Probabilistic models for the (sub)tree(s) of life
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Abstract: 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), culminating in the -family of Aldous' branching models. We next introduce real trees (trees as metric spaces) and show how to study them through their contour, provided they are properly measured and ordered. We then focus on the reduced tree, or coalescent tree, which is the tree spanned by individuals/species alive at the same fixed time. We show how reduced trees, like any compact ultrametric space, can be represented in a simple way via the so-called comb metric. Beautiful examples of random combs include the Kingman coalescent and coalescent point processes. We end up displaying some recent biological applications of coalescent point processes to the inference of species diversification, to conservation biology and to epidemiology.
Recommendations
- Probability and real trees. Ecole d'Eté de Probabilités de Saint-Flour XXXV -- 2005. Lecture given at the Saint-Flour probability summer school, July 6--23, 2005.
- Random trees. Abstracts from the workshop held January 18th -- January 24th, 2009.
- Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
- Phylogeny. Discrete and random processes in evolution
- Random ultrametric trees and applications
Cited in
(15)- Totally ordered measured trees and splitting trees with infinite variation
- Pruning the tree of life: \(k\)-core percolation as selection mechanism
- Trees within trees: simple nested coalescents
- The split-and-drift random graph, a null model for speciation
- Trees within trees. II: Nested fragmentations
- Revisiting Shao and Sokal's B₂ index of phylogenetic balance
- Random ultrametric trees and applications
- Reduced Critical Branching Processes for Small Populations
- scientific article; zbMATH DE number 2086868 (Why is no real title available?)
- Combinatorial and stochastic properties of ranked tree‐child networks
- A branching process with coalescence to model random phylogenetic networks
- Algebraic two-level measure trees
- The critical beta-splitting random tree. I: Heights and related results
- The coalescent of a sample from a binary branching process
- Ancestral diversity in fragmentation trees
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