Combinatorial and stochastic properties of ranked tree‐child networks
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Publication:6074698
Abstract: Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical properties, many combinatorial questions concerning them remain intractable. In this paper, we show that endowing these networks with a biologically relevant ranking structure yields mathematically tractable objects, which we term ranked tree-child networks (RTCNs). We explain how to derive exact and explicit combinatorial results concerning the enumeration and generation of these networks. We also explore probabilistic questions concerning the properties of RTCNs when they are sampled uniformly at random. These questions include the lengths of random walks between the root and leaves (both from the root to the leaves and from a leaf to the root); the distribution of the number of cherries in the network; and sampling RTCNs conditional on displaying a given tree. We also formulate a conjecture regarding the scaling limit of the process that counts the number of lineages in the ancestry of a leaf. The main idea in this paper, namely using ranking as a way to achieve combinatorial tractability, may also extend to other classes of networks.
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Cites work
- A bound for the distribution of the sum of discrete associated or negatively associated random variables.
- Combinatorial stochastic processes. Ecole d'Eté de Probabilités de Saint-Flour XXXII -- 2002.
- Counting and enumerating tree-child networks and their subclasses
- Counting phylogenetic networks
- Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks
- Fundamentals of Stein's method
- scientific article; zbMATH DE number 52632 (Why is no real title available?)
- scientific article; zbMATH DE number 1099195 (Why is no real title available?)
- scientific article; zbMATH DE number 2237386 (Why is no real title available?)
- On the asymptotic growth of the number of tree-child networks
- Phylogeny. Discrete and random processes in evolution
- Probabilistic models for the (sub)tree(s) of life
- Properties of phylogenetic trees generated by Yule-type speciation models
- Stochastic Calculus
- Unique determination of some homoplasies at hybridization events
Cited in
(20)- On the performance of randomized embedding of reproduction trees in static networks
- Asymptotic enumeration and distributional properties of galled networks
- Bijections for ranked tree-child networks
- Counting phylogenetic networks with few reticulation vertices: a second approach
- Distributions of cherries and pitchforks for the Ford model
- Enumeration of rooted binary unlabeled galled trees
- A branching process with coalescence to model random phylogenetic networks
- Limit theorems for patterns in ranked tree‐child networks
- A lattice structure for ancestral configurations arising from the relationship between gene trees and species trees
- The space of equidistant phylogenetic cactuses
- Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees
- Enumerative and distributional results for d-combining tree-child networks
- Counting rankings of tree-child networks
- Asymptotic enumeration of rooted binary unlabeled galled trees with a fixed number of galls
- Spaces of ranked tree-child networks
- Asymptotic enumeration of normal and hybridization networks via tree decoration
- Lifted inference beyond first-order logic
- Sackin indices for labeled and unlabeled classes of galled trees
- Combinatorial comparison of general galled trees, time-consistent galled trees, and simplex time-consistent galled trees
- Enumerative combinatorics of unlabeled and labeled time-consistent galled trees
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