EvoEvo workshop 2016

2nd EvoEvo workshop


Tuesday 20 Sep 2016

Satellite workshop of the 2016 Conference on Complex Systems

Beurs Van Berlage, Amsterdam, The Netherlands



Variation and Selection are the two core processes of Darwinian Evolution. Yet, both are directly regulated by many processes that are themselves products of evolution (e.g. DNA repair, mutator genes, transposable elements, horizontal transfer, stochasticity of gene expression, sex, network modularity, niche construction…). This results in the ability of evolution to self-modify its operators, hence its dynamics. We call this process “Evolution of Evolution” orEvoEvo. Different EvoEvo strategies have been proposed in the literature, including regulation of variability, robustness/evolvability strategies and bet-hedging, but finding traces of these strategies in extant organisms is difficult. Moreover all these strategies are likely to interact one with the others, blurring their respective outcomes. However, new tools are now available that help understanding EvoEvo. On the one hand, large scale bioinformatic data analysis can be used to recognize signatures of evolution of evolution. On the other hand, large scale computational modelling of multi-level evolution is now becoming feasible, and promises to shed light on the conditions under which evolutionary mechanisms evolve as well as their consequences.

The aim of the EvoEvo workshop is to seek for a unified theory of Evolution of Evolution and bring together researchers from various fields in computational biology to tackle this challenge. The workshop will take place as a satellite workshop of CCS 2016, Amsterdam, NL. The EvoEvo workshop is an initiative of the EvoEvo consortium funded by the FP7 EU-FET grant EvoEvo (ICT-610427).



9h30 – 9h50

Introduction talk: Paulien Hogeweg (Utrecht University)

What’s EvoEvo?

9h50 – 10h30

Invited talk: François Blanquart (Imperial College)

Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model?


10h30 – 11h
Coffee break

11h – 11h40

Invited talk: Nobuto Takeuchi (University of Tokyo)

The origin of genes through spontaneous symmetry breaking

11h40 – 13h

Contribution session 1 “EvoEvo at the molecular level”

11h40 – 12h Guillaume Beslon (Université de Lyon and Rhône-Alpes Complex Systems Institute, FR)
Evolvability drives innovation in viral genomes
12h – 12h20 Enrico Sandro Colizzi (Utrecht University, NL)
Mutational load is ameliorated by increased transcriptional load-associated mutations,
if these are biased towards duplications and deletions
12h20 – 12h40 Jacob Pieter Rutten (Utrecht University and Université de Lyon, NL)
Evolution of mutator populations in constant environments
12h40 – 13h Susan Stepney (University of York and York Centre for Complex Systems Analysis, UK)
Open-Endedness: Definitions and Shortcuts
13h – 14h45
Lunch & CCS Keynote Lecture

14h45 – 15h30

Invited talk: Eors Szathmary (Parmenides Center for the Concecptual Foundations of Science, Pullach/Munich, Germany)

Evolution of Evolvable Systems

15h30 – 16h30

Contribution session 2 “EvoEvo at the population level”

15h30 – 15h50 Charles Rocabert (INRIA Grenoble-Rhône Alpes, FR)
In-silico experimental evolution highlights the influence of environmental seasonality on bacterial diversification
15h50 – 16h10 Bram van Dijk (Utrecht University, NL)
Evolution of r- and K-selected species of Virtual Microbes: a case study in a simple fluctuating 2-resource environment
16h10 – 16h30 Simon Carrignon (Barcelona Supercomputing Center, SP)
Modeling the co-evolutionary dynamics of the Lobaria pulmonaria lichen symbiosis
16h30 – 17h
Coffee break

17h – 18h

Contribution session 3 “Using EvoEvo to built artificial systems”

17h – 17h20 Tim Hoverd (University of York and York Centre for Complex Systems Analysis, UK)
EvoMachina: a novel evolutionary algorithm inspired by bacterial genome reorganisation
17h20 – 17h40 Simon Hickinbotham (University of York, UK)
Evolution towards extinction in replicase models: inevitable unless…
17h40 – 18h Jonas Abernot (INRIA Grenoble-Rhône Alpes)
Physical interaction with automated music composition platforms



  • Guillaume Beslon, INSA-Lyon, Université de Lyon (FR), LIRIS/Beagle team
  • Santiago Elena, CSIC and Polytechnic University of Valencia (SP), IBMCP
  • Paulien Hogeweg, Utrecht University (NL), Bioinformatics group
  • Dominique Schneider, Université Grenoble Alpes (FR), TIMC-IMAG
  • Susan Stepney, University of York (UK), Centre for Complex Systems Analysis



Abstract for François Blanquart’s talk

Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model?

The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher’s model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher’s model was able to explain several statistical properties of the landscapes—including the mean and SD of selection and epistasis coefficients—it was often unable to explain the full structure of fitness landscapes.

Abstract for Nobuto Takeuchi’s talk

The origin of genes through spontaneous symmetry breaking

The heredity of the modern cell is provided by a small number of non-catalytic template molecules—the gene. This basic feature of modern-type heredity, however, is believed to have been absent at the earliest stages of evolution. The RNA world hypothesis posits that the heredity of the first, primitive cell (protocell, for short) was provided by a population of dual-functional molecules serving as both templates and catalysts. How could genes originate in protocells? Here, I will discuss the possibility that gene-like molecules emerge in protocells through spontaneous symmetry breaking between the complementary strands of replicating molecules. Our model assumes a population of primitive cells, each containing a population of replicating molecules. Protocells are selected towards maximizing the catalytic activity of internal molecules, whereas molecules tend to evolve towards minimizing it. This conflicting evolutionary tendencies at different levels induce symmetry breaking, whereby one strand of replicating molecules maintains catalytic activity and increases its copy number, whereas the other completely loses catalytic activity and decreases its copy number—like genes. The evolution of these gene-like molecules increases the equilibrium fitness of protocells. Our results implicate conflicting multilevel evolution as a key cause of the evolution of genetic complexity.

Abstract for Eors Szathmary’s talk

Evolution of Evolvable Systems

I shall survey experimental and theoretical results from an ERC Advanced project with that name (https://www.parmenides-foundation.org/research/projects/evoevo/). I shall focus on three issues:

  • Experimental approach to infrabiological systems,
  • Major transitions theory 2.0 (especially the filial transitions),
  • Learning in evolution versus Evolution in learning.





EvoEvo is an Information and Communication Technologies initiative funded by the European Commission under FP7.
Background image - Young Tree, 1932, Paul Klee