Related papers: Species Trees Forcing Parsimony to Fail
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Consider a random recusive tree with n vertices. We show that the number of vertices with even depth is asymptotically normal as n tends to infinty. The same is true for the number of vertices of depth divisible by m for m=3, 4 or 5; in all…
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…
Trees without vertices of degree $2$ are sometimes named topological trees. In this work, we bring forward the study of the inducibility of (rooted) topological trees with a given number of leaves. The inducibility of a topological tree $S$…
The parsimony score of a character on a tree equals the number of state changes required to fit that character onto the tree. We show that for unordered, reversible characters this score equals the number of tree rearrangements required to…
Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
Besides serving as prediction models, classification trees are useful for finding important predictor variables and identifying interesting subgroups in the data. These functions can be compromised by weak split selection algorithms that…
We prove non-asymptotic stretched exponential tail bounds on the height of a randomly sampled node in a random combinatorial tree, which we use to prove bounds on the heights and widths of random trees from a variety of models. Our results…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Tree spanners approximate distances within graphs; a subtree of a graph is a tree $t$-spanner of the graph if and only if for every pair of vertices their distance in the subtree is at most $t$ times their distance in the graph. When a…
The pseudoforest version of the Strong Nine Dragon Tree Conjecture states that if a graph $G$ has maximum average degree $\text{mad}(G) = 2 \max_{H \subseteq G} \frac{e(G)}{v(G)}$ at most $2(k + \frac{d}{k+d+1})$, then it has a…
We study the fundamental question of how likely it is that two randomly chosen trees are isomorphic to each other for different models of random trees. We show that the probability decays exponentially for rooted labeled trees as well as…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…