Biology subjects

Wolfe, T. M.

Publications and source records attributed to Wolfe, T. M..

5 recordsLinked to original sources

bioRxiv2024

Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza)

O_LIHybridization and polyploidy are major drivers of plant diversification, often accompanied by shifts in gene expression and genome composition. Small RNAs (smRNAs) are thought to influence such genomic changes, particularly through their interactions with transposable elements (TEs). C_LIO_LIWe comparatively quantified smRNAs in established sibling allopolyploids Dactylorhiza majalis and D. traunsteineri and their diploid progenitors to assess how independent allopolyploidization events shaped smRNA landscapes. C_LIO_LIDespite independent origins, the allotetraploids exhibited substantial overlap in smRNA composition, including transgressive accumulation of smRNA near genes related to transcriptional regulation, cell division and stress response. Consistently, TE-associated 24 nt smRNAs more closely resembled the paternal and larger genome, while shorter smRNAs typically reflected the maternal and smaller genome. Nevertheless, distinct patterns were also evident: the older D. majalis showed greater accumulation of smRNAs near genes involved in transcriptional and translational regulation, while the younger D. traunsteineri displayed stronger non-additive patterns, suggesting ongoing resolution of post-polyploid meiotic and mitotic instability. C_LIO_LIOur results reveal both convergence and divergence in smRNA landscapes among independently formed allopolyploids. Our study highlights the central role of smRNAs in resolving genomic conflict, with possible implications for functional divergence and ecological innovation during polyploid evolution. C_LI Plain-language summaryWe studied two sibling marsh orchid species that arose through hybridization and genome doubling. By comparing their small RNA molecules and how these associate with genes, we found both shared and species-specific patterns. These differences reflect how the orchids genomes have changed since formation, and may explain how repeated polyploidy events contribute to genetic and ecological diversity in plants.

evolutionary biology↗

bioRxiv2024

Microbiome impact of ibezapolstat and other Clostridioides difficile infection relevant antibiotics using humanized mice

BackgroundIbezapolstat (IBZ) is a competitive inhibitor of the bacterial Pol IIIC enzyme in clinical development for treatment of Clostridioides difficile infection (CDI). Previous studies demonstrated IBZ carries a favorable microbiome diversity profile compared to vancomycin (VAN). However, head-to-head comparisons with other CDI antibiotics have not been done. The purpose of this study was to compare microbiome changes associated with IBZ to other clinically used CDI antibiotics. MethodsGroups of germ-free (GF) mice received a fecal microbiota transplant from one of two healthy human donors and were subsequently exposed to either IBZ, VAN, fidaxomicin (FDX), metronidazole (MET), or no antibiotic (control). 16S rRNA encoding gene sequencing of temporally collected stool samples was used to compare gut microbiome perturbation between treatment and no-drug control groups. ResultsAmong the tested antibiotics, the most significant change in microbiome diversity was observed in MET-treated mice. Each antibiotic had a unique effect, but changes in alpha and beta diversity following FDX- and IBZ-treated groups were less pronounced compared to those observed in VAN-or MET-treated groups. By the end of therapy, both IBZ and FDZ increased the relative abundance of Bacteroidota (phylum), with IBZ additionally increasing the relative abundance of Actinomycetota (phylum). ConclusionIn microbiome-humanized mice, IBZ and FDX had smaller effects on gut microbiome diversity compared to VAN and MET. Notable differences were observed between the microbiome of IBZ- and FDX-treated groups, which may allow for differentiation of these two antibiotics in future studies.

microbiology↗

bioRxiv2024

Ecological divergence is marked by specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species. Significance statementThis study highlights the role of phenotypic plasticity in the persistence and distribution of sibling allopolyploid marsh orchids (Dactylorhiza majalis s.l.). By examining gene expression and the diversity of root mycobiome across reciprocal transplantations in native environments, we uncover high plasticity that facilitates adaptation and gene flow, thereby promoting both diversification and homogenization. These findings underscore the importance of plasticity in the establishment and long-term survival of allopolyploid species across the landscape.

evolutionary biology↗

bioRxiv2021

Recurrent allopolyploidization events diversify eco-physiological traits in marsh orchids

Whole-genome duplication, in particular allopolyploidy, has shaped the evolution of angiosperms and other organisms. Structural reorganization of chromosomes and repatterning of gene expression is frequently observed in early generation allopolyploids, with potential ecological consequences. The relative contributions of environmental and intrinsic drivers to these changes are unknown. We show here that in marsh orchids (Dactylorhiza, Orchidaceae), recurrently-formed allopolyploids are characterized by distinct eco-physiologies matching their respective environments, providing us with an excellent study system to address this question. Here we integrate eco-physiological and transcriptomic comparative studies to reveal a complex suite of intertwined, pronounced differences between sibling allopolyploids. We show that Dactylorhiza majalis that is distributed in Central and Southern Europe favors meadows with mesic soils. Its sibling allopolyploid D. traunsteineri occurs in fens, characterized by soils depleted by macro- and micronutrients, mainly in previously glaciated European areas. We further uncover distinct features in their nutrient transport, leaf elemental chemistry, light-harvesting, photoprotection, and stomata activity, that appear all linked to their distinct ecologies, in particular soil chemistry differences at their native sites. Recurrent polyploidization hence enriches biodiversity through eco-physiological diversification, providing the opportunity for sibling allopolyploids to evolve as distinct evolutionary units, despite pervasive interspecific gene flow. Significance StatementWhole-genome duplication resulting in polyploidy has underpinned the evolution of flowering plants and other organisms, and is important for many crops. However, the ecological implications of polyploidy remain little understood. Here, we demonstrate that two sibling allopolyploid marsh orchid species prefer distinct habitats, and have evolved a suite of distinctive ecophysiological characters (e.g. nutrient transport, energy harvesting and photoprotection). We argue that the divergence of these characters in the nascent polyploids drove adaptation into distinct ecological niches (low nutrient fens versus meadows with mesic soils), generating ecological barriers that maintains distinct, independent lineages, even in the presence of interspecific gene flow.

evolutionary biology↗

bioRxiv2021

Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

evolutionary biology↗