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Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
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 study the portraits of isometries of rooted trees - the labelling of the tree, at each vertex, by the permutation of its descendants - in terms of languages. We characterize regularly branched self-similar groups in terms of…
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…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
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…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
Accurate and consistent methods for counting trees based on remote sensing data are needed to support sustainable forest management, assess climate change mitigation strategies, and build trust in tree carbon credits. Two-dimensional remote…
We propose a novel tree classification system called Treelogy, that fuses deep representations with hand-crafted features obtained from leaf images to perform leaf-based plant classification. Key to this system are segmentation of the leaf…
Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely…
Tree perception is an essential building block toward autonomous forestry operations. Current developments generally consider input data from lidar sensors to solve forest navigation, tree detection and diameter estimation problems. Whereas…