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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Eco‐evolution from deep time to contemporary dynamics: The role of timescales and rate modulators

Ecology Letters, Год журнала: 2023, Номер 26(S1)

Опубликована: Сен. 1, 2023

Eco-evolutionary dynamics, or eco-evolution for short, are often thought to involve rapid demography (ecology) and equally heritable phenotypic changes (evolution) leading novel, emergent system behaviours. We argue that this focus on contemporary dynamics is too narrow: Eco-evolution should be extended, first, beyond pure include all environmental dimensions and, second, slow which unfolds over thousands millions of years. This extension allows us conceptualise biological systems as occupying a two-dimensional time space along axes capture the speed ecology evolution. Using Hutchinson's analogy: Time 'theatre' in evolution two interacting 'players'. therefore dynamic: identify modulators ecological evolutionary rates, like temperature sensitivity mutation, can change evolution, hence impact eco-evolution. Environmental may synchronise via these rate modulators, increasing occurrence represents substantial challenges prediction, especially context global change. Our perspective attempts integrate across disciplines, from gene-regulatory networks geomorphology timescales, today deep time.

Язык: Английский

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Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs

eLife, Год журнала: 2024, Номер 13

Опубликована: Сен. 10, 2024

There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common evolution and occur when, for example, resistance one drug results sensitivity another. Major questions remain about the extent which reliable, specifically, whether mutants provide a given all suffer similar tradeoffs. This question difficult because drug-resistant observed clinic, even those evolved controlled laboratory settings, often biased towards large fitness benefits. Thus, mutations (and mechanisms) may be more diverse than current data suggests. Here, we perform experiments utilizing lineage-tracking capture fuller spectrum of give yeast cells advantage fluconazole, antifungal drug. We then quantify each 774 across 12 environments, finding these group into classes with characteristically different Their unique imply affects through underlying mechanisms. Some groupings find surprising. For some resist single drugs do not their combination, while others do. And same gene have others. These findings, on hand, demonstrate difficulty relying consistent or intuitive when treatments. On other by demonstrating hundreds adaptive can reduced few groups characteristic tradeoffs, our findings yet empower strategies More generally speaking, grouping likely affect mechanisms, work guides efforts map phenotypic effects mutation.

Язык: Английский

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Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails

Science Advances, Год журнала: 2024, Номер 10(41)

Опубликована: Окт. 11, 2024

Predicting the outcomes of adaptation is a major goal evolutionary biology. When temporal changes in environment mirror spatial gradients, it opens up potential for predicting course adaptive evolution over time based on patterns genetic and phenotypic variation. We assessed this approach 30-year transplant experiment intertidal snail Littorina saxatilis . In 1992, snails were transplanted from predation-dominated to one dominated by wave action. On basis patterns, we predicted transitions shell size morphology, allele frequencies at positions throughout genome, chromosomal rearrangement frequencies. Observed closely agreed with predictions transformation was both dramatic rapid. Hence, can be knowledge variation among populations.

Язык: Английский

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Revisiting the Role of Genetic Variation in Adaptation

The American Naturalist, Год журнала: 2023, Номер 202(4), С. 486 - 502

Опубликована: Май 18, 2023

AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood organization code, provenance variation, and how such influenced phenotypes on which natural selection acts. Half century after discovery structure DNA unraveling rich understanding these problems means to both delve deeper widen our perspective across organisms populations. The 2022 Vice Presidential Symposium American Society Naturalists highlighted examples recent insights into in adaptive processes, are compiled this special section. work was conducted different parts world, included theoretical empirical studies with diverse organisms, addressed distinct aspects influences adaptation. In introductory article section, discuss some important generation maintenance its impacts phenotype fitness, fate populations, driving By placing section articles broader context developments, hope that overview will also serve as useful introduction field.

