistent with previously reported differences in aggressiveness and infection biology. Detailed morphological comparisons also provided support for the two groupings. Although the results revealed the existence of two lineages among isolates currently treated as C. manginecans , discordance among loci and signals of admixture in a subset of isolates were consistent with evidence for mixed ancestry and/or incomplete lineage sorting. This suggests incomplete reproductive isolation that is contributing to current taxonomic ambiguity and confusion. The results support treating the isolates in the two groups as distinct lineages (Lineage 1 and 2) within C. manginecans , recognising their differences while maintaining a conservative taxonomic approach and thus facilitating important quarantine considerations and future studies focused on disease management.