Functional biology in its natural context: A search for emergent simplicity

Bergelson, Joy; Kreitman, Martin; Petrov, Dmitri A.; Sánchez, Álvaro; Tikhonov, Mikhail

doi:10.7554/elife.67646

Cited by 45 publications

(54 citation statements)

References 91 publications

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“…Ecological interactions may not open up or close down any major adaptive paths; nevertheless, by altering the benefits of mutations and their rank order, interactions may canalize evolutionary trajectories at the community level. Thus, our results support the view ( 58 ) that despite the daunting complexity at the genetic level, evolution at the community level may be relatively simple and repeatable.…”

supporting

confidence: 89%

Mutualism-enhancing mutations dominate early adaptation in a microbial community

Venkataram

Kuo

Hom

et al. 2021

Preprint

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Evolutionary dynamics in ecological communities are often repeatable, but how species interactions affect the distribution of evolutionary outcomes at different levels of biological organization is unclear. Here, we use barcode lineage tracking to experimentally address this gap in a facultatively mutualistic community formed by the alga Chlamydomonas reinhardtii and the yeast Saccharomyces cerevisiae. We find that interactions with the alga alter the magnitude but not the sign of the fitness effects of adaptive mutations in yeast, changing the distribution of mutants contending for fixation. In the presence of alga, most contending mutants reinforce the mutualism and make evolution more repeatable at the community level. Thus, ecological interactions not only alter the trajectory of evolution but also dictate its repeatability at multiple levels of biological organization.One-sentence summaryThe mutualistic interaction between two species drives evolution to increase both species’ yields.

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supporting

confidence: 89%

Mutualism-enhancing mutations dominate early adaptation in a microbial community

Venkataram

Kuo

Hom

et al. 2021

Preprint

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“…A common thread that emerged from our investigations is that "standard laboratory conditions" turned out to be ill-suited for teasing out the widespread effects of H3K4 monomethylation. These results highlight that incorporating realistic ecological and environmental contexts into our experimental design is essential for understanding the regulatory genome and its contribution to evolution and development 44 . In the future, insights from phenomics and the inclusion of ecologically relevant conditions will allow us to explore how modulating elements embedded in densely connected biological networks could lead to the emergence of novel traits and influence the evolutionary dynamics of entire populations [45][46][47] .…”

Section: Discussionmentioning

confidence: 91%

Developmental phenomics suggests that H3K4 monomethylation catalyzed by Trr functions as a phenotypic capacitor

Gándara¹,

Tsai²,

Ekelöf

et al. 2022

Preprint

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How epigenetic modulators of gene regulation affect the development and evolution of animals has been difficult to ascertain. Despite the widespread presence of histone 3 lysine 4 monomethylation (H3K4me1) on enhancers, hypomethylation appears to have minor effects on animal development and viability. In this study, we performed quantitative, unbiased and multi-dimensional explorations of key phenotypes on Drosophila melanogaster with genetically induced hypomethylation. Hypomethylation reduced transcription factor enrichment in nuclear microenvironments, leading to reduced gene expression, and phenotypes outside of standard laboratory conditions. Our developmental phenomics survey further showed that H3K4me1 hypomethylation led to context-dependent changes in morphology, metabolism, and behavior. Therefore, H3K4me1 may contribute to phenotypic evolution as a phenotypic capacitor by buffering the effects of chance, genotypes and environmental conditions on transcriptional enhancers.

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“…In conclusion, there are many reasons to believe that analyzing a species in artificial laboratory environments might be of limited utility for understanding its function or interactions in the natural environment [56]. Usually, however, the concern is that the laboratory conditions are too simple, and in reality, many more details may matter.…”

Section: Discussionmentioning

confidence: 99%

Defining coarse-grainability in a model of structured microbial ecosystems

Moran

Tikhonov

2021

Preprint

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Any description of an ecosystem necessarily ignores some details of the underlying diversity. What predictions can be robust to such omissions? Here, building on the theoretical framework of resource competition, we introduce an eco-evolutionary model that allows organisms to be described at an arbitrary, potentially infinite, level of detail, enabling us to formally study the hierarchy of possible coarse-grained descriptions. Within this model, we demonstrate that a coarse-graining scheme may enable ecological predictions despite grouping together functionally diverse strains. However, this requires two conditions: the strains we study must remain in a diverse ecological context, and this diversity must be derived from a sufficiently similar environment. Our model suggests that studying individual strains of a species away from their natural eco-evolutionary context may eliminate the very reasons that make a species-level characterization an adequate coarse-graining of the natural diversity.

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Functional biology in its natural context: A search for emergent simplicity

Cited by 45 publications

References 91 publications

Mutualism-enhancing mutations dominate early adaptation in a microbial community

Mutualism-enhancing mutations dominate early adaptation in a microbial community

Developmental phenomics suggests that H3K4 monomethylation catalyzed by Trr functions as a phenotypic capacitor

Defining coarse-grainability in a model of structured microbial ecosystems

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