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| Open AccessIncreasing our ability to predict contemporary evolution
Classic debates concerning the extent to which scientists can predict evolution have gained new urgency as environmental changes force species to adapt or risk extinction. We highlight how our ability to predict evolution can be constrained by data limitations that cause poor understanding of deterministic natural selection. We then emphasize how such data limits can be reduced with feasible empirical effort involving a combination of approaches.
- Patrik Nosil
- , Samuel M. Flaxman
- & Zachariah Gompert
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Article
| Open AccessThe evolution of tit-for-tat in bacteria via the type VI secretion system
Game theory has contributed much to the understanding of social evolution. In an elegant combination of experimental tests and modelling, this study suggests that when bacteria face intense competition, repeated retaliation outcompetes a single tit-for-tat response to attack.
- William P. J. Smith
- , Maj Brodmann
- & Kevin R. Foster
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Article
| Open AccessEvolving cooperation in multichannel games
Most evolutionary game theory focuses on isolated games. Here, Donahue et al. present a general framework for ‘multichannel games’ in which individuals engage in a set of parallel games with a partner, and show that such parallel interactions favor the evolution of reciprocity across games.
- Kate Donahue
- , Oliver P. Hauser
- & Christian Hilbe
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Article
| Open AccessEvolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management
Mixtures of antibiotics or pesticides can help reduce the evolution of resistance to individual compounds. Here, Comont et al. show that in blackgrass, an important agricultural weed, herbicide mixtures do reduce specialized resistance but instead can select for a generalized resistance mechanism.
- David Comont
- , Claudia Lowe
- & Paul Neve
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Article
| Open AccessA mechanistic explanation of the transition to simple multicellularity in fungi
Multicellularity is one of the major transitions in evolution. Here, authors use a model to show that compared to unicellular bacteria, multicellular fungi can more rapidly colonise immobile, nutrient poor resources because exoenzymes provide greater or longer lasting benefits to mycelial organisms.
- Luke L. M. Heaton
- , Nick S. Jones
- & Mark D. Fricker
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Article
| Open AccessChild volunteers in a women's paramilitary organization in World War II have accelerated reproductive schedules
Life history theory predicts that females will adjust reproductive timing in response to environmental challenges. Here the authors show that young girls exposed to higher mortality rates during war give birth earlier and more often than their peers who were not exposed to these conditions.
- Robert Lynch
- , Virpi Lummaa
- & John Loehr
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Article
| Open AccessTurbulent coherent structures and early life below the Kolmogorov scale
Models of the origin of life generally require a mechanism to structure emerging populations. Here, Krieger et al. develop spatial models showing that coherent structures arising in turbulent flows in aquatic environments could have provided compartments that facilitated the origin of life.
- Madison S. Krieger
- , Sam Sinai
- & Martin A. Nowak
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Article
| Open AccessMinimum epistasis interpolation for sequence-function relationships
High-throughput combinatorial mutagenesis assays are useful to screen the function of many different sequences but they are not exhaustive. Here, Zhou and McCandlish develop a method to impute such missing genotype-phenotype data based on inferring the least epistatic sequence-function relationship.
- Juannan Zhou
- & David M. McCandlish
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Article
| Open AccessMeasuring single cell divisions in human tissues from multi-region sequencing data
Quantifying somatic evolutionary processes in cancer and healthy tissue is a challenge. Here, the authors use single time point multi-region sampling of cancer and normal tissue, combined with evolutionary theory, to quantify in vivo mutation and cell survival rates per cell division.
- Benjamin Werner
- , Jack Case
- & Andrea Sottoriva
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Article
| Open AccessEvolutionary games with environmental feedbacks
Strategic game payoffs often depend on the state of the environment, which in turn can be influenced by game strategies. Here, Tilman et al. develop a general framework for modeling strategic games with environmental feedbacks and analyze case studies from decision-making, ecology, and economics.
- Andrew R. Tilman
- , Joshua B. Plotkin
- & Erol Akçay
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Article
| Open AccessGene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence
A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.
- Jaime Iranzo
- , Yuri I. Wolf
- & Itamar Sela
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Article
| Open AccessAdaptation is maintained by the parliament of genes
The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.
- Thomas W. Scott
- & Stuart A. West
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Article
| Open AccessCoevolution of male and female mate choice can destabilize reproductive isolation
Models of mate choice have mainly focused on the implications of female mate choice for reproductive isolation. Here, Aubier et al. develop a population genetic model of coevolution between female and male mate choice, which can lead the population to oscillate between assortative and random mating.
