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1. Characterizing biological responses to climate variability and extremes to improve biodiversity projections

   https://doi.org/10.1371/journal.pclm.0000226  

   Buckley, Lauren B.; Carrington, Emily; Dillon, Michael E.; García-Robledo, Carlos; Roberts, Steven B.; Wegrzyn, Jill L.; Urban, Mark C. (June 2023, PLOS Climate)

   Moura, Mario R. (Ed.)

   Projecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current modeling approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic understanding of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales. 

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2. Characterizing biological responses to climate variability and extremes to improve biodiversity projections

   Buckley, L.; Carrington, E.; Dillon, M.E.; Garcia-Robledo, C; Roberts, S.B; Wegrzyn, J.; Urban, M.C. (June 2023, PLOS climate)

   Projecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current model- ing approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic under- standing of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales. 

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3. The Divergent Responses of Salinity Generalists to Hyposaline Stress Provide Insights Into the Colonisation of Freshwaters by Diatoms

   https://doi.org/10.1111/mec.17556  

   Judy, Kathryn J; Pinseel, Eveline; Downey, Kala M; Lewis, Jeffrey A; Alverson, Andrew J (November 2024, Molecular Ecology)

   Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time‐resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long‐term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage‐specific environmental responses in phytoplankton have shaped marine–freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions. 

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4. Roadmap on biology in time varying environments

   https://doi.org/10.1088/1478-3975/abde8d  

   Murugan, Arvind; Husain, Kabir; Rust, Michael J; Hepler, Chelsea; Bass, Joseph; Pietsch, Julian M; Swain, Peter S; Jena, Siddhartha G; Toettcher, Jared E; Chakraborty, Arup K; et al (May 2021, Physical Biology)

   Abstract Biological organisms experience constantly changing environments, from sudden changes in physiology brought about by feeding, to the regular rising and setting of the Sun, to ecological changes over evolutionary timescales. Living organisms have evolved to thrive in this changing world but the general principles by which organisms shape and are shaped by time varying environments remain elusive. Our understanding is particularly poor in the intermediate regime with no separation of timescales, where the environment changes on the same timescale as the physiological or evolutionary response. Experiments to systematically characterize the response to dynamic environments are challenging since such environments are inherently high dimensional. This roadmap deals with the unique role played by time varying environments in biological phenomena across scales, from physiology to evolution, seeking to emphasize the commonalities and the challenges faced in this emerging area of research. 

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5. Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium

   https://doi.org/10.1093/molbev/msaa256  

   Walworth, Nathan G; Lee, Michael D; Dolzhenko, Egor; Fu, Fei-Xue; Smith, Andrew D; Webb, Eric A; Hutchins, David A (October 2020, Molecular Biology and Evolution)

   null (Ed.)

   Abstract A major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO2, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO2 exposure and were maintained for at least 4.5 years of CO2 selection. After 7 years of CO2 selection, however, m5C methylation levels that initially responded to high-CO2 returned to ancestral, ambient CO2 levels. Concurrently, high-CO2 adapted growth and N2 fixation rates remained significantly higher than those of ambient CO2 adapted cell lines irrespective of CO2 concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO2-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change. 

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