The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.

The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamomi from natural and agricultural outbreaks and the long-distance movement of individual genotypes were studied using four microsatellite markers to genotype 159 isolates of Californian, Mexican, and worldwide origins. Allelic profiles identified 75 multilocus genotypes. A STRUCTURE analysis placed them in three groups characterized by different geographic and host ranges, different genic and genotypic diversity, and different reproductive modes. When relationships among genotypes were visualized on a minimum spanning network (MSN), genotypes belonging to the same STRUCTURE group were contiguous, with rare exceptions. A putatively ancestral group 1 had high genic diversity, included all A1 mating type isolates and all Papuan isolates in the sample, was rarely isolated from natural settings in California and Mexico, and was positioned at the center of the MSN. Putatively younger groups 2 and 3 had lower genic diversity, were both neighbors to group 1 but formed two distinct peripherical sectors of the MSN, and were equally present in agricultural commodities and natural settings in Mexico and California. A few genotypes, especially in groups 2 and 3, were isolated multiple times in different locations and settings. The presence of identical genotypes from the same hosts in different continents indicated that long-distance human-mediated movement of P. cinnamomi had occurred. The presence of identical genotypes at high frequencies in neighboring wildlands and agricultural settings suggest that specific commodities may have been the source of recent wild infestations caused by novel invasive genotypes.

Recognition of Tylopilus alboater once relied heavily on the morphological features of the basidiomata, which resulted in considerable confusion due to morphological stasis and plasticity. In this study, we examined specimens morphologically identified as T. alboater from Asia, North America, and Australia using phylogenomics and multi-locus sequence data. To clarify its phylogenetic placement within Boletaceae , we conducted a phylogenomic analysis based on 45 genomes (including three newly sequenced T. alboater genomes) comprising representatives from the eight subfamilies of Boletaceae . Additionally, we constructed a concatenated dataset (nrLSU + tef1-α + rpb1 + rpb2 ), incorporating representative species from all genera within the subfamily to which T. alboater belongs, to infer its phylogeny. Our phylogenomic analysis revealed that specimens morphologically identified as T. alboater exhibit polyphyly, clustering entirely within the subfamily Boletoideae . Our multi-locus phylogenetic analyses further indicated that these specimens represent eight distinct species distributed across five generic lineages within the subfamily Boletoideae , including one new genus, Neoporphyrellus , proposed in this study, as well as one new species, N. sinoalboater , and two new combinations, N. alboater and N. atronicotianus . The remaining five species are nested in four known genera, including two new species of Abtylopilus , Ab. indonesiensis and Ab. australiensis , and three known species belonging to Anthracoporus , Indoporus , and Tylopilus , respectively. These findings highlight the taxonomic complexity of the T. alboater complex and emphasize the importance of integrating phylogenomic and multi-locus approaches for accurate fungal systematics. Color photos of fresh basidiomata, line drawings of microscopic features, and detailed descriptions of the new taxa are presented.

Epidemiological models are important for the understanding of disease progression in plants and for the design of control strategies. Phytophthora ramorum, the pathogen responsible for the disease known as Sudden Oak Death, causes lethal infection on several oaks but relies on California bay laurels for transmission. Here, repeated surveys of bay laurels and oaks indicated that bay laurel disease incidence was positively correlated with rainfall, bay laurel density, and an eastern aspect, and negatively correlated with bay laurel basal area. Oak infection only occurred in years when rainfall was higher than the 30-year average, and although infection rates were greater among larger trees, mortality was greater among smaller trees. Additionally, larger oaks closer to infected bay laurels exhibited greater infection rates. Disease incidence differed among sites, and only a fraction of bay laurels were disease superspreaders, while even fewer individuals were refugial trees harboring active infections during dry periods. Based on this study, reducing bay laurel density in denser stands and the number of superspreaders or refugial trees in less dense stands may reduce disease incidence. However, the selective removal of bay laurel trees 0–10 m from oaks is likely to be more effective in preventing infection of specific oaks.

The COVID-19 pandemic ushered in an unprecedented period of both crisis and innovation in higher education. The shift to an online learning environment was particularly problematic for courses in which students learn disciplinary practices. Scientific practice requires hands-on training and collaborative engagement with instructors and peers, dimensions of the learning environment that were challenging to recreate online. Here, we describe the resulting instructional innovations and challenges experienced in shifting multiple undergraduate- and graduate-level molecular bioscience labs, including Genetics, Cell Biology, Bioinformatics, and Advanced Microscopy, to an online learning environment. Instructors pursued novel approaches, techniques, and at-home lab tools with varying success. Many innovations were retained after the transition back to an in-person learning environment because they uniquely supported previously overlooked aspects of student learning. Consistent with other reports, we found that marginalized students pursuing science were disproportionately burdened by COVID-19 and the shift to an online learning environment. A description of what worked for online learning, what didn’t, and what is worth holding onto in the future is valuable for constructing learning environments that effectively support learners in their disciplinary practice.