1
|
Abreu CI, Mathur S, Petrov DA. Environmental memory alters the fitness effects of adaptive mutations in fluctuating environments. Nat Ecol Evol 2024:10.1038/s41559-024-02475-9. [PMID: 39020024 DOI: 10.1038/s41559-024-02475-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Evolution in a static laboratory environment often proceeds via large-effect beneficial mutations that may become maladaptive in other environments. Conversely, natural settings require populations to endure environmental fluctuations. A sensible assumption is that the fitness of a lineage in a fluctuating environment is the time average of its fitness over the sequence of static conditions it encounters. However, transitions between conditions may pose entirely new challenges, which could cause deviations from this time average. To test this, we tracked hundreds of thousands of barcoded yeast lineages evolving in static and fluctuating conditions and subsequently isolated 900 mutants for pooled fitness assays in 15 environments. Here we find that fitness in fluctuating environments indeed often deviates from the time average, leading to fitness non-additivity. Moreover, closer examination reveals that fitness in one component of a fluctuating environment is often strongly influenced by the previous component. We show that this environmental memory is especially common for mutants with high variance in fitness across tested environments. We use a simple mathematical model and whole-genome sequencing to propose mechanisms underlying this effect, including lag time evolution and sensing mutations. Our results show that environmental fluctuations impact fitness and suggest that variance in static environments can explain these impacts.
Collapse
Affiliation(s)
- Clare I Abreu
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Shaili Mathur
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Schmidlin, Apodaca, Newell, Sastokas, Kinsler, Geiler-Samerotte. Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.17.562616. [PMID: 37905147 PMCID: PMC10614906 DOI: 10.1101/2023.10.17.562616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common in evolution and occur when, for example, resistance to one drug results in sensitivity to another. Major questions remain about the extent to which tradeoffs are reliable, specifically, whether the mutants that provide resistance to a given drug all suffer similar tradeoffs. This question is difficult because the drug-resistant mutants observed in the clinic, and even those evolved in controlled laboratory settings, are often biased towards those that provide large fitness benefits. Thus, the mutations (and mechanisms) that provide drug resistance may be more diverse than current data suggests. Here, we perform evolution experiments utilizing lineage-tracking to capture a fuller spectrum of mutations that give yeast cells a fitness advantage in fluconazole, a common antifungal drug. We then quantify fitness tradeoffs for each of 774 evolved mutants across 12 environments, finding these mutants group into 6 classes with characteristically different tradeoffs. Their unique tradeoffs may imply that each group of mutants affects fitness through different underlying mechanisms. Some of the groupings we find are surprising. For example, we find some mutants that resist single drugs do not resist their combination, while others do. And some mutants to the same gene have different tradeoffs than others. These findings, on one hand, demonstrate the difficulty in relying on consistent or intuitive tradeoffs when designing multidrug treatments. On the other hand, by demonstrating that hundreds of adaptive mutations can be reduced to a few groups with characteristic tradeoffs, our findings may yet empower multidrug strategies that leverage tradeoffs to combat resistance. More generally speaking, by grouping mutants that likely affect fitness through similar underlying mechanisms, our work guides efforts to map the phenotypic effects of mutation.
Collapse
Affiliation(s)
- Schmidlin
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe AZ
| | - Apodaca
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe AZ
| | - Newell
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe AZ
| | - Sastokas
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe AZ
| | - Kinsler
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Geiler-Samerotte
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe AZ
| |
Collapse
|
3
|
Hulse SV, Bruns EL. The Emergence of Non-Linear Evolutionary Trade-offs and the Maintenance of Genetic Polymorphisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.595890. [PMID: 38853830 PMCID: PMC11160725 DOI: 10.1101/2024.05.29.595890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Evolutionary models of quantitative traits often assume trade-offs between beneficial and detrimental traits, requiring modelers to specify a function linking costs to benefits. The choice of trade-off function is often consequential; functions that assume diminishing returns (accelerating costs) typically lead to single equilibrium genotypes, while decelerating costs often lead to evolutionary branching. Despite their importance, we still lack a strong theoretical foundation to base the choice of trade-off function. To address this gap, we explore how trade-off functions can emerge from the genetic architecture of a quantitative trait. We developed a multi-locus model of disease resistance, assuming each locus had random antagonistic pleiotropic effects on resistance and fecundity. We used this model to generate genotype landscapes and explored how additive versus epistatic genetic architectures influenced the shape of the trade-off function. Regardless of epistasis, our model consistently led to accelerating costs. We then used our genotype landscapes to build an evolutionary model of disease resistance. Unlike other models with accelerating costs, our approach often led to genetic polymorphisms at equilibrium. Our results suggest that accelerating costs are a strong null model for evolutionary trade-offs and that the eco-evolutionary conditions required for polymorphism may be more nuanced than previously believed.
