Related papers: Specieslike clusters based on identical ancestor p…
The idea that all life on earth traces back to a common beginning dates back at least to Charles Darwin's {\em Origin of Species}. Ever since, biologists have tried to piece together parts of this `tree of life' based on what we can observe…
In abstract terms, ecosystem ecology is about determining when two ecosystems, superficially different, are alike in some deeper way. An external observer can choose any ecosystem property as being important. In contrast, two ecosystems are…
It is now commonly accepted that globular clusters (GCs) have undergone a complex formation and that they host at least two stellar generations. This is a recent paradigm and is founded on both photometric and spectroscopic evidence. We…
Existential rules, long known as tuple-generating dependencies in database theory, have been intensively studied in the last decade as a powerful formalism to represent ontological knowledge in the context of ontology-based query answering.…
The Hubble tuning fork diagram, based on morphology, has always been the preferred scheme for classification of galaxies and is still the only one originally built from historical/evolutionary relationships. At the opposite, biologists have…
Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
The Union Closed Sets Conjecture states that in every finite, nontrivial set family closed under taking unions there is an element contained in at least half of all the sets of the family. We investigate two new directions with respect to…
Single-level density-based approach has long been widely acknowledged to be a conceptually and mathematically convincing clustering method. In this paper, we propose an algorithm called "best-scored clustering forest" that can obtain the…
We consider the problem of characterizing isomorphisms of types, or, equivalently, constructive cardinality of sets, in the simultaneous presence of disjoint unions, Cartesian products, and exponentials. Mostly relying on results about…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
This is the second of two papers dedicated to the relationship between population models of competition and biodiversity. Here we consider species assembly models where the population dynamics is kept far from fixed points through the…
We investigate how the pattern of contacts between species in mutualistic ecosystems is affected by the phylogenetic proximity between the species of each guild. We develop several theoretical tools to measure that effect and we use them to…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…
We describe a framework for encoding cluster combinatorics using categorical methods. We give a definition of an abstract cluster structure, which captures the essence of cluster mutation at a tropical level and show that cluster algebras,…
Components of complex systems are often classified according to the way they interact with each other. In graph theory such groups are known as clusters or communities. Many different techniques have been recently proposed to detect them,…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…