Related papers: Necessary and sufficient conditions for consistent…
We consider the problem of inferring an ancestral state from observations at the leaves of a tree, assuming the state evolves along the tree according to a two-state symmetric Markov process. We establish a general branching rate condition…
Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the…
For a tree Markov random field non-reconstruction is said to hold if as the depth of the tree goes to infinity the information that a typical configuration at the leaves gives about the value at the root goes to zero. The distribution of…
Consider a Markov chain $(\xi_v)_{v \in V} \in [k]^V$ on the infinite $b$-ary tree $T = (V,E)$ with irreducible edge transition matrix $M$, where $b \geq 2$, $k \geq 2$ and $[k] = \{1,...,k\}$. We denote by $L_n$ the level-$n$ vertices of…
Consider a Markov chain on an infinite tree T=(V,E) rooted at \rho. In such a chain, once the initial root state \sigma(\rho) is chosen, each vertex iteratively chooses its state from the one of its parent by an application of a Markov…
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…
In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
We introduce regenerative tree growth processes as consistent families of random trees with n labelled leaves, n>=1, with a regenerative property at branch points. This framework includes growth processes for exchangeably labelled Markov…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
A stochastic forest model of young and old age class trees is studied. First, we prove existence, uniqueness and boundedness of global nonnegative solutions. Second, we investigate asymptotic behavior of solutions by giving a sufficient…
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…
Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely…
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree,…
Consider a collection of random variables attached to the vertices of a graph. The reconstruction problem requires to estimate one of them given `far away' observations. Several theoretical results (and simple algorithms) are available when…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a…
Consider $k$-colorings of the complete tree of depth $\ell$ and branching factor $\Delta$. If we fix the coloring of the leaves, as $\ell$ tends to $\infty$, for what range of $k$ is the root uniformly distributed over all $k$ colors? This…
In this work, we give a description of all sigma-finite measures on the space of rooted compact real trees which satisfy a certain regenerative property. We show that any infinite measure which satisfies the regenerative property is the…