Collapse
|
4
|
Yu G, Wong BH, Painting CJ, Li H, Yu L, Zhang Z, Zhang S, Li D. Males armed with big weapons win fights at limited cost in ant-mimicking jumping spiders. Curr Zool 2024; 70:98-108. [PMID: 38476142 PMCID: PMC10926263 DOI: 10.1093/cz/zoac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/18/2022] [Indexed: 03/14/2024] Open
Abstract
A core assumption of sexual selection theory is that sexually selected weapons, specialized morphological structures used directly in male contests, can improve an individual's reproductive success but only if the bearer can overcome associated costs, the negative effects on the bearer's fitness components. However, recent studies have shown that producing and wielding exaggerated weapons may not necessarily be costly. Rather, some traits can be selected for supporting, or compensating for, the expense of producing and wielding such exaggerated weapons. In the ant-mimicking jumping spider Myrmarachne gisti, exaggerated chelicerae are borne only by adult males and not females, showing sexual dimorphism and steep positive allometry with body size. Here, we determine the potential benefits of bearing exaggerated chelicerae during male contests and explore the potential for costs in terms of prey-capture efficiency and compensation between chelicera size and neighboring trait size. While males with longer chelicerae won most of their male-male contests, we found no significant differences in prey-capture efficiency between males and females regardless of whether prey was winged or flightless. Males' elongated chelicerae thus do not impede their efficiency at capturing prey. Furthermore, we found that the sizes of all neighboring traits are positively correlated with chelicera size, suggesting that these traits may be under correlational selection. Taken together, our findings suggest that M. gisti males armed with the exaggerated chelicerae that function as weapons win more fights at limited cost for performance in prey capture and compensate for neighboring structures.
Collapse
Affiliation(s)
- Guocheng Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Boon Hui Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Christina J Painting
- Te Aka Mātuatua School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Hongze Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Long Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zengtao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shichang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering and Centre for Behavioral Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Daiqin Li
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| |
Collapse
|
5
|
Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
Collapse
Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
6
|
Chen V, Johnson MS, Hérissant L, Humphrey PT, Yuan DC, Li Y, Agarwala A, Hoelscher SB, Petrov DA, Desai MM, Sherlock G. Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. eLife 2023; 12:e92899. [PMID: 37861305 PMCID: PMC10629826 DOI: 10.7554/elife.92899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023] Open
Abstract
Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well adapted to one environment finds itself in another, pleiotropic effects of mutations that made it well adapted to its former environment will affect its success. To better understand such pleiotropic effects, we evolved both haploid and diploid barcoded budding yeast populations in multiple environments, isolated adaptive clones, and then determined the fitness effects of adaptive mutations in 'non-home' environments in which they were not selected. We find that pleiotropy is common, with most adaptive evolved lineages showing fitness effects in non-home environments. Consistent with other studies, we find that these pleiotropic effects are unpredictable: they are beneficial in some environments and deleterious in others. However, we do find that lineages with adaptive mutations in the same genes tend to show similar pleiotropic effects. We also find that ploidy influences the observed adaptive mutational spectra in a condition-specific fashion. In some conditions, haploids and diploids are selected with adaptive mutations in identical genes, while in others they accumulate mutations in almost completely disjoint sets of genes.
Collapse
Affiliation(s)
- Vivian Chen
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityBostonUnited States
| | - Lucas Hérissant
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Parris T Humphrey
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - David C Yuan
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Yuping Li
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Atish Agarwala
- Department of Physics, Stanford UniversityStanfordUnited States
| | | | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityBostonUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
| | - Gavin Sherlock
- Department of Genetics, Stanford UniversityStanfordUnited States
| |
Collapse
|
7
|
Sunassee ED, Jardim-Perassi BV, Madonna MC, Ordway B, Ramanujam N. Metabolic Imaging as a Tool to Characterize Chemoresistance and Guide Therapy in Triple-Negative Breast Cancer (TNBC). Mol Cancer Res 2023; 21:995-1009. [PMID: 37343066 PMCID: PMC10592445 DOI: 10.1158/1541-7786.mcr-22-1004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
After an initial response to chemotherapy, tumor relapse is frequent. This event is reflective of both the spatiotemporal heterogeneities of the tumor microenvironment as well as the evolutionary propensity of cancer cell populations to adapt to variable conditions. Because the cause of this adaptation could be genetic or epigenetic, studying phenotypic properties such as tumor metabolism is useful as it reflects molecular, cellular, and tissue-level dynamics. In triple-negative breast cancer (TNBC), the characteristic metabolic phenotype is a highly fermentative state. However, during treatment, the spatial and temporal dynamics of the metabolic landscape are highly unstable, with surviving populations taking on a variety of metabolic states. Thus, longitudinally imaging tumor metabolism provides a promising approach to inform therapeutic strategies, and to monitor treatment responses to understand and mitigate recurrence. Here we summarize some examples of the metabolic plasticity reported in TNBC following chemotherapy and review the current metabolic imaging techniques available in monitoring chemotherapy responses clinically and preclinically. The ensemble of imaging technologies we describe has distinct attributes that make them uniquely suited for a particular length scale, biological model, and/or features that can be captured. We focus on TNBC to highlight the potential of each of these technological advances in understanding evolution-based therapeutic resistance.
Collapse
Affiliation(s)
- Enakshi D. Sunassee
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | | | - Megan C. Madonna
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Bryce Ordway
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL 33612, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nirmala Ramanujam
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27708, USA
| |
Collapse
|
8
|
Li F, Tarkington J, Sherlock G. Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. J Mol Evol 2023; 91:334-344. [PMID: 36877292 PMCID: PMC10276102 DOI: 10.1007/s00239-023-10098-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of different cellular components affects a cell's ability to reproduce. Here, we describe an improved approach, implemented in Python, for estimating fitness in high throughput via pooled competition assays.
