We revisit representation theory in type A, used previously to establish that the dissimilarity vectors of phylogenetic trees are points on the tropical Grassmannian variety. We use a different version of this construction to show that the space of phylogenetic trees Kn maps to the tropical varieties of every flag variety of GLn(C). Using this map, we find a tropical function on the space of ph...

1Texas Natural Science Center, 2400 Trinity Street, University of Texas, Austin TX 78619, U.S.A. 2Section of Integrative Biology, The University of Texas at Austin, 1 University Station (A6700), Austin, TX 78712, U.S.A. 3Plant Biology Graduate Program, The University of Texas at Austin, 1 University Station (A6700), Austin, TX 78712, U.S.A. 4Institute of Cellular and Molecular Biology, The Univ...

We present a system for the large scale induction of cognate groups. Our model explains the evolution of cognates as a sequence of mutations and innovations along a phylogeny. On the task of identifying cognates from over 21,000 words in 218 different languages from the Oceanic language family, our model achieves a cluster purity score over 91%, while maintaining pairwise recall over 62%.

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of ...

Resolving Hydractiniidae and Hydroidolina Phylogeny using Mitochondrial Genomes by Erica Dawn Blight Department of Biology Duke University Date:_______________________ Approved: ___________________________ Clifford W. Cunningham , Supervisor ___________________________ Kathleen M. Pryer ___________________________ Paul S. Manos ___________________________ Gregory A. Wray _______________________...

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phy-logenetics is the study of species evolution. A major goal of the field is to establish evolutionaryrelationships within groups of species, in order to infer the topology of an evolutionary treeformed by this group and common ancestors to some of these species.In this context, having means...