Contingency and determinism in evolution: Replaying life’s tape

Science, Journal Year: 2018, Volume and Issue: 362(6415)

Published: Nov. 8, 2018

Replaying the tape of life The evolutionary biologist Stephen Jay Gould once dreamed about replaying in order to identify whether evolution is more subject deterministic or contingent forces. Greater influence determinism would mean that outcomes are repeatable and less variations history. Contingency, on other hand, suggests specific events, making them repeatable. Blount et al. review numerous studies have been done since put forward this question, both experimental observational, find many patterns adaptation convergent. Nevertheless, there still much variation with regard mechanisms forms converge. Science , issue p. eaam5979

Language: Английский

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Reintroducing mothur: 10 Years Later

Applied and Environmental Microbiology, Journal Year: 2019, Volume and Issue: 86(2)

Published: Nov. 8, 2019

More than 10 years ago, we published the paper describing mothur software package in Applied and Environmental Microbiology . Our goal was to create a comprehensive that allowed users analyze amplicon sequence data using most robust methods available. has helped lead community through ongoing sequencing revolution continues provide this service microbial ecology community.

Language: Английский

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Biofilms: Understanding the structure and contribution towards bacterial resistance in antibiotics

Medicine in Microecology, Journal Year: 2023, Volume and Issue: 16, P. 100084 - 100084

Published: May 31, 2023

The biofilm is a bacterial colony wrapped in an auto-produced polymer matrix of polysaccharides, proteins, and DNA. Bacterial biofilms cause persistent infections because they are more resistant to antibiotics, disinfectants, the immune system body. Other significant characteristics gradient oxygen nutrition from top layer bottom biofilms. Lower cell metabolic activity longer doubling rates linked gradients; these quiescent cells responsible for some resistance antibiotics. Biofilms may be avoided cured with vigorous antibiotic prophylaxis or treatment early on continuous suppressive medication. This review discusses development tolerance bacteria due formation, mechanisms, that induce bacteria. Recent strategies combat also discussed.

Language: Английский

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Trade-Offs (and Constraints) in Organismal Biology

Physiological and Biochemical Zoology, Journal Year: 2021, Volume and Issue: 95(1), P. 82 - 112

Published: Nov. 4, 2021

AbstractTrade-offs and constraints are inherent to life, studies of these phenomena play a central role in both organismal evolutionary biology. Trade-offs can be defined, categorized, studied at least six, not mutually exclusive, ways. (1) Allocation caused by limited resource (e.g., energy, time, space, essential nutrients), such that increasing allocation one component necessarily requires decrease another (if only two components involved, this is referred as the Y-model, e.g., energy devoted size versus number offspring). (2) Functional conflicts occur when features enhance performance task relative lengths in-levers out-levers, force-velocity trade-offs related muscle fiber type composition). (3) Shared biochemical pathways, often involving integrator molecules hormones, neurotransmitters, transcription factors), simultaneously affect multiple traits, with some effects being beneficial for or more Darwinian fitness survival, age first reproduction, fecundity) others detrimental. (4) Antagonistic pleiotropy describes genetic variants increase (or lower-level trait) while decreasing another. (5) Ecological circumstances selective regime) may impose trade-offs, foraging behavior increases availability yet also decreases survival. (6) Sexual selection lead elaboration (usually male) secondary sexual characters improve mating success but handicap survival and/or energetic costs reduce other components. Empirical search negative correlations between traits expected outcomes will generally inadequate if than involved especially complex physiological networks interacting traits. Moreover, populations experiencing harsh environmental conditions challenges extremes phenotypic distributions, among individuals species have exceptional athletic abilities. (partially) circumvented through various compensatory mechanisms, depending on timescale ranging from acute evolutionary. Going forward, pluralistic view constraints, combined integrative analyses cross levels biological organization traditional boundaries disciplines, study

Language: Английский

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Two decades of bacterial ecology and evolution in a freshwater lake

Nature Microbiology, Journal Year: 2025, Volume and Issue: 10(1), P. 246 - 257

Published: Jan. 3, 2025

Language: Английский

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Long-term studies provide unique insights into evolution

Nature, Journal Year: 2025, Volume and Issue: 639(8055), P. 589 - 601

Published: March 19, 2025

Language: Английский

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Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

