Related papers: Quantifying the difference between phylogenetic di…
The dilemma which remained unsolved using Rao-Stirling diversity, namely of how variety and balance can be combined into "dual concept diversity" (Stirling, 1998, pp. 48f.) can be clarified by using Nijssen et al.'s (1998) argument that the…
Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be…
The demographic disparity of biometric systems has led to serious concerns regarding their societal impact as well as applicability of such systems in private and public domains. A quantitative evaluation of demographic fairness is an…
Given a collection $\tau$ of subsets of a finite set $X$, we say that $\tau$ is {\em phylogenetically flexible} if, for any collection $R$ of rooted phylogenetic trees whose leaf sets comprise the collection $\tau$, $R$ is compatible (i.e.…
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via automatic…
Phylogenetic comparative methods are new in our field and are shrouded, for most linguists, in at least a little mystery. Yet the path that led to their discovery in comparative biology is so similar to the methodological history of…
It follows from a classical result of Jordan that every tree with maximum degree at most $r$ containing a vertex set labeled by $[n]$, has a single-edge cut which separates two subsets $A,B \subset [n]$ for which $\min\{|A|,|B|\} \ge…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
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…
Texture can be defined as the change of image intensity that forms repetitive patterns, resulting from physical properties of the object's roughness or differences in a reflection on the surface. Considering that texture forms a complex…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
The Sackin index is an important measure for the balance of phylogenetic trees. We investigate two extensions of the Sackin index to the class of galled trees and two of its subclasses (simplex galled trees and normal galled trees) where we…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
Decomposition analysis is a critical tool for understanding the social and spatial dimensions of segregation and diversity. In this paper, I highlight the conceptual, mathematical, and empirical distinctions between segregation and…