Related papers: Species tree inference from gene splits by Unroote…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
We propose a new topological invariant of unlabeled trees of N nodes. The invariant is a set of Nx2 matrices of integers, with sum_j k^{d_{i,j}} and v_i as the matrix elements, where d_{i,j} are the elements of the distance matrix and v_i…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
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…
Various modifications of decision trees have been extensively used during the past years due to their high efficiency and interpretability. Tree node splitting based on relevant feature selection is a key step of decision tree learning, at…
We study the efficiency of genus statistics in differentiating between different models of structure formation. Simple models which reproduce the salient features of the structure seeded by topological defects are examined. We consider…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…
For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…
We study the problem of inferring network topology from information cascades, in which the amount of time taken for information to diffuse across an edge in the network follows an unknown distribution. Unlike previous studies, which assume…
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),…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
Model performance is frequently reported only for the overall population under consideration. However, due to heterogeneity, overall performance measures often do not accurately represent model performance within specific subgroups. We…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Multitype branching processes with immigration in one type are used to model the dynamics of stage-structured plant populations. Parametric inference is first carried out when count data of all types are observed. Statistical…