Related papers: Neutral phylogenetic models and their role in tree…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
We study a stochastic community model able to interpolate from a neutral regime to a niche partitioned regime upon varying a single parameter tuning the intensity of niche stabilization, namely the difference between intraspecific and…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…
Cyclic dominance of species has been identified as a potential mechanism to maintain biodiversity, see e.g. B. Kerr, M. A. Riley, M. W. Feldman and B. J. M. Bohannan [Nature {\bf 418}, 171 (2002)] and B. Kirkup and M. A. Riley [Nature {\bf…
In tropical regions, fires propagate readily in grasslands but typically consume only edges of forest patches. Thus forest patches grow due to tree propagation and shrink by fires in surrounding grasslands. The interplay between these…
This work investigates how biodiversity is affected in a cyclic spatial May-Leonard model with hierarchical and non-hierarchical rules. Here we propose a generalization of the traditional rock-paper-scissors model by considering highly…
According to the competitive exclusion principle, in a finite ecosystem, extinction occurs naturally when two or more species compete for the same resources. An important question that arises is: when coexistence is not possible, which…
The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of…
Phenotypic plasticity and its evolution may help evolutionary rescue in a novel and stressful environment, especially if environmental novelty reveals cryptic genetic variation that enables the evolution of increased plasticity. However,…
Competition is the main driver of population dynamics, which shapes the genetic composition of populations and the assembly of ecological communities. Neutral models assume that all the individuals are equivalent and that the dynamics is…
Measures of biodiversity change such as the Living Planet Index describe proportional change in the abundance of a typical species, which can be thought of as change in the size of a community. Here, I discuss the orthogonal concept of…
Positive density-dependence occurs when individuals experience increased survivorship, growth, or reproduction with increased population densities. Mechanisms leading to these positive relationships include mate limitation, saturating…
We study a model of a multi-species ecosystem described by Lotka-Volterra-like equations. Interactions among species form a network whose evolution is determined by the dynamics of the model. Numerical simulations show power-law…
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…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens in a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under…
We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…
Biodiversity widely observed in ecological systems is attributed to the dynamical balance among the competing species. The time-varying populations of the interacting species are often captured rather well by a set of deterministic…