EMBO Reports, Journal Year: 2019, Volume and Issue: 20(8)

Published: July 24, 2019

Review24 July 2019Open Access Microbial Experimental Evolution – a proving ground for evolutionary theory and tool discovery Michael J McDonald Corresponding Author [email protected] orcid.org/0000-0002-5735-960X School of Biological Sciences, Monash University, Melbourne, Vic., Australia Search more papers by this author Information *,1 1School *Corresponding author. Tel: +61 3 9905 1697; E-mail: EMBO Reports (2019)20:e46992https://doi.org/10.15252/embr.201846992 See the Glossary abbreviations used in article. PDFDownload PDF article text main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract experimental evolution uses controlled laboratory populations study mechanisms evolution. The molecular analysis evolved enables empirical tests that can confirm predictions theory, but also lead surprising discoveries. As with other fields life sciences, microbial has become tool, deployed as part suite techniques available biologist. Here, I provide review general findings evolution, especially those relevant microbiologists are new field. relate these results design considerations an experiment suggest future directions working at intersection biology. clonal interference slowed rates fixation asexual population due competition between lineages each carry beneficial mutation coverage length concatenated DNA-sequence read data divided genome de novo occurs spontaneously during period fixed state which allele given genetic locus is frequency 1 barcode short DNA sequence identify individual or lineage haplotype set variants physically linked on single chromosome HGT horizontal gene transfer individuals share common ancestor within time LN natural log LTEE long-term N size parallel similar phenotypes genotypes independently evolving selection coefficient(s) quantitative representation relative fitness reproductive success standing variation present before considered observer Introduction studies now constitute one foundations 1. In particular, bring greater power precision studies, providing means out elaborate explore ideas biology 2. A typical starts culture, just like any microbiology laboratory. Cells inoculated into media left grow until culture reaches high density. Instead throwing using all resultant population, evolutionist transfers dilutes allow continued growth division. This cycle be indefinitely, generations accumulate, will drive adapt environment. simple process carried range systems, summarised Fig Figure Mechanisms propagation evolution(A) Batch requires regular dilution fresh media. These experiments relatively easy establish, since vessels commonly batch culture. scaled large number replicates, example when 96-well plates. (B) Chemostat systems include constant supply medium. provides continuous cultures without fluctuations phase. (C) Microfluidics most precise control over supplements cell cultures. may need custom designed, replicates limited. (D) Emulsion take advantage small cell-containing vesicles form mixing oil, surfactant cells. cells vesicle determined ratio cell, oil. mixed back vortexing centrifuging solution. One select yield per-vesicle rather than rapid 144. (E) Mutation accumulation introduces regular, single-cell bottleneck replicate population. achieved streaking petri dish then choosing colony (founded cell) streak next plate. (F) introduced model organism, often plant mouse, propagate it recovered from organism. analysed subjected further mode allows testing unanticipated organism-specific features environment difficult Download figure PowerPoint Long- short-term approaches Perhaps striking microbes access long scales. generation times up tens pass every day. limited only how experimentalist maintain transfers. easily stored freezer, indefinite period, so saved frozen snapshot restart inevitable accidents happen. longest running, probably famous, (LTEE). comprised 12 E. coli, started 1987 still passaged daily 68,000 later (see here recent 4). What learned running long? Twenty years ago, biologist might have predicted coli would reached optimal after few thousand generations. However, we know continues 61,500 5, 6. key been utilisation citrate (cit+ phenotype), carbon source buffer phenotype significant because species-defining characteristic unable utilised under oxidising conditions 7. effect mutations explicitly cause cit+ dependent "potentiating" do not seem directly influence occurred first 20,000 8. words, particular trait unlikely experiment. there quicker routes many An alternative propagating term evolve shorter time. strong, rapidly. Adapting temperatures, Tenaillon et al propagated 115 2,000 9. Increasing another magnitude, Lang 1,000 Saccharomyces cerevisiae 10, 11. massive replication confers statistical detect change, hundreds shows some questions highly replicated cannot address; however, trends emerging consistent across both long- 12, 13, reviewed below. Repeatability, diminishing returns diversification: predictable Parallel same phenotypes, sometimes mutations, 14. Parallelism driven observed short- species 11, 15-19 (Fig 2A). Repeatability interesting suggests phenotypic outcomes could predictable. To anticipate response environmental changes major goal 20, capacity make accurate desirable. unclear whether about ever enough useful, subject ongoing models 21, 22. Three experiments(A) Genetic parallelism. signature repeated genes independent populations. expected multi-hit mutated six hypothetical 1000-generation (grey shaded) (orange line) Diminishing epistasis. negatively correlated background (figure adapted 25). Stable polymorphism evolve, whereby multiple ecotypes, different niche microcosm, coexist 27. possible outcome successive sweeps mutation, occasionally hampered (D). At onset experiment, adaptation tends slows down 23. LTEE, rate increase follows law, no attained 5. explained epistatic interactions effects lower better 24. Experiments show engineered low-fitness larger if they high-fitness 2B). "diminishing returns" epistasis M. extorquens S. 