Related papers: Distribution of phylogenetic diversity under rando…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Many species see their range shifted poleward in response to global warming and need to keep pace in order to survive. To understand the effect of climate change on species ranges and its consequences on population dynamics, we consider a…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Difficulties identifying appropriate biodiversity impact metrics remain a major barrier to inclusion of biodiversity considerations in environmentally responsible investment. We propose and analyse a simple science-based local metric: the…
Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because…
For taxonomic levels higher than species, the abundance distributions of number of subtaxa per taxon tend to approximate power laws, but often show strong deviationns from such a law. Previously, these deviations were attributed to…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Possibility to establish macroscopic phenomenological theory for biological systems, akin to the akin to the well-established framework of thermodynamics, is briefly reviewed. We introduce the concept of an evolutionary fluctuation-response…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
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…
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…
We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic, symmetric, finite site model of…
The random diffusion model is a continuum model for a conserved scalar density field driven by diffusive dynamics where the bare diffusion coefficient is density dependent. We generalize the model from one with a sharp wavenumber cutoff to…