The genus Lasiodiplodia, a member of the family Botryosphaeriaceae, is an important fungal disease genus in agriculture. However, the Lasiodiplodia species survey and genetic diversity in Taiwan remain unclear. This study aimed to investigate the Lasiodiplodia species associated with various fruit species to explore the cryptic Lasiodiplodia species diversity, validate species delimitation, and unveil cryptic genetic diversity. Overall, six Lasiodiplodia species were identified, with several new records of infection identified. Additionally, phylogenetic analyses indicated that the relations of all isolates of L. theobromae might be paraphyletic. They were grouped with L. brasiliense based on Automatic Barcode Gap Discovery (ABGD), Automatic Partitioning (ASAP) and structure-based clustering analyses. These analyses did not provide conclusive evidence for L. brasiliensis as a stable species. It may be necessary to gather more information to clarify the species delineation. The multiple new records of Lasiodiplodia species with high genetic diversity and differentiation revealed that the diversity of Lasiodiplodia in Taiwan was underestimated in the past. We found that L. theobromae has the highest number of haplotypes but the lowest number of haplotype and nucleotide diversities, indicating a recent population expansion. This was supported by the significant negative Tajima’s D and Fu and Li’s D* tests. The high genetic diversity, low gene flow, and host-associated differentiation of Lasiodiplodia species indicate that they might harbour powerful evolutionary potential in Taiwan. This study provided critical insights into genetic variation, host-associated differentiation, and demography of Lasiodiplodia species, which would be helpful for disease management of related pathogens.

Lasiodiplodia, a genus within the Botryosphaeriaceae family, comprises significant plant pathogens with a broad host range and global distribution, posing a substantial threat to agricultural production. Our recent study revealed the complexity of this genus by identifying numerous potential cryptic species within the seemingly generalist L. theobromae. To fully understand this species’ complexity, higher-resolution genetic markers are required. Therefore, this study employed a comprehensive analysis of multiple transferable microsatellite markers to verify Lasiodiplodia species delimitation and examine the fine-scale genetic structure and diversity of Lasiodiplodia species, particularly L. theobromae. The study identified four distinct genetic groups within L. theobromae, each showing high genetic diversity. The phylogenetic relationships of these groups align with the evolutionary history of their host plants. This finding suggests that host-pathogen co-evolution is shaped by shared ancestral variation, limited gene flow, isolation and natural selection. These insights enhance our understanding of managing economically important Lasiodiplodia plant pathogens and highlight the significance of genetic diversity and host preferences in developing effective control measures.

Salix kusanoi is an endangered riparian tree species endemic to Taiwan. This study aimed to evaluate the genetic diversity and population structure across eight fragmented populations employing 33 microsatellite loci. The findings revealed moderate genetic diversity (mean A_E = 3.85, H_O = 0.22) and significant deviations from the Hardy–Weinberg equilibrium. This indicated an evolutionary pressure, such as genetic drift and inbreeding. The Analysis of Molecular Variance (AMOVA) demonstrated evident genetic differentiation among populations (F_ST = 0.30). Principal Coordinates Analysis (PCoA) and Bayesian clustering (STRUCTURE) described distinct regional genetic patterns, with K = 5 providing a robust context for understanding localized genetic variation. Conservation interventions, including targeted in situ conservation for genetically unique populations (SBF) and genetic rescue strategies for genetically underprivileged populations (NW and NT), are proposed to safeguard the genetic integrity and adaptive potential of S. kusanoi.