Quantifying the local adaptive landscape of a nascent bacterial community

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 16, 2023

The fitness effects of all possible mutations available to an organism largely shape the dynamics evolutionary adaptation. Yet, whether and how this adaptive landscape changes over times, especially upon ecological diversification in community composition, remains poorly understood. We sought fill gap by analyzing a stable two closely related ecotypes ("L" "S") shortly after they emerged within E. coli Long-Term Evolution Experiment (LTEE). engineered genome-wide barcoded transposon libraries measure invasion gene knockouts coexisting strains as well their ancestor, for many different, ecologically relevant conditions. find consistent statistical patterns effect variation across both genetic background despite idiosyncratic behavior individual knockouts. Additionally, are correlated with outcomes number conditions, possibly revealing shifting Together, our results reveal epistatic combine nascent community.

Язык: Английский

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Epistasis and Adaptation on Fitness Landscapes

Annual Review of Ecology Evolution and Systematics, Год журнала: 2022, Номер 53(1), С. 457 - 479

Опубликована: Сен. 14, 2022

Epistasis occurs when the effect of a mutation depends on its carrier's genetic background. Despite increasing evidence that epistasis for fitness is common, role during evolution contentious. Fitness landscapes, which are mappings genotype or phenotype to fitness, capture full extent and complexity epistasis. landscape theory has shown how affects course outcome evolution. Moreover, by measuring competitive sets tens thousands connected genotypes, empirical landscapes have frequent measure, choice mutations landscape, environment in it was measured. In this article, I review experiments their implications adaptation. discuss theoretical expectations light highlight open challenges future directions toward integrating data incorporating ecological factors.

Язык: Английский

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Epistasis and evolution: recent advances and an outlook for prediction

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Май 24, 2023

Abstract As organisms evolve, the effects of mutations change as a result epistatic interactions with other accumulated along line descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances measuring, modeling, and predicting epistasis evolutionary trajectories, both microbial cells single proteins. We focus on simple patterns global emerge this data, which be predicted by small number variables. The emergence these offers promise for efforts model predict

Язык: Английский

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Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

eLife, Год журнала: 2020, Номер 9

Опубликована: Дек. 2, 2020

Building a genotype-phenotype-fitness map of adaptation is central goal in evolutionary biology. It difficult even when adaptive mutations are known because it hard to enumerate which phenotypes make these adaptive. We address this problem by first quantifying how the fitness hundreds yeast mutants responds subtle environmental shifts. then model number collectively influence decomposing patterns variation. find that small inferred can predict near their original glucose-limited evolution condition. Importantly, matter little at or condition strongly distant environments. This suggests locally modular - affecting environment where they evolved yet globally pleiotropic additional may reduce improve new

Язык: Английский

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Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 293 - 310

Опубликована: Май 27, 2023

The phrase "survival of the fittest" has become an iconic descriptor how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed utilizing DNA barcodes, all are limited their precision differentiate strains with small fitness differences. In this study, we rule out some major sources imprecision, but still find that measurements vary substantially from replicate replicate. Our data suggest very subtle and difficult avoid environmental differences between replicates create systematic variation across measurements. We conclude by discussing should be interpreted given extreme environment dependence. This work was inspired scientific community who followed us gave tips as live tweeted high-replicate measurement experiment at #1BigBatch.

Язык: Английский

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An ultra high‐throughput, massively multiplexable, single‐cell RNA‐seq platform in yeasts

