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SUMMARY Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation ofin situselection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population ofPenicillium solitumover eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in thealb1gene, which encodes the first protein in the DHN-melanin biosynthesis pathway, explained the green to white shift. A similar phenotypic shift was recapitulated with analb1knockout and experimental evolution in laboratory populations. The most common genetic disruption of thealb1genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light, suggesting that loss of melanin is only adaptive in dark conditions. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. Unintentional domestication of microbes by cheesemakers may provide opportunities to generate new strains for innovation in traditional cheese production. 

For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment. 

Abstract Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait‐related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof‐of‐principle analysis ofPenicilliumgenomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome‐wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions. 

1. Climate change is projected to cause shifts in precipitation regimes globally, leading to intensified periods of precipitation and droughts. Most studies that have explored the influence of changing precipitation regimes on ecosystems have focused on changes in mean annual precipitation, rather than the variance around the mean. Soil fungi are ubiquitous organisms that drive ecosystem processes, but it is unknown how they respond to long-term increased interannual precipitation variability. 2. Here, we investigated the influence of long-term increased precipitation variability and host type on soil fungal diversity and community composition in a dryland ecosystem. We collected 300 soil samples from two time points and different host type substrate types at a long-term precipitation variability experiment at the Jornada Long Term Ecological Research site. Next, we used amplicon sequencing to characterize soil fungal communities. 3. Soil fungal alpha diversity and community composition were strongly affected by host type and sampling year, and increased precipitation variability caused a modest, statistically insignificant, decrease in soil fungal evenness. Furthermore, results from our structural equational model showed that the decrease in grass-associated soil fungal richness was likely an indirect result of host decline in response to increased precipitation variability. 4. Synthesis. Our work demonstrates effects of increase in interannual precipitation variability on soil fungi, and that plant hosts play a key role in mediating soil fungal responses.