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| Open AccessEvolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages
In this work, Yang et al. provide evidence of triclosan exposure resulting in increased evolvability of K. pneumoniae in experimental evolution studies. They utilize sequencing and transcriptomics to explore the chromosomally and horizontally acquired antimicrobial resistance mechanisms.
- Qiu E. Yang
- , Xiaodan Ma
- & Timothy R. Walsh
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Article
| Open AccessHigh temperature delays and low temperature accelerates evolution of a new protein phenotype
The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.
- Jia Zheng
- , Ning Guo
- & Andreas Wagner
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Article
| Open AccessBee-pollination promotes rapid divergent evolution in plants growing in different soils
In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.
- Thomas Dorey
- & Florian P. Schiestl
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Article
| Open AccessSynthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.
- Pavel Dvořák
- , Barbora Burýšková
- & Martin Benešík
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Article
| Open AccessPlasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria
In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
- J. Carlos R. Hernandez-Beltran
- , Jerónimo Rodríguez-Beltrán
- & Rafael Peña-Miller
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Article
| Open AccessDuplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria
Mobile genetic elements can promote the duplication of antibiotic resistance genes which may in turn accelerate the evolution of resistance to new drugs. Here, the authors show that duplicated antibiotic resistance genes are enriched in bacterial isolates from environments associated with rampant antibiotic use.
- Rohan Maddamsetti
- , Yi Yao
- & Lingchong You
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Article
| Open AccessCompetition-driven eco-evolutionary feedback reshapes bacteriophage lambda’s fitness landscape and enables speciation
Niche theory is often invoked to explain biodiversity, but it does not explain how species evolve to exploit unique niches. Using a combination of experimental and computational approaches, this study shows that resource competition can deform fitness landscapes, opening new pathways that promote ecological speciation.
- Michael B. Doud
- , Animesh Gupta
- & Justin R. Meyer
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Article
| Open AccessEffects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen
Bottleneck effects of plant barriers on pathogenic invasions remain unclear. Using a random barcoding approach, this study investigates how plant root permeability limits the invasion and population bottlenecks of a phytopathogenic Ralstonia.
- Gaofei Jiang
- , Yuling Zhang
- & Zhong Wei
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Article
| Open AccessInferring bacterial transmission dynamics using deep sequencing genomic surveillance data
Studying rare genetic changes that arose as an infectious bacterium spread between lab mice, here the authors show that using the relative abundance of any changes rather than just whether they occurred can more precisely identify who likely infected who.
- Madikay Senghore
- , Hannah Read
- & Siouxsie Wiles
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Article
| Open AccessUnaltered hepatic wound healing response in male rats with ancestral liver injury
How much the environment influences inherited adaptive traits is debated and challenging to demonstrate in mammals. Here the authors performed a multigeneration study that failed to morphologically replicate enhanced wound healing response following ancestral liver injury in rats. However, heritable transcriptional effects suggest transmission at the molecular level, albeit of unclear functional relevance.
- Johanna Beil
- , Juliane Perner
- & Rémi Terranova
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Article
| Open AccessDeep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
Mutations in an RNA polymerase fragment, frequently found in lab adaptation, cluster in two modules favoring growth or maintenance via loss of interactions. Combining mutations in both modules enhances both traits, promoting compensatory evolution.
- Alaksh Choudhury
- , Benoit Gachet
- & Olivier Tenaillon
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Article
| Open AccessMixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients
Here, Caballero et al. provide an in depth characterisation of patients colonized with single or mixed strains of Pseudomonas aeruginosa to demonstrate the impact of within-host diversity on the development of antibiotic resistance.
- Julio Diaz Caballero
- , Rachel M. Wheatley
- & R. Craig MacLean
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Article
| Open AccessCoexisting ecotypes in long-term evolution emerged from interacting trade-offs
Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.
- Avik Mukherjee
- , Jade Ealy
- & Markus Basan
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Article
| Open AccessBacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering
Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.
