Related papers: Specieslike clusters based on identical ancestor p…
Consider a continuous-time binary branching process conditioned to have population size n at some time t, and with a chance p for recording each extinct individual in the process. Within the family tree of this process, we consider the…
Darwin claims in the {\em Origin} that similarity is evidence for common ancestry, but that adaptive similarities are "almost valueless" as evidence. This claim seems reasonable for some adaptive similarities but not for others. Here we…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
The problem of clustering is considered, for the case when each data point is a sample generated by a stationary ergodic process. We propose a very natural asymptotic notion of consistency, and show that simple consistent algorithms exist,…
The problem of clustering is considered, for the case when each data point is a sample generated by a stationary ergodic process. We propose a very natural asymptotic notion of consistency, and show that simple consistent algorithms exist,…
Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for…
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have…
Cluster analysis requires many decisions: the clustering method and the implied reference model, the number of clusters and, often, several hyper-parameters and algorithms' tunings. In practice, one produces several partitions, and a final…
Source-sink systems are metapopulations of patches that can be of variable habitat quality. They can be seen as graphs, where vertices represent the patches, and the weighted oriented edges give the probability of dispersal from one patch…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
We propose a variation of the GMS model of evolution of species. In this version, as in the GMS model, at each birth, the new species in the system is labeled with a random fitness mark, but in our variation, to each extinction event is…
Two new criteria, that involve the microscopic dynamics of the system, are proposed for the identification of clusters in continuum systems. The first one considers a residence time in the definition of the bond between pairs of particles,…
This paper provides a complete suite of axioms for a version of set theory that I call Explication. Explication borrows from the two most prominent existing systems of set theory. Explication starts with class variables. After several…
Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify…
If predictions for species extinctions hold, then the `tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as…
Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…
After surveying classical results, we introduce a generalized notion of inference system to support structural recursion on non-well-founded data types. Besides axioms and inference rules with the usual meaning, a generalized inference…
This paper considers networks where relationships between nodes are represented by directed dissimilarities. The goal is to study methods for the determination of hierarchical clusters, i.e., a family of nested partitions indexed by a…
We introduce a generalized notion of inference system to support more flexible interpretations of recursive definitions. Besides axioms and inference rules with the usual meaning, we allow also coaxioms, which are, intuitively, axioms which…
The aim of this paper is to offer the first systematic exploration and definition of equivalent causal models in the context where both models are not made up of the same variables. The idea is that two models are equivalent when they agree…