Filippo Disanto

Exact enumeration of cherries and pitchforks in ranked trees under the coalescent model

We consider exact enumerations and probabilistic properties of ranked trees when generated under the random coalescent process. Using a new approach, based on generating functions, we derive several statistics such as the exact probability of finding k cherries in a ranked tree of fixed size n. We then extend our method to consider also the number of pitchforks. We find a recursive formula to calculate the joint and conditional probabilities of cherries and pitchforks when the size of the tree is fixed. These results provide insights into structural properties of coalescent trees under the model of neutral evolution.

The Effect of Single Recombination Events on Coalescent Tree Height and Shape

The coalescent with recombination is a fundamental model to describe the genealogical history of DNA sequence samples from recombining organisms. Considering recombination as a process which acts along genomes and which creates sequence segments with shared ancestry, we study the influence of single recombination events upon tree characteristics of the coalescent. We focus on properties such as tree height and tree balance and quantify analytically the changes in these quantities incurred by recombination in terms of probability distributions. We find that changes in tree topology are often relatively mild under conditions of neutral evolution, while changes in tree height are on average quite large. Our results add to a quantitative understanding of the spatial coalescent and provide the neutral reference to which the impact by other evolutionary scenarios, for instance tree distortion by selective sweeps, can be compared.

Catalan structures and Catalan pairs

A Catalan pair is a pair of binary relations (S,R) satisfying some axioms. These pairs are enumerated by the well-known Catalan numbers, and have been introduced in Disanto et al. (2010) [2] with the aim of giving a common language to many structures counted by Catalan numbers. Here, a simple method is given to pass from the recursive definition of a generic Catalan structure to the recursive definition of the Catalan pair on the same structure, thus giving an automatic way of interpreting Catalan structures in terms of Catalan pairs. Our method is applied to several well-known Catalan structures, focusing on the combinatorial meaning of the relations S and R in each case considered.

Yule-generated trees constrained by node imbalance.

The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance is defined by an integer 0 ≤ ω. For caterpillars, the extreme case of unbalanced trees, ω = 0. Under models of neutral evolution, for instance the Yule model, trees with small ω are unlikely to occur by chance. Indeed, imbalance can be a signature of permanent selection pressure, such as observable in the genealogies of certain pathogens. From a mathematical point of view it is interesting to observe that the space of Ω-trees maintains several statistical invariants although it is drastically reduced in size compared to the space of unconstrained Yule trees. Using generating functions, we study here some basic combinatorial properties of Ω-trees. We focus on the distribution of the number of subtrees with two leaves. We show that expectation and variance of this distribution match those for unconstrained trees already for very small values of ω.

Catalan Lattices on Series Parallel Interval Orders

Using the notion of series parallel interval order, we propose a unified setting to describe Dyck lattices and Tamari lattices (two well-known lattice structures on Catalan objects) in terms of basic notions of the theory of posets. As a consequence of our approach, we find an extremely simple proof of the fact that the Dyck order is a refinement of the Tamari one. Moreover, we provide a description of both the weak and the strong Bruhat order on 312-avoiding permutations, by recovering the proof of the fact that they are isomorphic to the Tamari and the Dyck order, respectively; our proof, which simplifies the existing ones, relies on our results on series parallel interval orders.

Combinatorial properties of Catalan pairs

We define the notion of a Catalan pair, which is a pair of (strict) order relations (S,R) satisfying certain axioms. We show that Catalan pairs of size n are counted by Catalan numbers. We study some combinatorial properties of the relations R and S. In particular, we show that the second component R uniquely determines the pair, and we give a characterization of the poset R in terms of forbidden configurations. We also propose some generalizations of Catalan pairs arising from the modification of one of the axioms.

Permutations with few internal points

Abstract Let the records of a permutation σ be its left-right minima, right-left minima, left-right maxima and right-left maxima. Conversely let a point ( i , j ) with j = σ ( i ) be an internal point of σ if it is not a record. Permutations without internal points have recently attracted attention under the name square permutations. We consider here the enumeration of permutations with a fixed number of internal points. We show that for each fixed i the generating function of permutations with i internal points with respect to the size is algebraic of degree 2. More precisely it is a rational function in the Catalan generating function. Our approach is constructive, yielding a polynomial uniform random sampling algorithm, and it can be refined to enumerate permutations with respect to each of the four types of records.