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The concept of neutral evolutionary networks being a significant factor in evolutionary dynamics was first proposed by Huynen {\em et al.} about 7 years ago. In one sense, the principle is easy to state -- because most mutations to an…
Evolutionary game dynamics is one of the most fruitful frameworks for studying evolution in different disciplines, from Biology to Economics. Within this context, the approach of choice for many researchers is the so-called replicator…
The rise of trait-based ecology has led to an increased focus on the distribution and dynamics of traits in communities. However, a general theory of trait-based ecology, that can apply across different scales (e.g., species that differ in…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
Policy gradient is a generic and flexible reinforcement learning approach that generally enjoys simplicity in analysis, implementation, and deployment. In the last few decades, this approach has been extensively advanced for fully…
It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer…
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
The delayed logistic equation (also known as Hutchinson's equation or Wright's equation) was originally introduced to explain oscillatory phenomena in ecological dynamics. While it motivated the development of a large number of mathematical…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
If the gradient of a probability distribution on a landscape of vacua aligns with the variation of some fundamental parameter, the parameter may be likely to take some non-generic value. Such non-generic values can be associated to critical…
An increasing number of dissident voices claim that the standard neo-Darwinian view of genes as 'leaders' and phenotypes as 'followers' during the process of adaptive evolution should be turned on its head. This idea is older than the…
Despite the significant recent progress in deep generative models, the underlying structure of their latent spaces is still poorly understood, thereby making the task of performing semantically meaningful latent traversals an open research…
Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock…
We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic…
In the present article the recent works to formulate laws in Darwinian evolutionary dynamics are discussed. Although there is a strong consensus that general laws in biology may exist, opinions opposing such suggestion are abundant. Based…
The long-time evolution of a system in interaction with an external environment is usually described by a family of linear maps g_t, generated by master equations of Block-Redfield type. These maps are in general non-positive; a widely…
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…
The purpose of this roadmap article is to draw attention to a paradigm shift in our understanding of evolution towards a perspective of ecological-evolutionary feedback, highlighted through two recent highly simplified examples of rapid…
Our planet is experiencing an accelerated process of change associated to a variety of anthropogenic phenomena. The future of this transformation is uncertain, but there is general agreement about its negative unfolding that might threaten…