Related papers: The case of the missing neutrality
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally…
We review the task of aligning simple models for language dynamics with relevant empirical data, motivated by the fact that this is rarely attempted in practice despite an abundance of abstract models. We propose that one way to meet this…
Although the origin of the fat-tail characteristic of the degree distribution in complex networks has been extensively researched, the underlying cause of the degree distribution characteristic across the complete range of degrees remains…
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals' fitness, usually the basic driving…
We propose a minimal model of the dynamics of diversity -- replicator equations with extinction, invasion and mutation. We numerically study the behavior of this simple model and show that it displays completely different behavior from the…
Mutualistic interactions, which are beneficial for both interacting species, are recurrently present in ecosystems. Observations of natural systems showed that, if we draw mutualistic relationships as binary links between species, the…
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a…
Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We…
Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with…
Despite its radical assumption of ecological equivalence between species, neutral biodiversity theory can often provide good fits to species abundance distributions observed in nature. Major criticisms of neutral theory have focused on…
Niche and neutral theory are two prevailing, yet much debated, ideas in ecology proposed to explain the patterns of biodiversity. Whereas niche theory emphasizes selective differences between species and interspecific interactions in…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we analyze a spatially-explicit neutral model based on…