Collapse
Affiliation(s)
- Fangfei Li
- Department of Genetics, Stanford University, Stanford, USA
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, USA.
| |
Collapse
|
9
|
Kinsler G, Schmidlin K, Newell D, Eder R, Apodaca S, Lam G, Petrov D, Geiler-Samerotte K. Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. J Mol Evol 2023; 91:293-310. [PMID: 37237236 PMCID: PMC10276131 DOI: 10.1007/s00239-023-10114-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phrase "survival of the fittest" has become an iconic descriptor of 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 methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
Collapse
Affiliation(s)
| | - Kara Schmidlin
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Daphne Newell
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Rachel Eder
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Sam Apodaca
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | | | | | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA.
- School of Life Sciences, Arizona State University, Tempe, USA.
| |
Collapse
|
10
|
Ascensao JA, Wetmore KM, Good BH, Arkin AP, Hallatschek O. Quantifying the local adaptive landscape of a nascent bacterial community. Nat Commun 2023; 14:248. [PMID: 36646697 PMCID: PMC9842643 DOI: 10.1038/s41467-022-35677-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/16/2022] [Indexed: 01/17/2023] Open
Abstract
The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes ("L" and "S") shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.
Collapse
Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103, Leipzig, Germany.
| |
Collapse
|
11
|
Mononen T, Kuosmanen T, Cairns J, Mustonen V. Understanding cellular growth strategies via optimal control. J R Soc Interface 2023; 20:20220744. [PMID: 36596459 PMCID: PMC9810423 DOI: 10.1098/rsif.2022.0744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Evolutionary prediction and control are increasingly interesting research topics that are expanding to new areas of application. Unravelling and anticipating successful adaptations to different selection pressures becomes crucial when steering rapidly evolving cancer or microbial populations towards a chosen target. Here we introduce and apply a rich theoretical framework of optimal control to understand adaptive use of traits, which in turn allows eco-evolutionarily informed population control. Using adaptive metabolism and microbial experimental evolution as a case study, we show how demographic stochasticity alone can lead to lag time evolution, which appears as an emergent property in our model. We further show that the cycle length used in serial transfer experiments has practical importance as it may cause unintentional selection for specific growth strategies and lag times. Finally, we show how frequency-dependent selection can be incorporated to the state-dependent optimal control framework allowing the modelling of complex eco-evolutionary dynamics. Our study demonstrates the utility of optimal control theory in elucidating organismal adaptations and the intrinsic decision making of cellular communities with high adaptive potential.
Collapse
Affiliation(s)
- Tommi Mononen
- Department of Computer Science, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
| | - Teemu Kuosmanen
- Department of Computer Science, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
| | - Johannes Cairns
- Department of Computer Science, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
| | - Ville Mustonen
- Department of Computer Science, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland,Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
12
|
Pfenninger M, Foucault Q. Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes. Integr Comp Biol 2022; 62:1812-1826. [PMID: 35762661 DOI: 10.1093/icb/icac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/05/2023] Open
Abstract
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.
Collapse
Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Quentin Foucault
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany
| |
Collapse
|
13
|
Schultz D, Stevanovic M, Tsimring LS. Optimal transcriptional regulation of dynamic bacterial responses to sudden drug exposures. Biophys J 2022; 121:4137-4152. [PMID: 36168291 PMCID: PMC9675034 DOI: 10.1016/j.bpj.2022.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Cellular responses to the presence of toxic compounds in their environment require prompt expression of the correct levels of the appropriate enzymes, which are typically regulated by transcription factors that control gene expression for the duration of the response. The characteristics of each response dictate the choice of regulatory parameters such as the affinity of the transcription factor to its binding sites and the strength of the promoters it regulates. Although much is known about the dynamics of cellular responses, we still lack a framework to understand how different regulatory strategies evolved in natural systems relate to the selective pressures acting in each particular case. Here, we analyze a dynamical model of a typical antibiotic response in bacteria, where a transcriptionally repressed enzyme is induced by a sudden exposure to the drug that it processes. We identify strategies of gene regulation that optimize this response for different types of selective pressures, which we define as a set of costs associated with the drug, enzyme, and repressor concentrations during the response. We find that regulation happens in a limited region of the regulatory parameter space. While responses to more costly (toxic) drugs favor the usage of strongly self-regulated repressors, responses where expression of enzyme is more costly favor the usage of constitutively expressed repressors. Only a very narrow range of selective pressures favor weakly self-regulated repressors. We use this framework to determine which costs and benefits are most critical for the evolution of a variety of natural cellular responses that satisfy the approximations in our model and to analyze how regulation is optimized in new environments with different demands.
Collapse
Affiliation(s)
- Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San Diego, La Jolla, California
| |
Collapse
|
14
|
Miller JH, Fasanello VJ, Liu P, Longan ER, Botero CA, Fay JC. Using colony size to measure fitness in Saccharomyces cerevisiae. PLoS One 2022; 17:e0271709. [PMID: 36227888 PMCID: PMC9560512 DOI: 10.1371/journal.pone.0271709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/15/2022] [Indexed: 01/05/2023] Open
Abstract
Competitive fitness assays in liquid culture have been a mainstay for characterizing experimental evolution of microbial populations. Growth of microbial strains has also been extensively characterized by colony size and could serve as a useful alternative if translated to per generation measurements of relative fitness. To examine fitness based on colony size, we established a relationship between cell number and colony size for strains of Saccharomyces cerevisiae robotically pinned onto solid agar plates in a high-density format. This was used to measure growth rates and estimate relative fitness differences between evolved strains and their ancestors. After controlling for edge effects through both normalization and agar-trimming, we found that colony size is a sensitive measure of fitness, capable of detecting 1% differences. While fitnesses determined from liquid and solid mediums were not equivalent, our results demonstrate that colony size provides a sensitive means of measuring fitness that is particularly well suited to measurements across many environments.
Collapse
Affiliation(s)
- James H. Miller
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Vincent J. Fasanello
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Ping Liu
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Emery R. Longan
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Carlos A. Botero
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Justin C. Fay
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
15
|
Brettner L, Ho WC, Schmidlin K, Apodaca S, Eder R, Geiler-Samerotte K. Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes. Curr Opin Genet Dev 2022; 75:101951. [PMID: 35797741 DOI: 10.1016/j.gde.2022.101951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
All organisms are defined by the makeup of their DNA. Over billions of years, the structure and information contained in that DNA, often referred to as genetic architecture, have been honed by a multitude of evolutionary processes. Mutations that cause genetic elements to change in a way that results in beneficial phenotypic change are more likely to survive and propagate through the population in a process known as adaptation. Recent work reveals that the genetic targets of adaptation are varied and can change with genetic background. Further, seemingly similar adaptive mutations, even within the same gene, can have diverse and unpredictable effects on phenotype. These challenges represent major obstacles in predicting adaptation and evolution. In this review, we cover these concepts in detail and identify three emerging synergistic solutions: higher-throughput evolution experiments combined with updated genotype-phenotype mapping strategies and physiological models. Our review largely focuses on recent literature in yeast, and the field seems to be on the cusp of a new era with regard to studying the predictability of evolution.
Collapse
|
16
|
Cesar S, Willis L, Huang KC. Bacterial respiration during stationary phase induces intracellular damage that leads to delayed regrowth. iScience 2022; 25:103765. [PMID: 35243217 PMCID: PMC8858994 DOI: 10.1016/j.isci.2022.103765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Corresponding author
| |
Collapse
|
17
|
Lutz S, Van Dyke K, Feraru MA, Albert FW. Multiple epistatic DNA variants in a single gene affect gene expression in trans. Genetics 2022; 220:iyab208. [PMID: 34791209 PMCID: PMC8733636 DOI: 10.1093/genetics/iyab208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/09/2021] [Indexed: 01/08/2023] Open
Abstract
DNA variants that alter gene expression in trans are important sources of phenotypic variation. Nevertheless, the identity of trans-acting variants remains poorly understood. Single causal variants in several genes have been reported to affect the expression of numerous distant genes in trans. Whether these simple molecular architectures are representative of trans-acting variation is unknown. Here, we studied the large RAS signaling regulator gene IRA2, which contains variants with extensive trans-acting effects on gene expression in the yeast Saccharomyces cerevisiae. We used systematic CRISPR-based genome engineering and a sensitive phenotyping strategy to dissect causal variants to the nucleotide level. In contrast to the simple molecular architectures known so far, IRA2 contained at least seven causal nonsynonymous variants. The effects of these variants were modulated by nonadditive, epistatic interactions. Two variants at the 5'-end affected gene expression and growth only when combined with a third variant that also had no effect in isolation. Our findings indicate that the molecular basis of trans-acting genetic variation may be considerably more complex than previously appreciated.
Collapse
Affiliation(s)
- Sheila Lutz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Krisna Van Dyke
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew A Feraru
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
18
|
Ardell SM, Kryazhimskiy S. The population genetics of collateral resistance and sensitivity. eLife 2021; 10:73250. [PMID: 34889185 PMCID: PMC8765753 DOI: 10.7554/elife.73250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/06/2021] [Indexed: 12/05/2022] Open
Abstract
Resistance mutations against one drug can elicit collateral sensitivity against other drugs. Multi-drug treatments exploiting such trade-offs can help slow down the evolution of resistance. However, if mutations with diverse collateral effects are available, a treated population may evolve either collateral sensitivity or collateral resistance. How to design treatments robust to such uncertainty is unclear. We show that many resistance mutations in Escherichia coli against various antibiotics indeed have diverse collateral effects. We propose to characterize such diversity with a joint distribution of fitness effects (JDFE) and develop a theory for describing and predicting collateral evolution based on simple statistics of the JDFE. We show how to robustly rank drug pairs to minimize the risk of collateral resistance and how to estimate JDFEs. In addition to practical applications, these results have implications for our understanding of evolution in variable environments. Drugs known as antibiotics are the main treatment for most serious infections caused by bacteria. However, many bacteria are acquiring genetic mutations that make them resistant to the effects of one or more types of antibiotics, making them harder to eliminate. One way to tackle drug-resistant bacteria is to develop new types of antibiotics; however, in recent years, the rate at which new antibiotics have become available has been dwindling. Using two or more existing drugs, one after another, can also be an effective way to eliminate resistant bacteria. The success of any such ‘multi-drug’ treatment lies in being able to predict whether mutations that make the bacteria resistant to one drug simultaneously make it sensitive to another, a phenomenon known as collateral sensitivity. Different resistance mutations may have different collateral effects: some may increase the bacteria’s sensitivity to the second drug, while others might make the bacteria more resistant. However, it is currently unclear how to design robust multi-drug treatments that take this diversity of collateral effects into account. Here, Ardell and Kryazhimskiy used a concept called JDFE (short for the joint distribution of fitness effects) to describe the diversity of collateral effects in a population of bacteria exposed to a single drug. This information was then used to mathematically model how collateral effects evolved in the population over time. Ardell and Kryazhimskiy showed that this approach can predict how likely a population is to become collaterally sensitive or collaterally resistant to a second antibiotic. Drug pairs can then be ranked according to the risk of collateral resistance emerging, so long as information on the variety of resistance mutations available to the bacteria are included in the model. Each year, more than 700,000 people die from infections caused by bacteria that are resistant to one or more antibiotics. The findings of Ardell and Kryazhimskiy may eventually help clinicians design multi-drug treatments that effectively eliminate bacterial infections and help to prevent more bacteria from evolving resistance to antibiotics. However, to achieve this goal, more research is needed to fully understand the range collateral effects caused by resistance mutations.
Collapse
Affiliation(s)
- Sarah M Ardell
- Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Sergey Kryazhimskiy
- Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| |
Collapse
|
19
|
Amicone M, Gordo I. Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation. Evolution 2021; 75:2641-2657. [PMID: 34341983 PMCID: PMC9292366 DOI: 10.1111/evo.14315] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/08/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022]
Abstract
Microbial ecosystems harbor an astonishing diversity that can persist for long times. To understand how such diversity is structured and maintained, ecological and evolutionary processes need to be integrated at similar timescales. Here, we study a model of resource competition that allows for evolution via de novo mutation, and focus on rapidly adapting asexual populations with large mutational inputs, as typical of many bacteria species. We characterize the adaptation and diversification of an initially maladapted population and show how the eco-evolutionary dynamics are shaped by the interaction between simultaneously emerging lineages - clonal interference. We find that in large populations, more intense clonal interference can foster diversification under sympatry, increasing the probability that phenotypically and genetically distinct clusters coexist. In smaller populations, the accumulation of deleterious and compensatory mutations can push further the diversification process and kick-start speciation. Our findings have implications beyond microbial populations, providing novel insights about the interplay between ecology and evolution in clonal populations.
Collapse
Affiliation(s)
- Massimo Amicone
- Evolutionary Biology, Instituto Gulbenkian de Ciência (IGC)OeirasPortugal
| | - Isabel Gordo
- Evolutionary Biology, Instituto Gulbenkian de Ciência (IGC)OeirasPortugal
| |
Collapse
|
20
|
Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. eLife 2021; 10:e70918. [PMID: 34596043 PMCID: PMC8579951 DOI: 10.7554/elife.70918] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time.
Collapse
Affiliation(s)
- Christopher W Bakerlee
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard University, CambridgeCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard University, CambridgeCambridgeUnited States
| |
Collapse
|
21
|
Vasquez KS, Willis L, Cira NJ, Ng KM, Pedro MF, Aranda-Díaz A, Rajendram M, Yu FB, Higginbottom SK, Neff N, Sherlock G, Xavier KB, Quake SR, Sonnenburg JL, Good BH, Huang KC. Quantifying rapid bacterial evolution and transmission within the mouse intestine. Cell Host Microbe 2021; 29:1454-1468.e4. [PMID: 34473943 PMCID: PMC8445907 DOI: 10.1016/j.chom.2021.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/25/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022]
Abstract
Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.
Collapse
Affiliation(s)
- Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nate J Cira
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Katharine M Ng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Miguel F Pedro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
22
|
Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun 2021; 12:5193. [PMID: 34465770 PMCID: PMC8408183 DOI: 10.1038/s41467-021-25440-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2021] [Indexed: 01/17/2023] Open
Abstract
Historical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step. Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
Collapse
|
23
|
Visher E, Evensen C, Guth S, Lai E, Norfolk M, Rozins C, Sokolov NA, Sui M, Boots M. The three Ts of virulence evolution during zoonotic emergence. Proc Biol Sci 2021; 288:20210900. [PMID: 34375554 PMCID: PMC8354747 DOI: 10.1098/rspb.2021.0900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022] Open
Abstract
There is increasing interest in the role that evolution may play in current and future pandemics, but there is often also considerable confusion about the actual evolutionary predictions. This may be, in part, due to a historical separation of evolutionary and medical fields, but there is a large, somewhat nuanced body of evidence-supported theory on the evolution of infectious disease. In this review, we synthesize this evolutionary theory in order to provide a framework for clearer understanding of the key principles. Specifically, we discuss the selection acting on zoonotic pathogens' transmission rates and virulence at spillover and during emergence. We explain how the direction and strength of selection during epidemics of emerging zoonotic disease can be understood by a three Ts framework: trade-offs, transmission, and time scales. Virulence and transmission rate may trade-off, but transmission rate is likely to be favoured by selection early in emergence, particularly if maladapted zoonotic pathogens have 'no-cost' transmission rate improving mutations available to them. Additionally, the optimal virulence and transmission rates can shift with the time scale of the epidemic. Predicting pathogen evolution, therefore, depends on understanding both the trade-offs of transmission-improving mutations and the time scales of selection.
