Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1197444 | ENA |
REPOSITORIES: ENA
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Project description:Although the relationship between phenotypic plasticity and evolutionary dynamics has attracted large interest, very little is known about the contribution of phenotypic plasticity to adaptive evolution. In this study, we analyzed phenotypic and genotypic changes in E. coli cells during adaptive evolution to ethanol stress. To quantify the phenotypic changes, transcriptome analyses were performed. We previously obtained 6 independently evolved ethanol tolerant E. coli strains, strains A through F, by culturing cells under 5% ethanol stress for about 1000 generations and found a significantly larger growth rate than the parent strains (Horinouchi et al, 2010, PMID: 20955615). To elucidate the phenotypic changes that occurred during adaptive evolution, we quantified the time-series of the expression changes by microarray analysis. Starting from frozen stocks obtained at 6 time points (0, 384, 744, 1224, 1824 and 2496 hours) in laboratory evolution, cells were cultured under 5% ethanol stress, and mRNA samples were obtained in the exponential growth phase for microarray analysis.
2014-07-21 | E-GEOD-59050 | biostudies-arrayexpress
Project description:Although the relationship between phenotypic plasticity and evolutionary dynamics has attracted large interest, very little is known about the contribution of phenotypic plasticity to adaptive evolution. In this study, we analyzed phenotypic and genotypic changes in E. coli cells during adaptive evolution to ethanol stress. To quantify the phenotypic changes, transcriptome analyses were performed.
2014-07-21 | GSE59050 | GEO
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
2018-07-27 | PXD008057 | Pride
Project description:<p>Understanding metabolic plasticity of animal evolution is a fundamental challenge in evolutionary biology. Owing to the diversification of insect wing morphology and dynamic energy requirements, the molecular adaptation mechanisms underlying the metabolic pathways in wing evolution remain largely unknown. This study reveals the pivotal role of the duplicated Apolipoprotein D (ApoD) gene in lipid and energy homeostasis in the lepidopteran wing. ApoD underwent significant expansion in insects, with gene duplication and consistent retention observed in Lepidoptera. Notably, duplicated ApoD2 was highly expressed in lepidopteran wings and encoded a unique C-terminal tail, conferring distinct ligand-binding properties. Using Bombyx mori as a model system, we integrated evolutionary analysis, multiomics, and in vivo functional experiments to elucidate the way duplicated ApoD2 mediates lipid trafficking and homeostasis via the AMP-activated protein kinase pathway in wings. Moreover, we revealed the specific expression and functional divergence of duplicated ApoD as a key mechanism regulating juvenile hormone levels and lipid homeostasis in the lepidopteran wing. These findings highlight an evolutionary scenario in which functional divergence and neofunctionalization conferred a novel role of ApoD in shaping adaptive lipid metabolic regulatory networks during wing phenotypic evolution. Overall, we provide in vivo evidence for the functional differentiation of duplicate genes in shaping adaptive metabolic regulatory networks during phenotypic evolution.</p>
2026-03-29 | MTBLS11285 | MetaboLights
Project description:<p>Understanding metabolic plasticity of animal evolution is a fundamental challenge in evolutionary biology. Owing to the diversification of insect wing morphology and dynamic energy requirements, the molecular adaptation mechanisms underlying the metabolic pathways in wing evolution remain largely unknown. This study reveals the pivotal role of the duplicated Apolipoprotein D (ApoD) gene in lipid and energy homeostasis in the lepidopteran wing. ApoD underwent significant expansion in insects, with gene duplication and consistent retention observed in Lepidoptera. Notably, duplicated ApoD2 was highly expressed in lepidopteran wings and encoded a unique C-terminal tail, conferring distinct ligand-binding properties. Using Bombyx mori as a model system, we integrated evolutionary analysis, multiomics, and in vivo functional experiments to elucidate the way duplicated ApoD2 mediates lipid trafficking and homeostasis via the AMP-activated protein kinase pathway in wings. Moreover, we revealed the specific expression and functional divergence of duplicated ApoD as a key mechanism regulating juvenile hormone levels and lipid homeostasis in the lepidopteran wing. These findings highlight an evolutionary scenario in which functional divergence and neofunctionalization conferred a novel role of ApoD in shaping adaptive lipid metabolic regulatory networks during wing phenotypic evolution. Overall, we provide in vivo evidence for the functional differentiation of duplicate genes in shaping adaptive metabolic regulatory networks during phenotypic evolution.</p>
2026-03-29 | MTBLS4308 | MetaboLights
Project description:Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria. Six animals each originating from four different islands were reared in either constant or reduced water conditions and hepatic mRNA levels of Gosner stage 37 animals evaluated by MAGEX DNA array analysis.