- Thomas G. Aubier
- , Hanna Kokko
- & Mathieu Joron
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Article
| Open AccessEvolutionary games on isothermal graphs
The spatial structure of a population is often critical for the evolution of cooperation. Here, Allen and colleagues show that when spatial structure is represented by an isothermal graph, the effective number of neighbors per individual determines whether or not cooperation can evolve.
- Benjamin Allen
- , Gabor Lippner
- & Martin A. Nowak
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Article
| Open AccessStepwise shifts underlie evolutionary trends in morphological complexity of the mammalian vertebral column
The mammalian vertebral column has become more complex over evolutionary time. Here, Jones and colleagues use phylogenetic modelling to show that this complexity increased in stepwise shifts likely driven by adaptations for increased aerobic capacity.
- Katrina E. Jones
- , Kenneth D. Angielczyk
- & Stephanie E. Pierce
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Article
| Open AccessDisease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals
Modern humans and Neanderthals coexisted in the Levant for tens of thousands of years before modern humans spread and replaced Neanderthals. Here, Greenbaum et al. develop a model showing that transmission of disease and genes can explain the maintenance and then collapse of this contact zone.
- Gili Greenbaum
- , Wayne M. Getz
- & Oren Kolodny
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Article
| Open AccessHow conflict shapes evolution in poeciliid fishes
The viviparity driven conflict hypothesis predicts the evolution of the placenta will suppress the evolution of traits associated with pre-copulatory mate choice and accelerate speciation rate. Furness et al. support the former and disprove the latter predictions with comparative analyses of the poecilid fishes.
- Andrew I. Furness
- , Bart J. A. Pollux
- & David N. Reznick
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Article
| Open AccessMutation bias and GC content shape antimutator invasions
Mutators are expected to re-evolve low mutation rates to reduce deleterious load, but empirical evidence is mixed. Here, the authors show that load can vary across mutators and genetic backgrounds, which their simulations suggest can substantially alter antimutator dynamics.
- Alejandro Couce
- & Olivier Tenaillon
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Article
| Open AccessSurvival of the simplest in microbial evolution
In asexual populations selection at different genomic loci can interfere with each other. Here, using a biophysical model of molecular evolution the authors show that interference results in long-term degradation of molecular function, an effect that strongly depends on genome size.
- Torsten Held
- , Daniel Klemmer
- & Michael Lässig
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Article
| Open AccessFeed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise
Feed‐forward loops (FFLs) can filter out noise, but whether their overrepresentation in GRNs reflects adaptive evolution for this function is debated. Here, the authors develop a null model of regulatory evolution and find that FFLs evolve readily under selection for the noise filtering function.
- Kun Xiong
- , Alex K. Lancaster
- & Joanna Masel
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Article
| Open AccessSignatures of echolocation and dietary ecology in the adaptive evolution of skull shape in bats
What drives changes in morphological diversity? Here, Arbour et al. analyse skull 3D shape evolution across the bat radiation using µCT scan data, finding two phases of skull shape diversification, early adaptive shifts related to echolocation, and more recent shifts related to diet transitions.
- Jessica H. Arbour
- , Abigail A. Curtis
- & Sharlene E. Santana
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Article
| Open AccessThe coevolution of lifespan and reversible plasticity
Reversible phenotypic plasticity is expected to be favoured by long lifespan, as this increases the environmental variation individuals experience. Here, the authors develop a model showing how phenotypic plasticity can drive selection on lifespan, leading to coevolution of these traits.
- Irja I. Ratikainen
- & Hanna Kokko
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Article
| Open AccessModeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
The catalytic efficiency of many enzymes is lower than the theoretical maximum. Here, the authors combine genome-scale metabolic modeling with population genetics models to simulate enzyme evolution, and find that strong epistasis limits turnover numbers due to diminishing returns of fitness gains.
- David Heckmann
- , Daniel C. Zielinski
- & Bernhard O. Palsson
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Article
| Open AccessIntralocus sexual conflict can resolve the male-female health-survival paradox
Although men have lower survival across ages, women have poorer health than men as they age. Here, Archer et al. suggest that this pattern is explained by intralocus sexual conflict and provide supporting evidence from a mathematical model and experiments with Drosophila.