- Yashraj Chavhan
- , Sutirth Dey
- & Peter A. Lind
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Article
| Open AccessDirected natural evolution generates a next-generation oncolytic virus with a high potency and safety profile
Compromised killing effects of oncolytic viruses due to attenuation of virulence remains a challenge. Here, the authors use a directed natural evolution approach to increase the oncolytic effect of the oncolytic virus M1 attributed to mutations in the E2 and nsP3 genes.
- Li Guo
- , Cheng Hu
- & Yuan Lin
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Article
| Open AccessMutation-induced infections of phage-plasmids
Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.
- Xiaoyu Shan
- , Rachel E. Szabo
- & Otto X. Cordero
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Article
| Open AccessA Vaccinia-based system for directed evolution of GPCRs in mammalian cells
G protein-coupled receptors are a major class of drug targets. Here, the authors develop a method whereby their biophysical and functional properties can be altered through directed evolution in mammalian cells, leading to variants exhibiting features such as high stability and expression, or increased allosteric coupling.
- Christoph Klenk
- , Maria Scrivens
- & Andreas Plückthun
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Article
| Open AccessQuantifying the local adaptive landscape of a nascent bacterial community
Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.
- Joao A. Ascensao
- , Kelly M. Wetmore
- & Oskar Hallatschek
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Article
| Open AccessMultistep diversification in spatiotemporal bacterial-phage coevolution
Bacteria and their viruses coexist and coevolve in nature, but maintaining them together in the lab is challenging. Here, a spatially structured environment allowed prolonged coevolution, with bacteria and phage diversifying into multiple ecotypes, uncovering gene mechanisms affecting phage-bacteria interactions.
- Einat Shaer Tamar
- & Roy Kishony
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Article
| Open AccessEvolutionary rescue of resistant mutants is governed by a balance between radial expansion and selection in compact populations
Antibiotic and anti-cancer therapy are challenged by mutation-mediated treatment resistance despite many mutations being maladaptive. Here, the authors introduce a system that shows how the probability of the long-term persistence of drug-resistant mutant lineages can be increased in dense microbial populations by acquiring multiple mutations.
- Serhii Aif
- , Nico Appold
- & Jona Kayser
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Article
| Open AccessEnvironmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli
Novel traits without immediate fitness benefit evolve frequently but we don’t know whether mutation or environment-driven selection drives this evolution. Here, using experimental evolution of E. coli populations, the authors demonstrate the importance of selection in the evolution of latent novel traits.
- Shraddha Karve
- & Andreas Wagner
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Article
| Open AccessTwo modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations
Here, the authors show that a colonizing bacterial strain evolves in the gut by either generating ecotypes or continuously fixing beneficial mutations. They associate the first mode to metabolic mutations and the second to domestication of bacteriophages that are incorporated into the bacterial genome.
- N. Frazão
- , A. Konrad
- & I. Gordo
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Article
| Open AccessExperimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning
Neutral networks, which are sets of genotypes connected via single mutations that share the same phenotype, are important for evolvability. Here, the authors provide experimental evidence of a neutral network in an RNA enzyme using a high-throughput assay and deep learning.
- Rachapun Rotrattanadumrong
- & Yohei Yokobayashi
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Article
| Open AccessRapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges
How rapidly the mutation rate responds evolutionarily to ecological and population-genetic factors over time is unclear. Here, the authors show that the evolution of mutation rates in E. coli proceeds rapidly in response to these factors with substantial bidirectional shifts.
- Wen Wei
- , Wei-Chin Ho
- & Michael Lynch
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Article
| Open AccessAdaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits
Phenotypic and genotypic evolution in worrisome Klebsiella spp. is influenced by the capsule. Here the authors show that adaptation outside the host can impact virulence-associated traits, including de novo emergence of hypermucoviscosity.
- Amandine Nucci
- , Eduardo P. C. Rocha
- & Olaya Rendueles
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Article
| Open AccessGenome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod
Using time-series whole-genome sequencing data from a laboratory evolution experiment, along with extensive computer simulations, the authors show that synergistic epistasis could drive rapid parallel freshwater adaptation in a saline copepod.
