Related papers: Predicting the ancestral character changes in a tr…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…
If one goes backward in time, the number of ancestors of an individual doubles at each generation. This exponential growth very quickly exceeds the population size, when this size is finite. As a consequence, the ancestors of a given…
Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…