- C. Ruth Archer
- , Mario Recker
- & David J. Hosken
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Review Article
| Open AccessEcology and evolution of facilitation among symbionts
Facilitation is a well-known ecological interaction among free-living species, but symbionts residing in or on a host can also positively affect other symbiont species. Here, the authors review examples of facilitation among symbionts, revealing how facilitation theory can improve understanding of these interactions.
- Flore Zélé
- , Sara Magalhães
- & Alison B. Duncan
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Article
| Open AccessSchedule and magnitude of reproductive investment under immune trade-offs explains sex differences in immunity
Females and males tend to emphasize different defenses against pathogens: pathogen detection and pathogen killing, respectively. Here, Metcalf and Graham show that these alternate strategies can be explained by immune trade-offs only because the sexes differ in reproductive life history.
- C. Jessica E. Metcalf
- & Andrea L. Graham
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Correspondence
| Open AccessThe role of MHC supertypes in promoting trans-species polymorphism remains an open question
- Maciej J. Ejsmond
- , Karl P. Phillips
- & Jacek Radwan
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Article
| Open AccessThe dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification
The degree to which species diversity is bounded by limited niche space is under debate. Here, Larcombe and colleagues show that bounded and unbounded processes contribute more-or-less equally to conifer diversification, and that it may be niche dimensionality that facilitates these opposing forces.
- Matthew J. Larcombe
- , Gregory J. Jordan
- & Steven I. Higgins
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Article
| Open AccessClade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates
The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.
- Robin Aguilée
- , Fanny Gascuel
- & Regis Ferriere
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Article
| Open AccessCollapse and rescue of cooperation in evolving dynamic networks
The evolution of cooperation depends on social structure, which may evolve in response. Here, Akçay models coevolution between cooperation and social network formation strategies, showing that coevolutionary feedbacks lead cooperation to collapse unless constrained by costs of social connections.
- Erol Akçay
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Article
| Open AccessUncertainty about social interactions leads to the evolution of social heuristics
Humans are known to use social heuristics to make intuitive decisions on whether to cooperate. Here, the authors show with evolutionary simulations that social heuristics can be an adaptive solution to uncertainties about the consequences of cooperation and can greatly increase cooperation levels.
- Pieter van den Berg
- & Tom Wenseleers
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Article
| Open AccessCultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck
A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.
- Tian Chen Zeng
- , Alan J. Aw
- & Marcus W. Feldman
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Article
| Open AccessConditional privatization of a public siderophore enables Pseudomonas aeruginosa to resist cheater invasion
Pyoverdine is secreted by the opportunistic pathogen Pseudomonas aeruginosa to scavenge iron from its hosts. Here, the authors show that under stress conditions P. aeruginosa uses a ‘conditional privatization’ strategy, reserving pyoverdine intracellularly to protect against oxidative damage.
- Zhenyu Jin
- , Jiahong Li
- & Fan Jin
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Article
| Open AccessDynamics of starvation and recovery predict extinction risk and both Damuth’s law and Cope’s rule
Energetic constraints produce a fundamental tradeoff in starvation and recovery rates, impacting eco-evolutionary dynamics. Here, Yeakel et al. develop a nutritional state-structured model that predicts population size as a function of body mass known as Damuth’s law, and a mechanism for Cope’s rule, the evolutionary trend towards larger body mass.
- Justin D. Yeakel
- , Christopher P. Kempes
- & Sidney Redner
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Review Article
| Open AccessAdvancing behavioural genomics by considering timescale
Gene expression and behaviours are intimately related, and their interactions can play out over timescales from developmental to evolutionary. Here, the authors review how temporal aspects of gene expression mediate behavioural responses to the environment, a key question in behavioural genomics.
- Clare C. Rittschof
- & Kimberly A. Hughes
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Article
| Open AccessAcculturation orientations affect the evolution of a multicultural society
Cross-cultural interactions can cause cultural change, a process known as acculturation. Here, Erten et al. develop a model of cultural change under immigration, considering individuals’ orientations towards acculturation, and find that willingness to interact cross-culturally and resident cultural conservatism favour cultural coexistence.
- E. Yagmur Erten
- , Pieter van den Berg
- & Franz J. Weissing
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Article
| Open AccessDynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity
How a trait evolves depends on the shape of its fitness trade-off. Here, Huang et al. demonstrate evolution of trade-off shape in an experimental predator-prey system and develop a mathematical model of trait evolution when the underlying trade-off can also evolve.