- David B. Stern
- , Nathan W. Anderson
- & Carol Eunmi Lee
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Article
| Open AccessMicrobiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis
This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.
- Laura Baldassarre
- , Hua Ying
- & Sebastian Fraune
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Article
| Open AccessMutational meltdown of putative microbial altruists in Streptomyces coelicolor colonies
In Streptomyces coelicolor, a subpopulation of cells can arise that produce metabolically costly antibiotics and a division of labor that maximizes colony fitness. This study uses experimental evolution to understand the reproductive and genomic fate of these mutant cells, showing that the arising altruistic cells are analogous to the reproductively sterile castes of social insects.
- Zheren Zhang
- , Shraddha Shitut
- & Daniel E. Rozen
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Article
| Open AccessEngineering artificial photosynthetic life-forms through endosymbiosis
The endosymbiotic theory posits that chloroplasts in eukaryotes arise from bacterial endosymbionts. Here, the authors engineer the yeast/cyanobacteria chimeras and show that the engineered cyanobacteria perform chloroplast-like functions to support the growth of yeast cells under photosynthetic conditions.
- Jason E. Cournoyer
- , Sarah D. Altman
- & Angad P. Mehta
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Article
| Open AccessImpact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium
Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.
- Erik Bakkeren
- , Ersin Gül
- & Médéric Diard
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Article
| Open AccessEvolutionary transition from a single RNA replicator to a multiple replicator network
Long-term experimental evolution shows that a single polymerase-encoding RNA replicator can evolve into a complex replicator network, shedding light on how a molecular replicator could have developed complexity before the emergence of life.
- Ryo Mizuuchi
- , Taro Furubayashi
- & Norikazu Ichihashi
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Article
| Open AccessIntralocus conflicts associated with a supergene
‘A supergene that underlies variation in male mating phenotypes has consequences for female reproduction. Here, the authors use evolutionary models to show that the rarest variant of this supergene is maintained by disproportionally high male reproductive success.’
- Lina M. Giraldo-Deck
- , Jasmine L. Loveland
- & Clemens Küpper
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Article
| Open AccessLoss of transcriptional plasticity but sustained adaptive capacity after adaptation to global change conditions in a marine copepod
Rapid adaptation will facilitate species resilience under global climate change, but its effects on plasticity are less commonly investigated. This study shows that 20 generations of experimental adaptation in a marine copepod drives a rapid loss of plasticity that carries costs and might have impacts on future resilience to environmental change.
- Reid S. Brennan
- , James A. deMayo
- & Melissa H. Pespeni
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Article
| Open AccessMutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis
Antibiotic persisters are phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Here, the authors provide evidence that cytoplasmic acidification, amplified by a compromised respiratory complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.
- Bram Van den Bergh
- , Hannah Schramke
- & Matthias Heinemann
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Article
| Open AccessObligate mutualistic cooperation limits evolvability
Cooperative mutualisms are widespread in many ecosystems but how they affect the ability of organisms to adapt to changing conditions was unclear. This study experimentally demonstrates that members of obligate cooperative mutualisms are less able to adapt evolutionarily to external selection pressures and are more likely to return to metabolic autonomy than their free-living counterparts.
- Benedikt Pauli
- , Leonardo Oña
- & Christian Kost
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Article
| Open AccessA mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes
Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Experiments in bacteria reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations, highlighting an underappreciated role for silent genetic variation in determining adaptive outcomes.
- James S. Horton
- , Louise M. Flanagan
- & Tiffany B. Taylor
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Article
| Open AccessTemporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors
Microbial evolution often involves transient phenotypes and sequential development of multiple mutations of unclear relevance. Here, the authors show that the evolution of non-growing E. coli cells can be driven by alterations in pyrimidine nucleoside levels associated with colony ageing and/or due to mutations in metabolic or regulatory genes.
- Ida Lauritsen
- , Pernille Ott Frendorf
- & Morten H. H. Nørholm
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Article
| Open AccessEpigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus
While a correlation between epigenetic modifications and mutation rates has been observed, experimental evidence of causality is limited. Here the authors measure the mutation rate in fungal mutants lacking histone modifications and confirm experimentally a causal effect of epigenetic modifications on mutation rates.
- Michael Habig
- , Cecile Lorrain
- & Eva H. Stukenbrock
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Article
| Open AccessChanges in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation
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.
- Dimitra Aggeli
- , Yuping Li
- & Gavin Sherlock
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Perspective
| Open AccessThe microbiome extends host evolutionary potential
The microbiome is becoming recognized as a key determinant of host phenotype. Here, Henry et al. present a framework for building our understanding of how the microbiome also influences host evolution, review empirical examples and research approaches, and highlight emerging questions.
- Lucas P. Henry
- , Marjolein Bruijning
- & Julien F. Ayroles
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Article
| Open AccessThe evolution of convex trade-offs enables the transition towards multicellularity
Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
- Joana P. Bernardes
- , Uwe John
- & Lutz Becks
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Article
| Open AccessRapid evolution of bacterial mutualism in the plant rhizosphere
Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.
- Erqin Li
- , Ronnie de Jonge
- & Alexandre Jousset
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Article
| Open AccessNatural selection increases female fitness by reversing the exaggeration of a male sexually selected trait
Natural and sexual selection can be in opposition favouring different trait sizes, but disentangling these processes empirically is difficult. Here Okada et al. show that predation on males shifts the balance of selection in experimentally evolving beetle populations, disfavoring a sexually-selected male trait but increasing female fitness.
- Kensuke Okada
- , Masako Katsuki
- & David J. Hosken
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Article
| Open AccessCompensatory evolution of Pseudomonas aeruginosa’s slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis
Long-term infection of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. Here, La Rosa et al. use adaptive laboratory evolution to increase the growth rate of clinical isolates, and identify mechanisms and evolutionary trajectories that, in reverse direction, may help the pathogen to adapt to the patients’ airways.
- Ruggero La Rosa
- , Elio Rossi
- & Søren Molin
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Article
| Open AccessThe neutral rate of whole-genome duplication varies among yeast species and their hybrids
The interaction between hybridisation and polyploidisation is thought to play an important role in eukaryote speciation. Here the authors sequence yeast crosses and show associations between hybridisation, genome instability, and genome duplication, suggesting these may have roles in the establishment of new hybrids.
- S. Marsit
- , M. Hénault
- & C. R. Landry
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Article
| Open AccessOxygen suppression of macroscopic multicellularity
The evolution of multicellular life is hypothesized to have been promoted by rising oxygen levels. Through experimental evolution and modeling, Bozdag et al. demonstrate that our planet’s first oxygenation would have strongly constrained, not promoted, the evolution of multicellular life.
- G. Ozan Bozdag
- , Eric Libby
- & William C. Ratcliff
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Article
| Open AccessCommunity composition of microbial microcosms follows simple assembly rules at evolutionary timescales
Evolution affects microbial community composition, but it is still unknown how commonly compositions change, and how predictable such changes are. Using experimental evolution, Meroz et al. show that compositional changes typically occur within ~400 generations, and are predictable by a bottom-up approach.
- Nittay Meroz
- , Nesli Tovi
- & Jonathan Friedman
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Article
| Open AccessMale fertility thermal limits predict vulnerability to climate warming
Trait-based approaches assume upper critical thermal limits (CTLs) are good predictors of climate change vulnerability. Here, the authors show that male fertility thermal limits, which are lower than CTLs, are better at predicting Drosophila extinction in the lab, suggesting species may be living close to their thermal limits.
- Belinda van Heerwaarden
- & Carla M. Sgrò
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Article
| Open AccessReversed evolution of grazer resistance to cyanobacteria
Anthropogenic changes, such as eutrophication from lake pollution, can lead to rapid evolution. Comparing Daphnia resurrected from generations adapted to historical pollution to contemporary, post-cleanup populations finds that Daphnia rapidly reversed their evolved resistance to harmful cyanobacteria.
- Jana Isanta-Navarro
- , Nelson G. Hairston Jr
- & Dominik Martin-Creuzburg