Related papers: Totally Ordered Measured Trees and Splitting Trees…
The monadic second-order theory of trees allows quantification over elements and over arbitrary subsets. We classify the class of trees with respect to the question: does a tree T have definable Skolem functions (by a monadic formula with…
We discuss several connections between discrete and continuous random trees. In the discrete setting, we focus on Galton-Watson trees under various conditionings. In particular, we present a simple approach to Aldous' theorem giving the…
Any Boolean function corresponds with a complete full binary decision tree. This tree can in turn be represented in a maximally compact form as a direct acyclic graph where common subtrees are factored and shared, keeping only one copy of…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
Random-cluster measures on infinite regular trees are studied in conjunction with a general type of `boundary condition', namely an equivalence relation on the set of infinite paths of the tree. The uniqueness and non-uniqueness of…
We consider a population model where individuals behave independently from each other and whose genealogy is described by a chronological tree called splitting tree. The individuals have i.i.d. (non-exponential) lifetime durations and give…
In [Aldous,Pitman,1998] a tree-valued Markov chain is derived by pruning off more and more subtrees along the edges of a Galton-Watson tree. More recently, in [Abraham,Delmas,2012], a continuous analogue of the tree-valued pruning dynamics…
We formalize an existing computability-theoretic method of presenting first-order structures whose domains have the cardinality of the continuum. Work using these methods until now has emphasized their topological properties. We shift the…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
We define symmetric and asymmetric branching trees, a class of processes particularly suited for modeling genealogies of inhomogeneous populations where individuals may reproduce throughout life. In this framework, a broad class of…
We show that the genealogy of any self-similar fragmentation process can be encoded in a compact measured real tree. Under some Malthusian hypotheses, we compute the fractal Hausdorff dimension of this tree through the use of a natural…
We study the local convergence of critical Galton-Watson trees and Levy trees under various conditionings. Assuming a very general monotonicity property on the functional of random trees, we show that random trees conditioned to have large…