25, well 26. While return makes specific does robust made although true experiencing fluctuating complex environments. Most use unicellular organisms adapting defined-nutrient diverse, co-existing subpopulations niches, evident 6, 27, 28 2C). Diverse heterogeneity experimenter, called eco-evolutionary feedback 29. happens populations, altered production waste products consumption modifications change ecology alters selective pressures experienced 30. observation emphasises its importance real communities mechanism experiments. facilitate fundamental parameters evolution: environment, Understanding, manipulating, factors benefit exerted size, founding genotype determines therefore drives while manipulating variable potentially subtle effects. interpreting setting discussed Population (N) strength forces minimum detected selection, expressed coefficient (s), 1/N, where "N" ineffective Ns < 31. likely experience drift, random sampling frequencies chance deleterious loss mutations. consequence expect slower and, extreme cases, extinction 32. Some designed consequences 33-36, deliberately 1–10 1). If avoid 103–104 recommended. Variation experimenter vary much variation, "fuel" supplied 37. proportional amount 38. start amounts 39-41, founded clone 3, 28, 42 adaptive must fuelled 43, 44, elevated artificially induced supplementing mutagen deleting required mismatch repair. antimicrobial resistance antibiotic global health challenge that, sits disciplines biology, microbiology, genomics 20. measure costs underlie 45-49, probability 49. Mutations occur important biological functions reduction viability 50. Fitness assays Box 1: How fitness) shown confer actually 47, 51-53, always come cost. When costly, resistant microbe secondary compensate primary 54. Since processes, strategies amelioration resistance, drugs, should account 55. promising line research characterise susceptibilities multidrug-resistant strains. order attain strains several compensatory It less able additional Knowledge multidrug targeted drug combinations based clinical pathogenic organism contribute offspring generation. determine degree validate experimentally wide assays. Growth 145, total carrying capacity, biomass 105 speed boundary expansion 141 measures gold standard measurement competitive starting point assay obtain construct marked reference strain. typically modified readily distinguished nature marker accuracy For instance, fluorescent differentiate strain, proportions measured flow cytometry 10 10s thousands counted ratios. Alternatively, mixture spread onto agar plates containing distinction 146, counting Initially, strain 1:1 ratio. Even care taken mix competitors ratio, very initial frequency, difference calculations fitness. Once portion aside competing diluted incubated time, allowing two compete. After competition, again. calculated measurements dividing individuals. done final point. (LN) quotient gives performance compared value passed points, yielding per-generation (s). chosen carefully. too long, extinction, thus reducing calculation s. short, changed detection differences genotypes. bacteriophages Bacteriophages therapies 56, bacteriophage provided insights genetics 57. Bacteriophage genomes small, whole-genome sequencing phage was rise next-generation technologies 58. head exploited 19, 59, 60. ease bacteria co-culture led co-evolutionary dynamics. infecting isolation 61, 62. diverse bacteriophage, increases types 63. bind membrane protein gain entry cell. facilitated detailed λ site 64, 65. Conversely, bacterial modifying encodes protein. conferred efflux pumps, hypothesised targets such pump tandem comprise "evolution proof" treatment strategy 56. principle demonstrated drove MEX pump, thereby restoring sensitivity P. aeruginosa 66. trait. applications. introduction useful properties reductions 67. yeast, crossed "wild-type" promote recombinants possess productivity fast-growing 68. Continuous passaging widely restore ethanol xylose 69-71. example, C321 replace UAG codons UAA. ideal biotechnological applications, incorporation non-standard amino acids code. engineering caused slow growth. 1,000-generation resulted restored rates. Moreover, re-sequencing revealed mutational causes reduced founder 72. novel hosts, conditions. Wolbachia quickly among their hosts conferring infected females. addition, induce insect pathogens. devised Dengue virus amongst mosquitos originally discovered D. melanogaster. suited dispersal mosquito A. aegypti mosquito's intracellular 2 years. newly establish stable infection 73 thereafter eventual public dengue 74. Next, introduce describing full historical recommend books 1, reviews 75-77 exhaustive treatments earlier periods non-microbial 78-81 aspects You get what you for: choices Setting beyond normally adaptation. Adaptation described, including temperatures 9, 82, gradients 55 even levels ionising radiation 83. imagination. parameter pressure differential survival relied upon regardless pressure, adaptations predict. Wildenberg 84 fluorescence-activated sorter brightest 24 h. anticipated expression modulate fluorescence. Instead, periodically multicellular clusters increased brightness advantage. unpredicted did diminish elegance serves demonstrate unpredictability thwart outcomes. general, complicated regime, unpredictable noted complicated, well-designed, elicit selection. sought traits selecting against germ progenitor cooperative mats fluorescens. Although were unexpected, successfully applied 85. Simple environments function Natural expose microorganisms nutrients stresses spatial temporal complexity reflected numbers utilise respond stress. Laboratory 86, inactivate superfluous 87. Many contain source, usually glucose. glucose sole concentration limits 3. h "lag time", enter via pykF, became 88. specialisation cost sources. Studies showed rbs operon, proteins ribose 89, disrupted deleted Measurements ~1% 90. then, disruption genes, sources, maltose, minimal Other yeast concentrations glucose, Genes 91. Whole-genome half disrupt encode negative regulators RAS/PKA pathway ac

