Phylogenetic Networks

DOI10.1007/978-3-030-37853-0_2zbMATH Open1448.92155arXiv1906.01586OpenAlexW4232319577MaRDI QIDQ5118413FDOQ5118413

Joseph Rusinko, Elizabeth Gross, Colby Long

Publication date: 8 September 2020

Published in: Foundations for Undergraduate Research in Mathematics (Search for Journal in Brave)

Abstract: Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these relationships. Developing practical and efficient methods for inferring phylogenetic trees has lead to a number of interesting mathematical questions across a variety of fields. However, due to hybridization and gene flow, a phylogenetic network may be a better representation of the evolutionary history of some groups of organisms. In this chapter, we introduce some of the basic concepts in phylogenetics, and present related undergraduate research projects on phylogenetic networks that touch on areas of graph theory and abstract algebra. In the first section, we describe several open research questions related to the combinatorics of phylogenetic networks. In the second, we describe problems related to understanding phylogenetic statistical models as algebraic varieties.

Full work available at URL: https://arxiv.org/abs/1906.01586

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zbMATH Keywords

graph theorynetworksphylogeneticsalgebraic geometryevolutionary tree

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15) Systems biology, networks (92C42)

Cites Work

• Phylogeny. Discrete and random processes in evolution
• Title not available (Why is that?)
• Title not available (Why is that?)
• Algebraic Statistics for Computational Biology
• Title not available (Why is that?)
• Phylogenetic networks with every embedded phylogenetic tree a base tree
• Basic Phylogenetic Combinatorics
• Combinatorial secant varieties
• Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network
• Invariants of phylogenies in a simple case with discrete states
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Invariants of some probability models used in phylogenetic inference
• On determining if tree-based networks contain fixed trees
• Title not available (Why is that?)
• Toric Ideals of Phylogenetic Invariants
• Mathematical Models in Biology
• Trinets encode tree-child and level-2 phylogenetic networks
• Inferring a level-1 phylogenetic network from a dense set of rooted triplets
• Distinguishing Phylogenetic Networks
• Reconstructing a phylogenetic level-1 network from quartets
• Quartet compatibility and the quartet graph
• Algebraic Statistics
• Title not available (Why is that?)
• New characterisations of tree-based networks and proximity measures
• Quarnet inference rules for level-1 networks
• Identifiability of 3-class Jukes-Cantor mixtures

Cited In (8)

• Biochemical and phylogenetic networks. I: Hypertrees and corona products
• Phylogenetic networks from multi-labelled trees
• Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models
• Folding and unfolding phylogenetic trees and networks
• The fine structure of galls in phylogenetic networks
• Phylogenetic networks that display a tree twice
• Species-Driven Persistent Phylogeny
• Groves of phylogenetic trees

Uses Software

• Macaulay2
• ASTRAL-II
• Quartets MaxCut

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