Empirical fitness landscapes reveal accessible evolutionary paths

  title={Empirical fitness landscapes reveal accessible evolutionary paths},
  author={Frank J. Poelwijk and Daniel J. Kiviet and Daniel M. Weinreich and Sander J. Tans},
When attempting to understand evolution, we traditionally rely on analysing evolutionary outcomes, despite the fact that unseen intermediates determine its course. A handful of recent studies has begun to explore these intermediate evolutionary forms, which can be reconstructed in the laboratory. With this first view on empirical evolutionary landscapes, we can now finally start asking why particular evolutionary paths are taken. 

Fitness Landscapes and Evolutionary Dynamics

This key note considers fitness landscapes and their use for understanding evolutionary dynamics in natural and artificial biological systems, with a main focus on evolutionary biology and evolutionary computation.

Revealing evolutionary pathways by fitness landscape reconstruction

This recent and timely marriage between systems biology and evolutionary biology is reviewed, which holds the promise to understand evolutionary dynamics in a more mechanistic and predictive manner.

Frontiers of Fitness Landscapes: A Summary of Open Questions

This chapter discusses challenges to a fitness landscape approach that result from recent experimental and theoretical findings about the information transfer in biological systems and sets out opportunities these results may open up.

The Changing Geometry of a Fitness Landscape Along an Adaptive Walk

It is shown that the relative prevalence of the various kinds of epistasis varies along an adaptive walk, and a simple and general explanation is proposed, confirming the role of mean regression.

What can we learn from fitness landscapes?

  • D. Hartl
  • Biology
    Current opinion in microbiology
  • 2014

Fitness Landscapes: From Evolutionary Biology to Evolutionary Computation

This chapter gives an introduction to the book and an overview of fundamental concepts, notions and mathematical descriptions of fitness landscapes and examples of computational and empirical landscapes are introduced.

Replaying the Tape of Life: Quantification of the Predictability of Evolution

It is becoming clear that evolutionary trajectories in static correlated fitness landscapes are substantially non-random but the relative contributions of determinism and stochasticity in the evolution of specific phenotypes strongly depend on the specific conditions, particularly the magnitude of the selective pressure and the number of available beneficial mutations.

Exploring protein fitness landscapes by directed evolution

Directed evolution studies have shown how rapidly some proteins can evolve under strong selection pressures and, because the entire 'fossil record' of evolutionary intermediates is available for detailed study, they have provided new insight into the relationship between sequence and function.

The competition between simple and complex evolutionary trajectories in asexual populations

The probability of valley crossing depends nonmonotonically on population size: intermediate size populations are most likely to follow a “greedy” strategy of acquiring immediately beneficial mutations even if they lead to evolutionary dead ends, while larger and smaller populations are more likely to cross fitness valleys to reach distant advantageous genotypes.

Repeatability of evolution on epistatic landscapes

This work investigates the mutational path probabilities of systems having epistatic effects on both fitness and mutation rates using a theoretical and computational framework and allows epistatic interactions to also affect mutation rates to create qualitatively non-trivial dynamics.



Metastable evolutionary dynamics: Crossing fitness barriers or escaping via neutral paths?

The analysis shows that crossing entropy barriers is faster by orders of magnitude than fitness barrier crossing, and when populations are trapped in a metastable phenotypic state, they are most likely to escape by crossing an entropy barrier, along a neutral path in genotype space.

Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments

It is shown that stochastic switching can be favored over sensing when the environment changes infrequently, and the optimal switching rates then mimic the statistics of environmental changes.

Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data

This analysis indicates that when a duplicated repressor co-diverges together with its binding site, the fitness landscape allows funneling to a new regulatory interaction with early increases in fitness, and finds that neutral mutations do not play an essential role.


The theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

It is demonstrated that 102 mutational trajectories linking β-lactamase alleles are inaccessible to Darwinian selection and that many of the remaining trajectories have negligible probabilities of realization, which implies that the protein tape of life may be largely reproducible and even predictable.

Resurrecting ancient genes: experimental analysis of extinct molecules

Ancient genes can now be reconstructed, expressed and functionally characterized, thanks to improved techniques for inferring and synthesizing ancestral sequences, and offers a powerful new way to empirically test hypotheses about the function of genes from the deep evolutionary past.

Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

The dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation are examined, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations are examined.

The Selective Cause of an Ancient Adaptation

The wildtype gene encoding the NADP‐dependent isocitrate dehydrogenase of Escherichia coli is replaced by an engineered one possessing the ancestral NAD‐dependent phenotype and the metabolic basis of an ancient adaptive event is revealed.

Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing

The existence of variants that are more stable than the extant proteins suggests that selection for maximum thermostability may not have been an important factor in the evolution of this enzyme.

Protein stability promotes evolvability.

This work uses simulations with model lattice proteins to demonstrate how extra stability increases evolvability by allowing a protein to accept a wider range of beneficial mutations while still folding to its native structure.