Collapse
Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Claire Evensen
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Edith Lai
- College of Natural Resources, University of California, Berkeley, CA 94720, USA
| | - Marina Norfolk
- College of Letters and Sciences, University of California, Berkeley, CA 94720, USA
| | - Carly Rozins
- Department of Science and Technology Studies, Division of Natural Science, York University, Toronto, Ontario, Canada M3J 1P3
| | - Nina A. Sokolov
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Melissa Sui
- College of Letters and Sciences, University of California, Berkeley, CA 94720, USA
| | - Michael Boots
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| |
Collapse
|
24
|
Fontana S, Rasmann S, de Bello F, Pomati F, Moretti M. Reconciling trait based perspectives along a trait-integration continuum. Ecology 2021; 102:e03472. [PMID: 34260747 DOI: 10.1002/ecy.3472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 11/08/2022]
Abstract
Trait based ecology has developed fast in the last decades, aiming to both explain mechanisms of community assembly, and predict patterns in nature, such as the effects of biodiversity shifts on key ecosystem processes. This body of work has stimulated the development of several conceptual frameworks and analytical methods, as well as the production of trait databases covering a growing number of taxa and organizational levels (from individuals to guilds). However, this breeding ground of novel concepts and tools currently lacks a general and coherent framework, under which functional traits can help ecologists organize their research aims, and serve as the common currency to unify several scientific disciplines. Specifically, we see a need to bridge the gaps between community ecology, ecosystem ecology, and evolutionary biology, in order to address the most pressing environmental issues of our time. To achieve this integration goal, we define a trait-integration continuum, which reconciles alternative trait definitions and approaches in ecology. This continuum outlines a coherent progression of biological scales, along which traits interact and hierarchically integrate from genetic information, to whole organism fitness-related traits, to trait syndromes and functional groups. Our conceptual scheme proposes that lower-level trait integration is closer to the inference of ecoevolutionary mechanisms determining population and community properties, whereas higher-level trait integration is most suited to the prediction of ecosystem processes. Within these two extremes, trait integration varies on a continuous scale, which relates directly to the inductive-deductive loop that should characterize the scientific method. With our proposed framework, we aim to facilitate scientists in contextualising their research based on the trait-integration levels that matter most to their specific goals. Explicitly acknowledging the existence of a trait-integration continuum is a promising way for framing the appropriate questions, thus obtaining reliable answers and results that are comparable across studies and disciplines.
Collapse
Affiliation(s)
- Simone Fontana
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland.,Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
| | - Sergio Rasmann
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, 2000, Switzerland
| | - Francesco de Bello
- Department of Botany, Faculty of Sciences, University of South Bohemia, Na Zlate Stoce 1, České Budějovice, 370 05, Czech Republic.,Desertification Research Centre (CIDE-CSIC), Carretera Moncada-Náquera, Km 4,5, Moncada (Valencia), 46113, Spain
| | - Francesco Pomati
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf, 8600, Switzerland
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| |
Collapse
|
25
|
Pinheiro F, Warsi O, Andersson DI, Lässig M. Metabolic fitness landscapes predict the evolution of antibiotic resistance. Nat Ecol Evol 2021; 5:677-687. [PMID: 33664488 DOI: 10.1038/s41559-021-01397-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/20/2021] [Indexed: 12/14/2022]
Abstract
Bacteria evolve resistance to antibiotics by a multitude of mechanisms. A central, yet unsolved question is how resistance evolution affects cell growth at different drug levels. Here, we develop a fitness model that predicts growth rates of common resistance mutants from their effects on cell metabolism. The model maps metabolic effects of resistance mutations in drug-free environments and under drug challenge; the resulting fitness trade-off defines a Pareto surface of resistance evolution. We predict evolutionary trajectories of growth rates and resistance levels, which characterize Pareto resistance mutations emerging at different drug dosages. We also predict the prevalent resistance mechanism depending on drug and nutrient levels: low-dosage drug defence is mounted by regulation, evolution of distinct metabolic sectors sets in at successive threshold dosages. Evolutionary resistance mechanisms include membrane permeability changes and drug target mutations. These predictions are confirmed by empirical growth inhibition curves and genomic data of Escherichia coli populations. Our results show that resistance evolution, by coupling major metabolic pathways, is strongly intertwined with systems biology and ecology of microbial populations.
Collapse
Affiliation(s)
- Fernanda Pinheiro
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Omar Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| |
Collapse
|
26
|
Host diversity slows bacteriophage adaptation by selecting generalists over specialists. Nat Ecol Evol 2021; 5:350-359. [PMID: 33432132 DOI: 10.1038/s41559-020-01364-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/12/2020] [Indexed: 01/28/2023]
Abstract
Most viruses can infect multiple hosts, yet the selective mechanisms that maintain multi-host generalists over single-host specialists remain an open question. Here we propagate populations of the newly identified bacteriophage øJB01 in coculture with many host genotypes and find that while phage can adapt to infect any of the new hosts, increasing the number of hosts slows the rate of adaptation. We quantify trade-offs in the capacity for individual phage to infect different hosts and find that phage from evolved populations with more hosts are more likely to be generalists. Sequencing of evolved phage reveals strong selection and the genetic basis of adaptation, supporting a model that shows how the addition of more potential hosts to a community can select for low-fitness generalists over high-fitness specialists. Our results show how evolution with multiple hosts alters the rate of viral adaptation and provides empirical support for an evolutionary mechanism that promotes generalists over specialists.
