Towards evolutionary predictions: Current promises and challenges

Evolutionary Applications, Год журнала: 2022, Номер 16(1), С. 3 - 21

Опубликована: Дек. 9, 2022

Abstract Evolution has traditionally been a historical and descriptive science, predicting future evolutionary processes long considered impossible. However, predictions are increasingly being developed used in medicine, agriculture, biotechnology conservation biology. Evolutionary may be for different purposes, such as to prepare the future, try change course of evolution or determine how well we understand processes. Similarly, exact aspect evolved population that want predict also differ. For example, could which genotype will dominate, fitness extinction probability population. In addition, there many uses not always recognized such. The main goal this review is increase awareness methods data research fields by showing breadth situations made. We describe diverse share common structure described predictive scope, time scale precision. Then, using examples ranging from SARS‐CoV2 influenza CRISPR‐based gene drives sustainable product formation biotechnology, discuss evolution, factors affect predictability can prevent undesirable directions promote beneficial (i.e. control). hope stimulate collaboration between establishing language predictions.

Язык: Английский

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Identifying Targets of Selection in Laboratory Evolution Experiments

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 345 - 355

Опубликована: Фев. 21, 2023

Язык: Английский

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Scaling up and down: movement ecology for microorganisms

Trends in Microbiology, Год журнала: 2022, Номер 31(3), С. 242 - 253

Опубликована: Окт. 22, 2022

Язык: Английский

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Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness

Applied and Environmental Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Март 11, 2025

ABSTRACT Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts in-soil fitness, particularly focusing incubation in liquid culture as an unavoidable phase inoculant production and pre-incubation target a potential method performance. We conducted experimental evolution phosphorus-solubilizing bacterial species, Priestia megaterium , (i) soil only, (ii) media (iii) followed by media, using population metagenomic sequencing track mutations over time. Several typical vitro evolutionary phenomena were observed media-incubated populations, including clonal interference, genetic hitchhiking, mutation parallelism between replicate the sporulation transcription factor spo0A . Liquid populations also developed clear fitness reduction compared ancestral isolate. However, soil-incubated grew slowly, experienced far fewer generations despite longer absolute time, accumulated minimal mutational changes. Correspondingly, did not display improved survival isolate their soils, though there appear be minor reductions unfamiliar soil. This work demonstrates that adaptation and/or native impact new more complex real-world habitats does closely resemble media. IMPORTANCE Innovative solutions are needed address emerging challenges agriculture while reducing its footprint. Management microbiomes could contribute this effort, plant growth-promoting microorganisms provide key ecosystem services support crops. Yet, inoculating beneficial farm yields unreliable results. require greater knowledge ecology these taxa functioning sustainable agroecosystems. In report, demonstrate laboratory lingering another negatively species. go further highlight underlying give rise patterns. These insights leveraged our understanding soil-dwelling adapt different pressures.

Язык: Английский

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Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 1, 2023

Abstract Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in specific environment which population evolving. However, environments are rarely constant or predictable. When an organism well adapted to one finds itself another, pleiotropic effects of made it its former will affect success. To better understand such effects, we evolved both haploid and diploid barcoded budding yeast populations multiple environments, isolated adaptive clones, then determined “non-home” they were not selected. We find pleiotropy common, with most lineages showing non-home environments. Consistent other studies, these unpredictable: some deleterious others. do same genes tend show similar effects. also ploidy influences observed mutational spectra condition-specific fashion. In conditions, haploids diploids selected identical genes, while others accumulate almost completely disjoint sets genes.

Язык: Английский

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Barcoding Populations of Pseudomonas fluorescens SBW25

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 254 - 262

Опубликована: Апрель 25, 2023

In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics lineages within evolving populations and communities. Although barcoded can deliver unprecedented insight into change, microbes presents specific technical challenges. Here, are described for model bacterium Pseudomonas fluorescens SBW25, including design cloning regions, preparation libraries amplicon sequencing, quantification resulting lineages. so doing, we hope aid implementation methodologies a broad range non-model organisms.

Язык: Английский

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Theoretical validation of growth curves for quantifying phage-bacteria interactions

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 29, 2023

Abstract Bacteria-infecting viruses, bacteriophages, are the most abundant biological entities on planet, frequently serving as model systems in basic research and increasingly relevant for medical applications such phage therapy. A common need is to quantify infectivity of a given bacterial host (or resistance phage). However, current methods suffer from low-throughput or low-precision. One method that has potential high-throughput high-precision quantification phage-bacteria interactions growth curves, where density measured over time presence absence phages. Recent work proposed several approaches these curves into metric infectivity. little known about how metrics relate one another underlying traits. To address this gap, we apply ecological modeling populations simulate across wide range trait values. Our findings show many curve provide parallel measures Informative include peak decline portions driven by between traits, correlate with conventional fitness. Moreover, intrapopulation variation can alter dynamics. Finally, test sensitivity inoculum densities, assess techniques compare different hosts. In all, our support use precise microbial sciences. Significance Bacteriophages viruses infect bacteria. Phages have long been laboratory models being explored antimicrobials. Commonly, well infects strain. Unfortunately, either laborious imprecise. could be better it remained unclear data produce single Here, used simulations match conditions. suggests rapid, measurement

Язык: Английский

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Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

eLife, Год журнала: 2023, Номер 12

Опубликована: Окт. 20, 2023

Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in specific environment which population evolving. However, environments are rarely constant or predictable. When an organism well adapted to one finds itself another, pleiotropic effects of made it its former will affect success. To better understand such effects, we evolved both haploid and diploid barcoded budding yeast populations multiple environments, isolated adaptive clones, then determined 'non-home' they were not selected. We find pleiotropy common, with most lineages showing non-home environments. Consistent other studies, these unpredictable: some deleterious others. do same genes tend show similar effects. also ploidy influences observed mutational spectra condition-specific fashion. In conditions, haploids diploids selected identical genes, while others accumulate almost completely disjoint sets genes.

Язык: Английский

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Experimental evolution in a warming world – the omics era

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(8)

Опубликована: Июль 18, 2024

A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions impacts climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) a highly effective tool has been increasingly employed elucidate basis adaptation. The number evolve resequence studies rising, yet there dearth efforts integrate this new wealth knowledge. Here, we review literature showing how these have contributed increase our We identify two major trends: polygenic adaptation general lack consistency in candidate targets selection between studies. These findings indicate adaptive specific environments are rather independent. reveals several gaps existing research. Firstly, paucity done organisms diverse taxa. Secondly, need apply dynamic ecologically relevant environments. Thirdly, genomic changes life history behavioral traits. Addressing issues would allow in-depth relationship genotype phenotype. highlight key methodological aspects can address some limitations omissions identified. include greater standardization methodologies utilization technologies focusing integration phenotypic context

Язык: Английский

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Bayesian inference of relative fitness on high-throughput pooled competition assays

PLoS Computational Biology, Год журнала: 2024, Номер 20(3), С. e1011937 - e1011937

Опубликована: Март 15, 2024

The tracking of lineage frequencies via DNA barcode sequencing enables the quantification microbial fitness. However, experimental noise coming from biotic and abiotic sources complicates computation a reliable inference. We present Bayesian pipeline to infer relative fitness high-throughput assays. Our model accounts for multiple propagates uncertainties throughout all parameters in systematic way. Furthermore, using modern variational inference methods based on automatic differentiation, we are able scale large number unique barcodes. extend this core analyze multi-environment assays, replicate experiments, barcodes linked genotypes. On simulations, our method recovers known within posterior credible intervals. This work provides generalizable framework experiments. accompanying open-source software library adoption principled statistical evolution.

Язык: Английский

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