Abstract : Phylogenetic trees and networks are used to elucidate the evolutionary history of genes or species. Data proliferation due to recent technological advancements has led to the pursuit of more efficient algorithms and novel approaches. Advances in the area can lead to breakthroughs in various disciplines of biology and life sciences, including genetics, cell biology, zoology, botany, microbiology, epidemiology, drug discovery, and biodiversity conservation, to name a few. This mini-symposium will cover recent topics related to phylogenetic research, from both theoretical and practical viewpoints, with results from algebra, algorithms, bioinformatics, combinatorics, computational complexity, geometry, statistics, and software development.
[04132] Navigating the Frontiers of Phylogenetic Research: Challenges and Applications
Format : Talk at Waseda University
Author(s) :
Momoko Hayamizu (Department of Applied Mathematics, Waseda University)
Abstract : This talk serves as an introduction to our mini-symposium on phylogenetic research. It emphasizes key challenges and applications in this rapidly evolving field from both theoretical and biological perspectives. After providing a brief overview of the symposium topics and presentations, I will discuss some of the recent results and open problems related to phylogenetic trees and networks, with a focus on combinatorial and algorithmic approaches.
[05050] Advances and challenges in statistical inference of phylogenetic networks
Format : Online Talk on Zoom
Author(s) :
Luay Nakhleh (Rice University)
Abstract : Evolutionary analyses of various groups of eukaryotic species have revealed evidence for reticulation. Reticulate evolutionary histories are best represented as phylogenetic networks. I will describe the multispecies network coalescent (MSNC) model, which allows for modeling vertical and horizontal evolutionary processes acting within and across species boundaries. I will then discuss progress we have made on developing statistical inference methods under the MSNC as well as challenges facing the inference in practice.
[03613] The Tree of Blobs of a Species Network: Identifiability
Format : Online Talk on Zoom
Author(s) :
Hector D Banos (California State University San Bernardino)
Elizabeth S Allman (University of Alaska Fairbanks)
John A Rhodes (University of Alaska Fairbanks)
Jonathan D Mitchell (Univeristy of Tasmania)
Abstract : As genealogical analyses of DNA data have progressed, more evidence has appeared showing that hybridization is often an important factor in evolution. Hybridization has played a crucial role in the evolutionary history of plants, some groups of fish, and frogs, among other species. In such cases, networks are the objects used to represent the relationships between species. The network multispecies coalescent model is a standard probabilistic model describing the formation of gene trees in the presence of hybridization and incomplete lineage sorting. We present a step toward inferring a general species network by showing the identifiability of its tree of blobs, in which all 'hybrid species relationships' are contracted to nodes, so only tree-like relationships between the taxa are shown.
[03991] Identifiability of phylogenetic networks
Format : Talk at Waseda University
Author(s) :
Leo van Iersel (TU Delft)
Abstract : Will we ever be able to reconstruct our own history and the history of other species? What can we reconstruct when we have enough data? And what cannot be reconstructed no matter how much data we collect? Evolutionary histories can be described using directed graphs called phylogenetic networks. Which phylogenetic networks can in principle be reconstructed from data of currently living species, like DNA data, under certain models of evolution? This is an important question to answer in order to be able to develop statistically-consistent methods. I will discuss algorithmic, graph theoretic and algebraic results that are important for answering this question.
[04778] Log-concave density estimation on tree space
Format : Talk at Waseda University
Author(s) :
Yuki Takazawa (The University of Tokyo)
Tomonari Sei (The University of Tokyo)
Abstract : A probability density is log-concave if its logarithm is concave. In recent decades, the maximum likelihood estimation method for log-concave densities has been developed in Euclidean spaces. In this talk, we introduce a generalization of this estimator to the space of phylogenetic trees. We provide a sufficient condition for the existence of the estimator, present the estimation algorithm, and discuss some challenges in the computation.
[03260] Tropical Logistic Regression Model on Space of Phylogenetic Trees
Format : Talk at Waseda University
Author(s) :
Ruriko Yoshida (Naval Postgraduate School)
George Aliatimis (University of Lancaster)
Burak Boyaci (University of Lancaster)
James Grant (University of Lancaster)
Abstract : In recent years, tropical geometry has found applications in statistical learning over the space of phylogenetic trees. In this talk, we propose an analogue of the logistic regression model in the setting of tropical geometry. Our proposed method is to classify gene trees over the space of ultrametrics, a tropical linear space. The generalization errors of our model is discussed. Experiment results with simulated and empirical data show our model works well.
[04319] From phylogenetics to semigroups, through set partitions
Format : Online Talk on Zoom
Author(s) :
Andrew Francis (Western Sydney University)
Abstract : We show that the set of all phylogenetic trees and forests are in correspondence with the set of all partitions of finite sets, extending Diaconis and Holmes (1998). This correspondence can be further extended to phylogenetic networks through a class of covers of finite sets. Partitions of finite sets can be represented as diagrams in a partition monoid, leading to applications of semigroups in phylogenetics. Joint work with Peter Jarvis and with Mike Steel.