Collapse
|
27
|
Boyer S, Hérissant L, Sherlock G. Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment. PLoS Genet 2021; 17:e1009314. [PMID: 33493203 PMCID: PMC7861553 DOI: 10.1371/journal.pgen.1009314] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/04/2021] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
The environmental conditions of microorganisms' habitats may fluctuate in unpredictable ways, such as changes in temperature, carbon source, pH, and salinity to name a few. Environmental heterogeneity presents a challenge to microorganisms, as they have to adapt not only to be fit under a specific condition, but they must also be robust across many conditions and be able to deal with the switch between conditions itself. While experimental evolution has been used to gain insight into the adaptive process, this has largely been in either unvarying or consistently varying conditions. In cases where changing environments have been investigated, relatively little is known about how such environments influence the dynamics of the adaptive process itself, as well as the genetic and phenotypic outcomes. We designed a systematic series of evolution experiments where we used two growth conditions that have differing timescales of adaptation and varied the rate of switching between them. We used lineage tracking to follow adaptation, and whole genome sequenced adaptive clones from each of the experiments. We find that both the switch rate and the order of the conditions influences adaptation. We also find different adaptive outcomes, at both the genetic and phenotypic levels, even when populations spent the same amount of total time in the two different conditions, but the order and/or switch rate differed. Thus, in a variable environment adaptation depends not only on the nature of the conditions and phenotypes under selection, but also on the complexity of the manner in which those conditions are combined to result in a given dynamic environment.
Collapse
Affiliation(s)
- Sébastien Boyer
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Lucas Hérissant
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
28
|
Kinsler G, Geiler-Samerotte K, Petrov DA. Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation. eLife 2020; 9:e61271. [PMID: 33263280 PMCID: PMC7880691 DOI: 10.7554/elife.61271] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Building a genotype-phenotype-fitness map of adaptation is a central goal in evolutionary biology. It is difficult even when adaptive mutations are known because it is hard to enumerate which phenotypes make these mutations adaptive. We address this problem by first quantifying how the fitness of hundreds of adaptive yeast mutants responds to subtle environmental shifts. We then model the number of phenotypes these mutations collectively influence by decomposing these patterns of fitness variation. We find that a small number of inferred phenotypes can predict fitness of the adaptive mutations near their original glucose-limited evolution condition. Importantly, inferred phenotypes that matter little to fitness at or near the evolution condition can matter strongly in distant environments. This suggests that adaptive mutations are locally modular - affecting a small number of phenotypes that matter to fitness in the environment where they evolved - yet globally pleiotropic - affecting additional phenotypes that may reduce or improve fitness in new environments.
Collapse
Affiliation(s)
- Grant Kinsler
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Kerry Geiler-Samerotte
- Department of Biology, Stanford UniversityStanfordUnited States
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State UniversityTempeUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| |
Collapse
|
29
|
Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
Collapse
Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
30
|
Visher E, Boots M. The problem of mediocre generalists: population genetics and eco-evolutionary perspectives on host breadth evolution in pathogens. Proc Biol Sci 2020; 287:20201230. [PMID: 32811306 PMCID: PMC7482275 DOI: 10.1098/rspb.2020.1230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/22/2020] [Indexed: 01/29/2023] Open
Abstract
Many of our theories for the generation and maintenance of diversity in nature depend on the existence of specialist biotic interactions which, in host-pathogen systems, also shape cross-species disease emergence. As such, niche breadth evolution, especially in host-parasite systems, remains a central focus in ecology and evolution. The predominant explanation for the existence of specialization in the literature is that niche breadth is constrained by trade-offs, such that a generalist is less fit on any particular environment than a given specialist. This trade-off theory has been used to predict niche breadth (co)evolution in both population genetics and eco-evolutionary models, with the different modelling methods providing separate, complementary insights. However, trade-offs may be far from universal, so population genetics theory has also proposed alternate mechanisms for costly generalism, including mutation accumulation. However, these mechanisms have yet to be integrated into eco-evolutionary models in order to understand how the mechanism of costly generalism alters the biological and ecological circumstances predicted to maintain specialism. In this review, we outline how population genetics and eco-evolutionary models based on trade-offs have provided insights for parasite niche breadth evolution and argue that the population genetics-derived mutation accumulation theory needs to be better integrated into eco-evolutionary theory.
