Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

Members of the fungal genus Microbotryum are well‐known parasites on eudicotyledonous plant hosts. However, recent studies focused exclusively on Microbotryum species being parasites in the anthers of Caryophyllaceae in which strong host‐specificity was confirmed by molecular analyses. Consequently, species numbers have risen considerably as multi‐host parasites were split up in so‐called cryptic species. We subjected three non‐caryophyllaceous Microbotryum groups to molecular phylogenetic analyses to see whether we would confirm multi‐host morphospecies or if host‐specific cryptic species in these selected groups could be revealed as well (i.e. a group of non‐caryophyllaceous anther smuts, parasites on different Fallopia species, and parasites on Polygonum bistorta and Polygonum vi‐viparum). We applied a multiple analysis strategy to correct for varying alignment effects on a two‐locus dataset (ITS and LSU rDNA). The results obtained by the different approaches are uniform; high host‐specificity exists in the non‐ caryophyllaceous anther smuts, but overlapping host ranges occur in the parasites of Fallopia species. Results for the parasites of Polygonum are similar, with Microbotryum bistortarum being separated into three lineages and M. marginale forming a lineage on P. bistorta which apparently is conspecific with M. bistortarum p.p. Our study shows that phylogenetic patterns within Microbotryum are much more complicated than deduced from morphological observations alone. Even though Microbotryum species are highly host‐specific, it is impossible to identify species based solely on host taxa affiliation. Species status is reinstated for the anther smut on Salvia pratensis.

Summary: Populations of diverse, unknown, and potentially pathogenic fungi and fungus‐like organisms are continuously introduced into new locations via asymptomatic infections (e.g. as endophytes or latent pathogens) within internationally traded live plants. Interactions between these asymptomatic fungi and novel recipient host trees can be unpredictable, and urban introductions may act as bridgeheads into natural and managed forests. Historical examples of novel, highly destructive forest tree diseases highlight the potential threat of this pathway. As the trade in live plants continues to expand, the likelihood of high‐impact incursions increases. This has led to calls for more proactive management, including more stringent treatment and regulatory standards, and even the phasing out of trade in plants determined to be an untenable risk to forest ecosystems. In this review, we discuss how biosecurity systems should consider advances in understanding the diversity and ecology of phytobiomes associated with asymptomatic plants and what measures can be considered to reduce this threat to global forest health.

The smut fungal genus Microbotryum (Microbotryales, Pucciniomycotina) contains species that parasitize plants from many different lineages of euasterids, with host specificity of individual parasite species in general being exceptionally high. Additionally, it has been shown that the location of spore production in some species is related to spore dispersal. In this phylogenetic study based on ITS and LSU rDNA data of 57 Microbotryum spp., host spectra and sorus location are mapped on the phylogeny of Microbotryum species in order to understand the macroevolutionary patterns of these two traits. We find that monophyletic parasite clades correspond well with monophyletic host clades and also that monophyletic parasite groups in general produce their spores in the same plant organ. Ancestral state reconstruction inferred the most probable ancestral trait for sorus location being leaves and the most probable ancestral host family for the genus Microbotryum as being the Polygonaceae. According to molecular analyses, a newly sequenced specimen of Ustilago ducellieri, a seed parasite on Arenaria leptoclados, previously treated as synonym of Microbotryum duriaeanum, belongs to a lineage distinct from specimens of M. duriaeanum. A new combination, Microbotryum ducellieri, is accordingly proposed. Taxonomic implications of the presented analyses for the genera Bauhinus and Haradaea are briefly discussed.