[04284] Learning from phylogenies to uncover evolutionary dynamics
Format : Talk at Waseda University
Author(s) :
Olivier GASCUEL (CNRS - Institut de Systématique, Evolution, Biodiversité (ISYEB))
Abstract : I will describe the work done in my group to estimate the parameters of models used in phylodynamics and macroevolution studies. In particular, we use neural networks combined with simulations to learn to predict the parameters of these models. This involves both adequate representations of phylogenies and the use of appropriate neural architectures. The results compare favourably with the state of the art, with extremely fast methods for analyzing very large trees.
[05365] Minimum Number of Leaf-Covering Subtrees Covering Phylogenetic Networks
Format : Talk at Waseda University
Author(s) :
Yuki Yoshida (The University of Tokyo)
Abstract : Several deviation measures of non-tree-based phylogenetic networks from tree-based have been defined and their characteristics have been studied. One of the measures is the minimum number of leaf-covering subtrees which cover the phylogenetic network. In this talk, I suggest the first polynomial-time and efficient algorithm to compute both the minimum number and the covering subtrees. This algorithm is based on flow algorithms on several networks transformed from the network used to compute another deviation measure.
[04243] Proximity measures for phylogenetic network classes
Format : Talk at Waseda University
Author(s) :
Yukihiro Murakami (TU Delft)
Leo van Iersel (TU Delft)
Mark Jones (TU Delft)
Esther Julien (TU Delft)
Abstract : Orchard networks represent the evolutionary history of species as a tree structure with horizontal arcs. In this talk, we will explore the extent to which a network departs from being orchard. We will examine this deviation through varying graph operations such as adding leaves and removing arcs, as well as via vertex labeling. To provide context, we will compare these findings to proximity measures for other classes of networks, including tree-based and tree-child networks.
[03534] Data reduction rules to compute distances between phylogenetic trees
Format : Online Talk on Zoom
Author(s) :
Simone Linz (University of Auckland)
Steven Kelk (Maastricht University)
Ruben Meuwese (Maastricht University )
Simone Linz (University of Auckland)
Abstract : In evolutionary biology, phylogenetic trees are widely used to unravel the ancestral history of entities such as species or viruses. However, it is not uncommon to obtain different trees for the same data set. For example this can be due to methodological reasons. These tree incongruences motivate the use of distance measures in phylogenetics to quantify the dissimilarities between two phylogenetic trees. One popular distance between phylogenetic trees is called the tree bisection and reconnection (TBR) distance. Although this distance is NP-hard to compute, it is also fixed-parameter tractable. In this talk, we describe a series of results on the size of the TBR kernel, i.e. the size of two phylogenetic trees after pre-processing.
[03576] Parsimony and the rank of phylogenetic flattenings
Format : Online Talk on Zoom
Author(s) :
David Bryant (University of Otago)
Abstract : The standard models of sequence evolution on a phylogeny determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for one set of taxa and columns corresponding to all site patterns for another. Flattenings have been used to prove difficult results in phylogenetic mathematics and form the basis of several methods of phylogenetic inference. We provide an exact formula for the rank of these matrices based on parsimony scores.
Abstract : In this talk we discuss X-cactus, a type of phylogenetic network which is essentially a cactus graph in which some vertices are labelled by elements from a set X of species. In this talk, we present a way to encode X-cactuses in terms of certain collections of X-partitions, and discuss a partial order on the set of X-cactuses, including an analysis of some properties of its least upper and greatest lower bounds.
[05034] On the Sackin index of galled trees
Format : Talk at Waseda University
Author(s) :
Michael Fuchs (National Chengchi University)
Bernhard Gittenberger (TU Wien)
Abstract : We will compute the Sackin index of some classes of phylogenetic networks that belong to so-called galled trees. In particular, we consider level-1 networks as well as the closely related one-component galled trees. The Sackin index is the sum of the vertex heights.
The method we approach the problem is specifying the networks in terms of combinatorial structures and performing a singularity analysis on the resulting generating functions.
[04250] Distribution of patterns in ranked tree-child networks
Format : Talk at Waseda University
Author(s) :
Michael Fuchs (National Chengchi University)
Hexuan Liu (National Sun Yat-sen University )
Tsan-Cheng Yu (National Chengchi University)
Abstract : In this talk, I will first review tree-child networks and ranked tree-child networks (RTCN), and then explain our results on the distributional behavior of certain patterns in random RTCNs. These results extend the limit law for cherries and give rise to a conjecture for general patterns. This is the first such study for a class of phylogenetic networks.
[04323] Counting phylogenetic networks with the component graph method
Format : Talk at Waseda University
Author(s) :
Michael Fuchs (National Chengchi University)
Abstract : The component graph method was proposed by Louxin Zhang in order to solve algorithmic problems for tree-child networks, galled networks, reticulation-visible networks and extensions. Moreover, the method was also used to obtain exact counting results of the number of networks with n leaves and k reticulations. In this talk, we will explain how we used the method to prove asymptotic counting results for tree-child networks with a fixed number of reticulation nodes and galled networks.
