Related papers: Possible and Impossible Inferences From Reconstruc…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
To assess the number of life-bearing worlds in astrophysical environments, it is necessary to take the intertwined processes of abiogenesis (birth), extinction (death), and transfer of life (migration) into account. We construct a…
Most phylogenetic models assume that the evolutionary process is stationary and reversible. As a result, the root of the tree cannot be inferred as part of the analysis because the likelihood of the data does not depend on the position of…
Mortality is an instrument of natural selection. Evolutionary motivated theories imply its irreversibility and life history dependence. This is inconsistent with mortality data for protected populations. Accurate analysis yields mortality…
Different classes of phenomenological universalities of environment dependent growths have been proposed. The logistic as well as environment dependent West-type allometry based biological growth can be explained in this proposed framework…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
We outline a phenomenological theory of evolution and origin of life by combining the formalism of classical thermodynamics with a statistical description of learning. The maximum entropy principle constrained by the requirement for…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
This article presents a comprehensive study of the continuous McKendrick model, which serves as a foundational framework in population dynamics and epidemiology. The model is formulated through partial differential equations that describe…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data…
Evolutionary graph theory has grown to be an area of intense study. Despite the amount of interest in the field, it seems to have grown separate from other subfields of population genetics and evolution. In the current work I introduce the…
Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success.…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
We provide a theoretical framework to understand when firms may benefit from exploiting previously abandoned technologies and brands. We model for the long run process of innovation, allowing for sustainable diversity and comebacks of old…
We finely describe the "coming down from infinity" for birth and death processes which eventually become extinct. Our biological motivation is to study the decrease of regulated populations which are initially large. Under general…