Related papers: Specieslike clusters based on identical ancestor p…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Although geographic isolation has been shown to play a key role in promoting reproductive isolation, it is now believed that speciation can also happen in sympatry and with considerable gene flow. Here we present a model of sympatric…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
We consider a stationary random field indexed by an increasing sequence of subsets of $\mathbb{Z}^d$ obeying a very broad geometrical assumption on how the sequence expands. Under certain mixing and local conditions, we show how the tail…
Cluster analysis has attracted more and more attention in the field of machine learning and data mining. Numerous clustering algorithms have been proposed and are being developed due to diverse theories and various requirements of emerging…
We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend…
We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime [Van Valen, L.,…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
We propose some axioms for hierarchical clustering of probability measures and investigate their ramifications. The basic idea is to let the user stipulate the clusters for some elementary measures. This is done without the need of any…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
A computational theory for clustering and a semi-supervised clustering algorithm is presented. Clustering is defined to be the obtainment of groupings of data such that each group contains no anomalies with respect to a chosen grouping…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
Self-similarity is the property of a system being similar to a part of itself. We posit that a special class of behaviourally self-similar systems exhibits a degree of resilience to adversarial behaviour. We formalise the notions of system,…
If evolution can be connected to the principle of least action, and if it is depicted in evolution space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate…