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Societal Impact StatementIt is important to recognize how our current understanding of plants has been shaped by diverse cultural contexts, as this underscores the importance of valuing and incorporating contributions from all knowledge systems in scientific pursuits. This approach emphasizes the ongoing bias, including within scientific practices, and the necessity of discussing problematic histories within spaces of learning. It is crucial to acknowledge and address biases, even within scientific endeavors. Doing so fosters a more inclusive and equitable scientific community. This article, while not comprehensive, serves as a starting point for conversation and an introduction to current work on these topics. SummaryIn response to a global dialog about systemic racism, ongoing inequalities, appeals to decolonize science, and the many recent calls for diversity, equity, accessibility, and inclusion, we draw on the narratives of plants to revisit the history of botany. Our goal is to uncover how exclusionary practices have functioned in the past and persist today. We also explore the numerous opportunities and challenges that arise in the era of information as we strive to establish a more inclusive field of botany. This approach recognizes and honors the contributions of historically marginalized groups, such as Black and Indigenous communities. We hope that this article can serve as a catalyst for raising awareness, fostering contemplation, and driving action toward a more equitable and just scientific community. 

ABSTRACT Gene expression divergence through evolutionary processes is thought to be important for achieving programmed development in multicellular organisms. To test this premise in filamentous fungi, we investigated transcriptional profiles of 3,942 single-copy orthologous genes (SCOGs) in five related sordariomycete species that have morphologically diverged in the formation of their flask-shaped perithecia. We compared expression of the SCOGs to inferred gene expression levels of the most recent common ancestor of the five species, ranking genes from their largest increases to smallest increases in expression during perithecial development in each of the five species. We found that a large proportion of the genes that exhibited evolved increases in gene expression were important for normal perithecial development in Fusarium graminearum . Many of these genes were previously uncharacterized, encoding hypothetical proteins without any known functional protein domains. Interestingly, the developmental stages during which aberrant knockout phenotypes appeared largely coincided with the elevated expression of the deleted genes. In addition, we identified novel genes that affected normal perithecial development in Magnaporthe oryzae and Neurospora crassa , which were functionally and transcriptionally diverged from the orthologous counterparts in F. graminearum . Furthermore, comparative analysis of developmental transcriptomes and phylostratigraphic analysis suggested that genes encoding hypothetical proteins are generally young and transcriptionally divergent between related species. This study provides tangible evidence of shifts in gene expression that led to acquisition of novel function of orthologous genes in each lineage and demonstrates that several genes with hypothetical function are crucial for shaping multicellular fruiting bodies. IMPORTANCE The fungal class Sordariomycetes includes numerous important plant and animal pathogens. It also provides model systems for studying fungal fruiting body development, as its members develop fruiting bodies with a few well-characterized tissue types on common growth media and have rich genomic resources that enable comparative and functional analyses. To understand transcriptional divergence of key developmental genes between five related sordariomycete fungi, we performed targeted knockouts of genes inferred to have evolved significant upward shifts in expression. We found that many previously uncharacterized genes play indispensable roles at different stages of fruiting body development, which have undergone transcriptional activation in specific lineages. These novel genes are predicted to be phylogenetically young and tend to be involved in lineage- or species-specific function. Transcriptional activation of genes with unknown function seems to be more frequent than ever thought, which may be crucial for rapid adaption to changing environments for successful sexual reproduction. 

ABSTRACT Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespreadQuercus macrocarpa, we conducted a rangewide survey ofQ. macrocarpaand four sympatric eastern North American white oak species. Using a Hyb‐Seq approach, we assembled a dataset of 3412 thinned single‐nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off‐target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure withinQ. macrocarpaassociated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.