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Abstract Traditional fermented foods often contain specialized microorganisms adapted to their unique environments. For example, the filamentous mold Aspergillus oryzae, used in saké fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae, used in soybean-based fermentations like miso and shochu, is hypothesized to have been domesticated from Aspergillus parasiticus. Here, we examined the effects of long-term A. sojae use in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 17 A. sojae and 24 A. parasiticus genomes (23 of which were sequenced for this study), alongside phenotypic traits of 9 isolates. Aspergillus sojae formed a distinct, low-diversity population, suggesting a recent clonal expansion. Interestingly, a population of A. parasiticus was more closely related to A. sojae than other A. parasiticus populations. Genome comparisons revealed loss-of-function mutations in A. sojae, notably in biosynthetic gene clusters encoding secondary metabolites, including the aflatoxin cluster. Interestingly though, A. sojae harbored a partial duplication of a siderophore biosynthetic cluster. Phenotypic assays showed A. sojae lacked aflatoxin production, while it was variable in A. parasiticus isolates. Additionally, certain A. sojae strains exhibited larger colony diameters under miso-like salt conditions. These findings support the hypothesis that A. parasiticus is the progenitor of A. sojae and that domestication significantly reduced genetic diversity. Future research should explore how wild and food-associated strains influence sensory attributes and microbial community dynamics in fermented soy products. 

Abstract Geochemical records generated from the calcite tests of benthic foraminifera, especially those of the generaCibicidoidesandUvigerina, provide the basis for proxy reconstructions of past climate. However, the extent to which benthic foraminifera are affected by postdepositional alteration is poorly constrained. Furthermore, how diagenesis may alter the geochemical composition of benthic foraminiferal tests, and thereby biasing a variety of proxy‐based climate records, is also poorly constrained. We present the Foraminiferal Preservation Index (FPI) as a new metric to quantify preservation quality based on objective, well‐defined criteria. The FPI is used to identify and quantify trends in diagenesis temporally, from late Pliocene to modern coretop samples (3.3–0 Ma), as well as spatially in the deep ocean. The FPI identifies the chemical composition of deep‐ocean water masses to be the primary driver of diagenesis through time, while also serving as a supplementary method of identifying periods of changing water mass influence at a given site. Additionally, we present stable isotope data (δ¹⁸O, δ¹³C) generated from individualCibicidoidesspecimens of various preservation quality that demonstrate the likelihood of significant biasing in a variety of geochemical proxy records, especially those used to reconstruct past changes in ice volume and sea level. These single‐test data further demonstrate that when incorporating carefully selected tests of only the highest preservation quality, robust paleorecords can be generated.