Yeast, Год журнала: 2024, Номер 41(4), С. 242 - 255

Опубликована: Янв. 28, 2024

Abstract Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies yeast transcriptomes have been limited by the processing capabilities traditional RNA sequencing techniques. Here we optimize a powerful, high‐throughput single‐cell (scRNAseq) platform, SPLiT‐seq (Split Pool Ligation‐based Transcriptome sequencing), for yeasts apply it 43,388 cells multiple species ploidies. This platform utilizes combinatorial barcoding strategy enable massively parallel hundreds genotypes growth conditions at once. method be applied most strains fraction cost scRNAseq approaches. Thus, our technology permits leverage “the awesome power yeast” allowing us survey transcriptome environments in short period time with no specialized equipment. The key this is sequential barcodes probabilistically appended cDNA copies while molecules remain trapped inside each cell. cell labeled unique combination barcodes. Since uses membrane as container reaction, many processed together without need physically isolate them from one another separate wells droplets. Further, first barcode sequence chosen intentionally identify samples different genetic backgrounds, enabling multiplexing perturbations single experiment. In addition greater capabilities, also facilitates deeper investigation biological heterogeneity, given its nature. For example, data presented here, detect transcriptionally distinct states related cycle, ploidy, metabolic strategies, so forth, all within clonal populations grown same environment. Hence, has two obvious impactful applications research: general study transcriptional phenotypes across second investigating cell‐to‐cell heterogeneity entire transcriptome.

Язык: Английский

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Decreased thermal niche breadth as a trade-off of antibiotic resistance

The ISME Journal, Год журнала: 2022, Номер 16(7), С. 1843 - 1852

Опубликована: Апрель 14, 2022

Abstract Evolutionary theory predicts that adaptations, including antibiotic resistance, should come with associated fitness costs; yet, many resistance mutations seemingly contradict this prediction by inducing no growth rate deficit. However, most assays comparing sensitive and resistant strains have been performed under a narrow range of environmental conditions, which do not reflect the variety contexts pathogenic bacterium might encounter when causing infection. We hypothesized reduced niche breadth, defined as diminished across diversity environments, can be cost resistance. Specifically, we test whether chloramphenicol-resistant Escherichia coli incur disproportionate deficits in novel thermal conditions. Here show bacteria greater costs at temperatures than their antibiotic-sensitive ancestors. In several cases, observed historic temperature but saw warmer colder temperatures. These results were consistent various genetic mechanisms Thus, propose decreased breadth is an under-documented Furthermore, these demonstrate shifts rapidly environment changes; context-dependent select for rapid gain loss evolutionary strategy.

Язык: Английский

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Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 21, 2024

Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult characterize in dominant gut species complex vivo environment. Here we show that fine-scale genome-wide transposon libraries enable quantitative inferences these evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains gnotobiotic mice, observed positive selection on thousands cryptic variants - most which were unrelated original gene knockouts. The spectrum fitness benefits varied between species, and displayed diverse tradeoffs over time different dietary conditions, enabling underlying function. These results suggest within-host adaptations arise from an intense competition numerous contending variants, strongly influence emergent tradeoffs.

Язык: Английский

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Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales

Annual Review of Biophysics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 19, 2025

All biological systems are subject to perturbations: due thermal fluctuations, external environments, or mutations. Yet, while composed of thousands interacting components, recent high-throughput experiments show that their response perturbations is surprisingly low-dimensional: confined only a few stereotyped changes out the many possible. Here, we explore unifying dynamical framework - soft modes explain and analyze low-dimensionality in biology, from molecules eco-systems. We argue this one makes non-trivial predictions generalize classic ideas developmental biology disparate systems, namely: phenocopying, dual buffering, global epistasis. While some these have been borne experiments, discuss how allow for far-reaching which data protein biophysics microbial ecology.

Язык: Английский

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Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

eLife, Год журнала: 2021, Номер 10

Опубликована: Окт. 1, 2021

Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have range unrealized pleiotropic effects in other environments. These consequences influence emergence specialists or generalists, and are critical for evolution temporally spatially fluctuating While many experiments examined at snapshot time, very few observed dynamics these emerge evolve. Here, we propagated hundreds diploid haploid laboratory budding yeast populations each three environments, then assayed their fitness multiple environments over 1000 generations evolution. We find that replicate evolved same condition share common patterns across within first several hundred However, also dynamic environment-specific variability trends: tends increase with extent depending on environment. results suggest shifting overlapping contributions chance contingency adaptation, could evolutionary trajectories complex fluctuate space time.

Язык: Английский

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