Collapse
Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Ringgold Standard Institution, Penryn, Cornwall, UK
| |
Collapse
|
31
|
Biselli E, Schink SJ, Gerland U. Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate. Mol Syst Biol 2020; 16:e9478. [PMID: 32500952 PMCID: PMC7273699 DOI: 10.15252/msb.20209478] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/09/2023] Open
Abstract
Fitness of bacteria is determined both by how fast cells grow when nutrients are abundant and by how well they survive when conditions worsen. Here, we study how prior growth conditions affect the death rate of Escherichia coli during carbon starvation. We control the growth rate prior to starvation either via the carbon source or via a carbon-limited chemostat. We find a consistent dependence where death rate depends on the prior growth conditions only via the growth rate, with slower growth leading to exponentially slower death. Breaking down the observed death rate into two factors, maintenance rate and recycling yield, reveals that slower growing cells display a decreased maintenance rate per cell volume during starvation, thereby decreasing their death rate. In contrast, the ability to scavenge nutrients from carcasses of dead cells (recycling yield) remains constant. Our results suggest a physiological trade-off between rapid proliferation and long survival. We explore the implications of this trade-off within a mathematical model, which can rationalize the observation that bacteria outside of lab environments are not optimized for fast growth.
Collapse
Affiliation(s)
- Elena Biselli
- Physics of Complex BiosystemsPhysics DepartmentTechnical University of MunichGarchingGermany
- Department of Systems BiologyHarvard Medical SchoolBostonMAUSA
| | - Severin Josef Schink
- Physics of Complex BiosystemsPhysics DepartmentTechnical University of MunichGarchingGermany
- Department of Systems BiologyHarvard Medical SchoolBostonMAUSA
| | - Ulrich Gerland
- Physics of Complex BiosystemsPhysics DepartmentTechnical University of MunichGarchingGermany
| |
Collapse
|
32
|
Bernhardt JR, Kratina P, Pereira AL, Tamminen M, Thomas MK, Narwani A. The evolution of competitive ability for essential resources. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190247. [PMID: 32200736 PMCID: PMC7133530 DOI: 10.1098/rstb.2019.0247] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 02/01/2023] Open
Abstract
Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species' minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered-to what extent are species' competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed Chlamydomonas reinhardtii for approximately 285 generations to seven environments in chemostats that differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in a common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Collapse
Affiliation(s)
- Joey R. Bernhardt
- Aquatic Ecology Department, Eawag, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Pavel Kratina
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aaron Louis Pereira
- Aquatic Ecology Department, Eawag, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Manu Tamminen
- Department of Biology, University of Turku, Natura, University Hill, 20014 Turku, Finland
| | - Mridul K. Thomas
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anita Narwani
- Aquatic Ecology Department, Eawag, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| |
Collapse
|
33
|
A model for the interplay between plastic tradeoffs and evolution in changing environments. Proc Natl Acad Sci U S A 2020; 117:8934-8940. [PMID: 32245811 DOI: 10.1073/pnas.1915537117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Performance tradeoffs are ubiquitous in both ecological and evolutionary modeling, yet they are usually postulated and built into fitness and ecological landscapes. However, tradeoffs depend on genetic background and evolutionary history and can themselves evolve. We present a simple model capable of capturing the key feedback loop: evolutionary history shapes tradeoff strength, which, in turn, shapes evolutionary future. One consequence of this feedback is that genomes with identical fitness can have different evolutionary properties shaped by prior environmental exposure. Another is that, generically, the best adaptations to one environment may evolve in another. Our simple framework bridges the gap between the phenotypic Fisher's Geometric Model and the genotypic properties, such as modularity and evolvability, and can serve as a rich playground for investigating evolution in multiple or changing environments.
Collapse
|
34
|
van Dijk B, Meijer J, Cuypers TD, Hogeweg P. Trusting the hand that feeds: microbes evolve to anticipate a serial transfer protocol as individuals or collectives. BMC Evol Biol 2019; 19:201. [PMID: 31684861 PMCID: PMC6829849 DOI: 10.1186/s12862-019-1512-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Experimental evolution of microbes often involves a serial transfer protocol, where microbes are repeatedly diluted by transfer to a fresh medium, starting a new growth cycle. This has revealed that evolution can be remarkably reproducible, where microbes show parallel adaptations both on the level of the phenotype as well as the genotype. However, these studies also reveal a strong potential for divergent evolution, leading to diversity both between and within replicate populations. We here study how in silico evolved Virtual Microbe "wild types" (WTs) adapt to a serial transfer protocol to investigate generic evolutionary adaptations, and how these adaptations can be manifested by a variety of different mechanisms. RESULTS We show that all WTs evolve to anticipate the regularity of the serial transfer protocol by adopting a fine-tuned balance of growth and survival. This anticipation is done by evolving either a high yield mode, or a high growth rate mode. We find that both modes of anticipation can be achieved by individual lineages and by collectives of microbes. Moreover, these different outcomes can be achieved with or without regulation, although the individual-based anticipation without regulation is less well adapted in the high growth rate mode. CONCLUSIONS All our in silico WTs evolve to trust the hand that feeds by evolving to anticipate the periodicity of a serial transfer protocol, but can do so by evolving two distinct growth strategies. Furthermore, both these growth strategies can be accomplished by gene regulation, a variety of different polymorphisms, and combinations thereof. Our work reveals that, even under controlled conditions like those in the lab, it may not be possible to predict individual evolutionary trajectories, but repeated experiments may well result in only a limited number of possible outcomes.
Collapse
Affiliation(s)
- Bram van Dijk
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Jeroen Meijer
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Thomas D. Cuypers
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| |
Collapse
|
35
|
Life on the frontline reveals constraints. Nat Ecol Evol 2019; 3:1501-1502. [PMID: 31611675 DOI: 10.1038/s41559-019-1010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|