Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep

Efficient recycled algorithms for quantitative trait models on phylogenies

We present an efficient and flexible method for computing likelihoods of phenotypic traits on a phylogeny. The method does not resort to Monte-Carlo computation but instead blends Felsenstein's discrete character pruning algorithm with methods for numerical quadrature. It is not limited to Gaussian models and adapts readily to model uncertainty in the observed trait values. We demonstrate the framework by developing efficient algorithms for likelihood calculation and ancestral state reconstruction under Wright's threshold model, applying our methods to a dataset of trait data for extrafloral n…

A Statistical Test for Clades in Phylogenies

We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and the use of SPRs for heuristically finding maximum likelihood trees. Through a number of simulations with the Jukes-Cantor model on various topologies, it is observed that the SPR tests are informative, and reasonably fast compared to searching for the maximum likelihood tree. This suggests that the SPR tests would be a useful addition to the suite of existi…

Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies

Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPP), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPP lead …

LvD：一种计算系统发育树似然的新算法

LvD: A New Algorithm for Computing the Likelihood of a Phylogeny

LvD算法通过分解方法提高系统发育树似然计算效率，实现O(log n)时间复杂度，适用于各种核苷酸模型，并在实际应用中显著提升计算速度。

Extracting Conflict-free Information from Multi-labeled Trees

A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain conflict-free information that is of interest and yet is not obvious. We define the information content of a MUL-tree T as the set of all conflict-free quartet topologies implied by T, and define the maximal reduced form of T as the smallest tree that can be obtained from T by pruning leaves and contracting edges while retaining the same information content. We …