Related papers: The evolution of genetic architectures underlying …
Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation…
We consider a stochastic individual-based model for the evolution of a haploid, asexually reproducing population. The space of possible traits is given by the vertices of a (possibly directed) finite graph $G=(V,E)$. The evolution of the…
We examine the feasibility of predicting and subsequently managing the future evolution of a Complex Adaptive System. Our archetypal system mimics a competitive population of mechanical, biological, informational or human objects. We show…
In genome-wide association studies (GWASs), there is an increasing need for detecting the associations between a genetic variant and multiple traits. In studies of complex diseases, it is common to measure several potentially correlated…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
To understand the effect of assortative mating on the genetic evolution of a population, we consider a finite population in which each individual has a type, determined by a sequence of n diallelic loci. We assume that the population…
Evolution in finite populations is often modelled using the classical Moran process. Over the last ten years this methodology has been extended to structured populations using evolutionary graph theory. An important question in any such…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
The layout of multi-dimensional data can have a significant impact on the efficacy of hardware caches and, by extension, the performance of applications. Common multi-dimensional layouts include the canonical row-major and column-major…
We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping…
The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…
Evolutionary adaptation is the process that increases the fit of a population to the fitness landscape it inhabits. As a consequence, evolutionary dynamics is shaped, constrained, and channeled, by that fitness landscape. Much work has been…
Although a number of studies have shown that natural and laboratory populations initially well-adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…
During the founding of the field of quantitative genetics, Fisher formulated in 1918 his ``infinitesimal model'' that provided a novel mathematical framework to describe the Mendelian transmission of quantitative traits. If the infinitely…
The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century there have been remarkable advances in the development of theory for this diversification, and the theory's success…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…