Related papers: The case of the missing neutrality
The possibility of complicated dynamic behaviour driven by non-linear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility…
Mutualistic interactions are widespread in nature, from plant communities and microbiomes to human organizations. Along with competition for resources, cooperative interactions shape biodiversity and contribute to the robustness of complex…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
This paper is a step towards a systematic theory of the transitivity (clustering) phenomenon in random networks. A static framework is used, with adjacency matrix playing the role of the dynamical variable. Hence, our model is a matrix…
Most non-synonymous mutations are thought to be deleterious because of their effect on protein sequence. These polymorphisms are expected to be removed or kept at low frequency by the action of natural selection, and rare deleterious…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
A quasispecies is a set of interrelated genotypes that have reached a situation of equilibrium while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible…
We propose a novel network growth model coupled with the competition interaction to simulate macroevolution. Our work shows that the competition plays an important role in macroevolution and it is more rational to describe the interaction…
Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…
Research on the vulnerability of electric networks with a complex network approach has produced significant results in the last decade, especially for transmission networks. These studies have shown that there are causal relations between…
Understanding how systems can be designed to be evolvable is fundamental to research in optimization, evolution, and complex systems science. Many researchers have thus recognized the importance of evolvability, i.e. the ability to find new…
The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev.…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Recently it has been shown that a large variety of different networks have power-law (scale-free) distributions of connectivities. We investigate the robustness of such a distribution in discrete threshold networks under neutral evolution.…