Язык: Английский

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Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications

Environmental Science and Pollution Research, Год журнала: 2024, Номер 31(15), С. 22199 - 22242

Опубликована: Фев. 27, 2024

Язык: Английский

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Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs

eLife, Год журнала: 2024, Номер 13

Опубликована: Март 18, 2024

There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common evolution and occur when, for example, resistance one drug results sensitivity another. Major questions remain about the extent which reliable, specifically, whether mutants provide a given all suffer similar tradeoffs. This question difficult because drug-resistant observed clinic, even those evolved controlled laboratory settings, often biased towards large fitness benefits. Thus, mutations (and mechanisms) may be more diverse than current data suggests. Here, we perform experiments utilizing lineage-tracking capture fuller spectrum of give yeast cells advantage fluconazole, antifungal drug. We then quantify each 774 across 12 environments, finding these group into classes with characteristically different Their unique imply affects through underlying mechanisms. Some groupings find surprising. For some resist single drugs do not their combination, while others do. And same gene have others. These findings, on hand, demonstrate difficulty relying consistent or intuitive when treatments. On other by demonstrating hundreds adaptive can reduced few groups characteristic tradeoffs, our findings yet empower strategies More generally speaking, grouping likely affect mechanisms, work guides efforts map phenotypic effects mutation.

Язык: Английский

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Substrate geometry affects population dynamics in a bacterial biofilm

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(17)

Опубликована: Апрель 15, 2024

Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by noneven surfaces. However, the impact surface irregularities on population dynamics biofilms remains elusive, most experiments are conducted flat Here, we show that shape which biofilm grows influences genetic drift and selection within biofilm. We culture E scherichia coli in microwells with corrugated bottom observe emergence clonal sectors whose size corresponds to corrugations, despite no physical barrier separating different areas The remarkably stable do not invade each other; attribute this stability characteristics velocity field biofilm, hinders mixing expansion. A microscopically detailed computer model fully reproduces these findings highlights role mechanical interactions adhesion friction microbial evolution. also predicts expansion be limited even for clones significant growth advantage—a finding confirm experimentally using mixture antibiotic-sensitive antibiotic-resistant mutants presence sublethal concentrations antibiotic rifampicin. strong suppression contrasts sharply behavior seen bacterial colonies grown agar. Our results can affected patterning demonstrate how better understanding physics used control

Язык: Английский

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Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

ISME Communications, Год журнала: 2023, Номер 3(1)

Опубликована: Авг. 28, 2023

Microbial evolution is driven by rapid changes in gene content mediated horizontal transfer (HGT). While mobile genetic elements (MGEs) are important drivers of flux, the nanobiome-the zoo Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts complex communities. A bioinformatic pipeline (xenoseq) was developed cross-compare metagenomic samples from consortia evolving parallel, aimed at identifying MGE dissemination, which applied compost communities underwent periodic mixing MGEs. We show xenoseq can distinguish movement demographic community composition otherwise confounds identification, and furthermore demonstrate discovery various unexpected entities. Of particular interest a nanobacterium candidate phylum radiation (CPR) closely related species identified groundwater ecosystems (Candidatus Saccharibacterium), appears have parasitic lifestyle. also highlight another prolific element, 313 kb plasmid hosted Cellvibrio lineage. The host predicted be capable nitrogen fixation, acquisition coincides with increased ammonia production. Taken together, data new experimental strategies combined analyses stand provide insight into nanobiome as driver evolution.

Язык: Английский

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Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution

Journal of Heredity, Год журнала: 2024, Номер unknown

Опубликована: Июль 30, 2024

Abstract A major goal of modern biology is connecting phenotype with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised surface ecotype and cave-derived ecotype, well suited as model to study the mechanisms adaptation extreme environments. Here, we map 206 previously published quantitative trait loci (QTL) for traits in A. mexicanus newest version genome assembly, AstMex3. These analyses revealed that QTL clusters more than expected by chance, this clustering not explained distribution genes genome. To investigate whether certain characteristics facilitate phenotypic evolution, tested genomic associated increased opportunities mutation, such highly mutagenic CpG sites, are reliable predictors sites evolution but did find any significant trends. Finally, combined collected expression selection data identify 36 candidate may underlie repeated cave phenotypes, including rgrb, which predicted be involved phototransduction. We found gene has disrupted exons all non-hybrid populations intact reading frames fish. Overall, our results suggest specific regions play roles driving environment demonstrate how compiled dataset can understanding basis cavefish.

Язык: Английский

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