Related papers: Assortativity in sympatric speciation and species …
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
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…
Single species population models and discrete stochastic gene frequency models are two standards of mathematical biology important for the evolution of populations. An agent based model is presented which reproduces these models and then…
We study the genetic behaviour of a population formed by haploid individuals which reproduce asexually. The genetic information for each individual is stored along a bit-string (or chromosome) with L bits, where 0-bits represent the…
We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate \lambda. We…
The outcome of competition among species is influenced by the spatial distribution of species and effects such as demographic stochasticity, immigration fluxes, and the existence of preferred habitats. We introduce an individual-based model…
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for…
The degree-degree correlation is crucial in understanding the structural properties of and dynamics occurring upon network, and is often measured by the assortativity coefficient $r$. In this paper, we first study this measure in detail and…
Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is developed using cell death or apoptosis in heterogeneous cell…
When studying the dynamics of trait distribution of populations in a heterogeneous environment, classical models from quantitative genetics choose to look at its system of moments, specifically the first two ones. Additionally, in order to…
In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…
Situations involving cooperative behaviour are widespread among animals and humans alike. Game theory and evolutionary dynamics have provided the theoretical and computational grounds to understand what are the mechanisms that allow for…
Core-periphery is a key feature of large-scale networks underlying a wide range of social, biological, and transportation phenomena. Despite its prevalence in empirical data, it is unclear whether this property is a consequence of more…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model…
The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment…
Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin…
This thesis responds to the challenges of using a large number, such as thousands, of features in regression and classification problems. There are two situations where such high dimensional features arise. One is when high dimensional…