2014-03-18 | E-GEOD-42274 | biostudies-arrayexpress
Project description:Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria.
2014-03-18 | GSE42274 | GEO
Project description:Many organisms can acclimate to new environments through phenotypic plasticity, a complex trait that can be heritable, subject to selection, and evolve. However, the rate and genetic basis of plasticity evolution remain largely unknown. We experimentally evolved outbred populations of the nematode Caenorhabditis remanei under an acute heat shock during early larval development. When raised in a non-stressful environment, ancestral populations were highly sensitive to a 36.8°C heat shock and exhibited high mortality. However, initial exposure to a non-lethal high temperature environment resulted in significantly reduced mortality during heat shock (hormesis). Lines selected for heat shock resistance rapidly evolved the capacity to withstand heat shock in the native environment without any initial exposure to high temperatures, and early exposure to high temperatures did not lead to further increases in heat resistance. This loss of plasticity would appear to have resulted from the genetic assimilation of the heat induction response in the non-inducing environment. However, analyses of transcriptional variation via RNA-sequencing from the selected populations revealed no global changes in gene regulation correlated with the observed changes in heat stress resistance. Instead, assays of the phenotypic response across a broader range of temperatures revealed that the induced plasticity was not fixed across environments, but rather the threshold for the response was shifted to higher temperatures over evolutionary time. These results demonstrate that apparent genetic assimilation can result from shifting thresholds of induction across environments and that analysis of the broader environmental context is critically important for understanding the evolution of phenotypic plasticity. mRNA profiles of ancestral and two experimentally evolved populations of C. remanei at 20°C or 30°C, 6 replicates/temperature for each population
2014-05-04 | E-GEOD-56510 | biostudies-arrayexpress
Project description:How environmentally induced traits become genetically stabilized during evolution remains a central question in biology. The teleost Astyanax mexicanus, comprising surface (SF) and cave (CF) morphotypes, provides a powerful system to link environmentally induced traits with evolved phenotypes. Here, we integrate morphometric, physiological, and transcriptomic analyses to investigate how sustained darkness reshapes phenotypic plasticity across generations. We show that plastic responses in SF are rapidly modified after only two generations of dark rearing (2dSF). Morphological changes in 2dSF are highly heterogeneous: some traits shift toward cavefish values, while others overshoot them, and key traits such as eye size and pigmentation respond in the opposite direction, indicating widespread maladaptive plasticity. In contrast, CF exhibit limited environmental responsiveness, consistent with canalized phenotypes. Traits exhibiting maladaptive plasticity in SF tend to be canalized in CF, suggesting that maladaptive responses are preferentially reduced during evolution. At the molecular level, transcriptional plasticity declines sharply from SF to 2dSF and is nearly absent in CF, suggesting rapid loss of environmental responsiveness. Gene expression analyses further reveal a mixture of maladaptive and adaptive trajectories. Most transcriptional changes in 2dSF deviate from cavefish expression patterns, including those related to visual function, consistent with maladaptive morphological trends. However, a subset of genes involved in lipid metabolism and heme homeostasis shows stepwise shifts from SF through 2dSF to CF, consistent with adaptive accommodation. Notably, anesthesia resistance increases in 2dSF to levels comparable to CF within only two generations, demonstrating rapid accommodation in neural traits. Together, our results show that plastic phenotypes are initially heterogeneous but are rapidly reshaped across generations, with maladaptive components reduced and adaptive components stabilized. This process bridges immediate plasticity and long-term evolutionary change, providing empirical support for phenotypic accommodation as a mechanism facilitating rapid adaptation and highlighting how plasticity can biasing evolutionary trajectories during the colonization of extreme environments.
2026-05-08 | GSE324281 | GEO