- Weini Huang
- , Arne Traulsen
- & Lutz Becks
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Article
| Open AccessPhenotypic plasticity promotes recombination and gene clustering in periodic environments
Selection for recombination requires genetic diversity and negative linkage disequilibrium, which can be produced by coevolutionary arms races. Here the authors propose a qualitatively different scenario that can favour recombination in seasonal environments through the ‘genomic storage effect’.
- Davorka Gulisija
- & Joshua B. Plotkin
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Article
| Open AccessGenome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities
The rise of metabolic interdependencies among microbes is still poorly understood. Here, taking the underlying biochemical networks into consideration, Zomorrodi and Segrè integrate genome-scale metabolic models with evolutionary game theory to study the rise of cross-feeding in microbial communities.
- Ali R. Zomorrodi
- & Daniel Segrè
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Article
| Open AccessParadoxes in leaky microbial trade
Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.
- Yoav Kallus
- , John H. Miller
- & Eric Libby
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Article
| Open AccessEvolution of drift robustness in small populations
Genetic drift can reduce fitness in small populations by counteracting selection against deleterious mutations. Here, LaBar and Adami demonstrate through a mathematical model and simulations that small populations tend to evolve to drift-robust fitness peaks, which have a low likelihood of slightly-deleterious mutations.
- Thomas LaBar
- & Christoph Adami
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Article
| Open AccessPredicting metabolic adaptation from networks of mutational paths
The structure and dynamics of microbial communities reflect trade-offs in the ability to use different resources. Here, Josephides and Swain incorporate metabolic trade-offs into an eco-evolutionary model to predict networks of mutational paths and the evolutionary outcomes for microbial communities.
- Christos Josephides
- & Peter S. Swain
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Article
| Open AccessThe origin of a primordial genome through spontaneous symmetry breaking
Early molecules of life likely served both as templates and catalysts, raising the question of how functionally distinct genomes and enzymes arose. Here, the authors show that conflict between evolution at the molecular and cellular levels can drive functional differentiation of the two strands of self-replicating molecules and lead to copy number differences between the two.
- Nobuto Takeuchi
- , Paulien Hogeweg
- & Kunihiko Kaneko
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Article
| Open AccessEvolution of new regulatory functions on biophysically realistic fitness landscapes
Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.
- Tamar Friedlander
- , Roshan Prizak
- & Gašper Tkačik
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Article
| Open AccessA unified model of Hymenopteran preadaptations that trigger the evolutionary transition to eusociality
The Hymenoptera are thought to have preadaptations responsible for the repeated evolution of eusociality in ants, bees, and wasps. Here, Quiñones and Pen model the evolution of primitively social insects and identify factors that synergistically promote the transition to eusociality.
- Andrés E. Quiñones
- & Ido Pen
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Article
| Open AccessDiversity spurs diversification in ecological communities
Diversification may be driven by diversity, a concept Calcagnoet al. explore using models of intra- and inter-specific ecological interactions. A threshold number of species is sometimes required before adaptive radiations can occur; a phenomenon they term diversity-dependent adaptive radiation.
- Vincent Calcagno
- , Philippe Jarne
- & Patrice David
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Article
| Open AccessKilling by Type VI secretion drives genetic phase separation and correlates with increased cooperation
The Type VI Secretory System (T6SS) is used by some bacteria to kill non-kin competitors. Here, McNally and colleagues combine mathematical modelling, experiments withVibrio choleraand phylogenetic analysis to show that by eliminating nearby non-kin the T6SS may also favour cooperation among kin.
- Luke McNally
- , Eryn Bernardy
- & William C. Ratcliff
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Article
| Open AccessMicrobes can help explain the evolution of host altruism
The origins of altruism have fascinated us for centuries. Here, the authors propose that altruistic behaviour could be explained by microbes manipulating their hosts to act altruistically towards other hosts that may carry related microbes, and show that microbe-mediated altruism can evolve in a wide range of circumstances.
- Ohad Lewin-Epstein
- , Ranit Aharonov
- & Lilach Hadany
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Article
| Open AccessThe evolution of sex-specific virulence in infectious diseases
Many infectious diseases are more likely to progress to serious illness or death in men than in women, which has been attributed to a stronger immune response in women. Here, the authors propose that pathogen transmission from mother to child favours the evolution of lower virulence in women, and argue that the higher risk of HTLV-1 infection progressing to leukaemia in Japanese men is due to prolonged breastfeeding in Japan.
- Francisco Úbeda
- & Vincent A. A. Jansen