Biology subjects

Bazzicalupo, A.

Publications and source records attributed to Bazzicalupo, A..

7 recordsLinked to original sources

bioRxiv2026

Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size

Ectomycorrhizal (EM) fungi are vital to forest ecosystems, supporting tree growth and survival. However, their inclusion in conservation policy and action remains limited and little is known about the status of their genetic diversity, which is essential for their long-term survival and adaptation. The Global Biodiversity Framework adopted a genetic indicator based on the effective population size, Ne, to monitor genetic diversity in all species. To date, it is still uncertain how Ne, a key parameter, can be reliably assessed in species with complex life history traits. Ectomycorrhizal fungi are a highly diverse group of taxa displaying haplodiplontic life cycles with partially clonal reproduction. Here, we review the literature to understand how these life history traits might affect Ne and its estimation in six species of EM fungi. We estimated Ne in 19 populations using eight genetic and genomic datasets from selected studies. We compared Ne estimates using Linkage Disequilibrium (LD) and Sibship Frequency (SF) methods. We tested how Ne estimates change due to partial clonality and genetic structure gradients and whether the number of genetic markers influence the precision of the estimates. We show a systematic bias in Ne estimations when large clones are present and when populations are not correctly delimited. We found both methods are not robust to these factors, which makes them unreliable for conservation assessment purposes in EM fungi. This study provides new perspectives for further research into the links between life history traits and the effective population size of ectomycorrhizal fungi.

genetics↗

bioRxiv2026

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

Human colonization since the 19th century has resulted in the global spread of pines across the Southern Hemisphere, well beyond their original northern boreal distribution. Such introductions moved not only the pines but also expanded the distribution of their symbiotic partners. Although the introduction of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, population genomic analyses of 208 individuals across both native and introduced ranges showed that all introductions originated from Europe, likely mediated by human activities along with pine introductions. With the exception of North America, introduced populations were genetically differentiated from the Europe population, with varying magnitudes of population expansion in different introduced regions, often linked to forestry practices. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial genetic patterns of native versus exotic habitats. This study provides insight into the population genetics of a globally introduced ectomycorrhizal fungus whose introduction process is likely applicable to other pine-co-introduced ectomycorrhizal fungi.

evolutionary biology↗

bioRxiv2025

Evolutionary responses to increased opportunity for sexual selection in yeast

Sexual selection contributes to biodiversity and the costs and benefits of sexual reproduction. In organisms where sex is infrequent, these impacts of sexual selection are likely to be limited. An increased frequency of obligate sex would increase the opportunity for sexual selection, which could promote the evolution of sexual traits and sexual differentiation. To study these dynamics, we conducted experimental evolution in the yeast Saccharomyces cerevisiae, which is predominantly asexual, with two isogamous mating types. We used selectable markers to impose frequent obligate sex in 96 populations. We manipulated the opportunity for sexual selection by imposing skewed mating-type ratios and by altering the degree to which mating occurred by selfing versus outcrossing. After just ten sexual cycles, we observed evolution in growth, cell size, pheromone production, and mating, with the mating types responding asymmetrically, but little evolutionary change in sporulation rate. Mating type dimorphism increased, with evident trade-offs between growth, attractiveness, and cell size. Genome sequences from a subset of populations revealed many mutations affecting sex-related genes. Unexpectedly, the selfing populations evolved to become sporulation-competent haploids, unlinking meiosis from ploidy change. Our results illustrate that sexual differentiation can evolve rapidly in response to an increased opportunity for sexual selection.

evolutionary biology↗

bioRxiv2025

Evolution of cross-tolerance to metals in yeast

Organisms often face multiple selective pressures simultaneously (e.g., mine tailings with multiple heavy metal contaminants), yet we know little about when adaptation to one stressor provides cross-tolerance or cross-intolerance to other stressors. To explore the potential for cross-tolerance, we first adapted Saccharomyces cerevisiae to high concentrations of six single metals in a short-term evolutionary rescue experiment. We then measured the cross-tolerance of each metal-adapted line in the other five metals. We generated and tested three predictors for the degree of cross-tolerance, based on the similarity between pairs of metal environments in (1) their physiochemical properties, (2) the overlap in genes known to impact tolerance to both metals, and (3) their co-occurrence in the environment. None of these predictors explained significant variation in cross-tolerance. Instead, we observed that adapted lines in one metal were frequently cross-tolerant to certain metals (manganese and nickel) and intolerant to others (cobalt and zinc). Furthermore, cross-tolerance between pairs of metals was not reciprocal, with mutations accumulating in one metal (e.g., copper) providing adaptation to another metal (e.g., manganese), but not vice versa. Evolved lines also differed in their degree of specialization, with lines evolved in manganese or copper more specialized to that metal, but lines evolved in cobalt or zinc more generally tolerant. To determine the genetic basis of these metal adaptations, we sequenced the genomes of 109 metal-adapted yeast lines. The SNP mutation spectrum was significantly different in cadmium, cobalt, and manganese than expected in a mutation accumulation experiment in S. cerevisiae. In addition, two lines were highly mutated, bearing defects in DNA repair genes (both in manganese). Thirteen genes exhibited parallel adaptation to different metals; three of these genes generated broad cross-tolerance. Several mutations were found in vacuolar transporter genes, suggesting an important role for vacuolar proteins in adapting to metal stress. Our results with these metal-adapted lines indicate that cross-tolerance is challenging to predict, depending on the combined stressors experienced and the nature of the mutations involved.

evolutionary biology↗

bioRxiv2023

Comparative transcriptomics provides insight into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Zinc is a major soil contaminant and high zinc levels can disrupt growth, survival, and reproduction of fungi. Some fungal species have evolved zinc tolerance through cell processes mitigating zinc toxicity, though the genes and detailed mechanisms underlying fungal zinc tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of zinc tolerance in the mycorrhizal fungus Suillus luteus. We found that zinc tolerance in this species is both a constitutive and environmentally dependent trait. Highly differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus zinc tolerance, while others are reported here for the first time. Overall, we found S. luteus zinc tolerance is associated with differences in expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of metal tolerance in mycorrhizal associations.

genomics↗

bioRxiv2021

Fungal communities from geothermal soils in Yellowstone National Park

Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 {degrees}C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.

ecology↗

bioRxiv2019

Incipient local adaptation in a fungus: evolution of heavy metal tolerance through allelic and copy-number variation

Human-altered environments can shape the evolution of organisms. Fungi are no exception, though little is known about how they withstand anthropogenic pollution. Here, we document incipient polygenic local adaptation in the mycorrhizal fungus Suillus luteus driven by recent soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed no evidence of population structure but detected allelic divergence and gene copy number variation in genes involved in metal exclusion, storage, immobilization, and reactive oxygen species detoxification. Standing genetic variation included multiple alleles of small effects contributing to heavy metal tolerance, suggesting the existence of different strategies to withstand contamination. These variants were shared across the whole population but under selection in isolates exposed to pollution. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.

evolutionary biology↗