相关论文: Tierra's missing neutrality: case solved
Does an ecological community allow stable coexistence? Identifying the general principles that determine the answer to this question is a central problem of theoretical ecology. Random matrix theory approaches have uncovered the general…
Quantifying the adaptive landscape in a given dynamical processes has been one of most important goals in theoretical biology. It can have immediate implications for many dynamical properties, such as robustness and plasticity. Based 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…
Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution, against a formal interpretation proposed…
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…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
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 origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
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…
Neutral dynamics, where taxa are assumed to be demographically equivalent and their abundance is governed solely by the stochasticity of the underlying birth-death process, has proved itself as an important minimal model that accounts for…
Ecological networks allow us to study the structure and function of ecosystems and gain insights on species resilience/stability. The study of this ecological networks is usually a snapshop focused in a limited specific range of space and…
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…
This article reviews and evaluates models of network evolution based on the notion of structural diversity. We show that diversity is an underlying theme of three principles of network evolution: the preferential attachment model,…
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…
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…
Similarity of competitors has been proposed to facilitate coexistence of species because it slows down competitive exclusion, thus making it easier for equalizing mechanisms to maintain diverse communities. On the other hand, chaos can…
A neutral ecology model is simulated on an island chain, in which neighbouring islands can exchange individuals but only the first island is able to receive immigrants from a metacommunity. It is found by several measures that biodiversity…
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…