Language: Английский

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Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(36), P. 17906 - 17915

Published: Aug. 20, 2019

Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution natural environments are largely unknown. Here, we study the ubiquitous process host colonization commensal bacteria. We show, experimental Escherichia coli mouse intestine, that ecology gut controls pace a new invading bacterial strain. If resident E. strain is present gut, evolves rapid horizontal gene transfer (HGT), which precedes outweighs mutations. HGT driven 2 bacteriophages carried strain, cause an epidemic phage infection invader. These dynamics followed subsequent clonal interference genetically diverse lineages phage-carrying (lysogenic) show genes uptaken enhance metabolism specific carbon sources provide fitness advantage to lysogenic invader lineages. A minimal dynamical model explains temporal pattern epidemics complex evolutionary outcome phage-mediated selection. conclude phage-driven key eco-evolutionary driving force colonization-it accelerates promotes genetic diversity

Language: Английский

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The Classification and Evolution of Bacterial Cross-Feeding

Frontiers in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 7

Published: May 14, 2019

Bacterial feeding has evolved towards specific evolutionary niches and the sources of energy differ between species strains. Although bacteria fundamentally compete for nutrients, excreted products from one strain may be preferred source or a essential nutrients another strain. The large variability in preferences bacterial strains often provides complex cross-feeding relationships bacteria, particularly environments such as human lower gut, which impacts on host's digestion nutrition. amount information is available strains, it important to consider evolution cross-feeding. Adaptation environmental stimuli continuous process, thus understanding microbial interactions allows us determine resilience populations changes this environment, nutrient supply, how new might emerge future. In review, we provide framework terminology dividing into four forms that can used classification analysis dynamics. Under proposed framework, discuss origins factors spatial structure influence their emergence subsequent persistence. This review draws both theoretical experimental literature cross-disciplinary perspective different types

Language: Английский

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Experimental Evolution as a High-Throughput Screen for Genetic Adaptations

mSphere, Journal Year: 2018, Volume and Issue: 3(3)

Published: May 8, 2018

Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving influenced all population genetic forces, including selection, mutation, drift, recombination, relative contributions these forces may be seen as mysterious. Here, I describe why outcomes experimental should viewed with greater certainty because force selection typically dominates. Importantly, any mutant rising rapidly high frequency large must have acquired adaptive traits selective environment. Sequencing genomes mutants can identify genes pathways that contribute an adaptation. review logic simple mathematics this evolve-and-resequence approach powerful way find mutations mutation combinations best increase fitness new

Language: Английский

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