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We adapt existing statistical modeling techniques for social networks to study consumption data observed in trophic food webs. These data describe the feeding volume (non-negative) among organisms grouped into nodes, called trophic species,…
Understanding how an extinction event affects ecosystem is fundamental to biodiversity conservation. For this reason, food web response to species loss has been investigated in several ways in the last years. Several studies focused on…
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical…
Few of food web theory hypotheses/predictions can be readily tested using empirical data. An exception is represented by simple probabilistic models for food web structure, for which the likelihood has been derived. Here I test the…
Real food web data available in the literature presents us with the relations between various species, sizes of these species, metabolic types of the species and other useful information, which allows us to define parameters for the…
Metacommunity theory is considered a promising approach for explaining species diversity and food web complexity. Recently Pillai et al. proposed a simple modeling framework for the dynamics of food webs at the metacommunity level. Here, we…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
We develop a stochastic, individual-based model for food web simulation which in the large-population limit reduces to the well-studied Webworld model, which has been used to successfully construct model food webs with several realistic…
We investigate in detail the model of a trophic web proposed by Amaral and Meyer [Phys. Rev. Lett. 82, 652 (1999)]. We focused on small-size systems that are relevant for real biological food webs and for which the fluctuations are playing…
Animal grouping behaviors have been widely studied due to their implications for understanding social intelligence, collective cognition, and potential applications in engineering, artificial intelligence, and robotics. An important…
Artificially evolving foraging behavior in simulated legged animals has proved to be a notoriously difficult task. Here, we co-evolve the morphology and controller for virtual organisms in a three-dimensional physically realistic…
The coupling between evolutionary and ecological changes (eco-evolutionary dynamics) has been shown to be relevant among diverse species, and is also of interest outside of ecology, i.e. in cancer evolution. These dynamics play an important…
Food webs represent the set of consumer-resource interactions among a set of species that co-occur in a habitat, but most food web studies have omitted parasites and their interactions. Recent studies have provided conflicting evidence on…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
One essential ingredient of evolutionary theory is the concept of fitness as a measure for a species' success in its living conditions. Here, we quantify the effect of environmental fluctuations onto fitness by analytical calculations on a…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Social network structures play an important role in the lives of animals by affecting individual fitness and the spread of disease and information. Nevertheless, we still lack a good understanding of how these structures emerge from the…