Overlaid species forests

DOI10.1016/J.DAM.2021.11.005MaRDI QIDQ2065769zbMATH OpenOpenAlexFDO

Authors Katharina T. Huber, G. E. Scholz, Vincent Moulton

Publication date 13 January 2022

Published in Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2006.14275

zbMATH Keywords

phylogenetic networkunfoldingintrogression modeloverlaid species forest (OSF)

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15)

Abstract: Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a fundamental role in speciation. Recently the concept of an overlaid species forest was introduced to represent introgression histories. Basically this approach takes a putative gene history in the form of a phylogenetic gene tree and tries to overlay this onto a forest which usually consists of a collection of lineage trees for the species of interest. The result is a network called an overlaid species forest in which genes jump or introgress between lineages. In this paper we study properties of overlaid species forests, showing that they have various connections with models for lateral gene transfer, maximum parsimony, and unfolding of phylogenetic networks. In particular, we show that a certain algorithm called OSF-B UILDER for constructing overlaid species forests is guaranteed to a produce a special type of overlaid species forest with a minimum number introgressions, as well as providing some characterizations for networks that can arise from overlaid species forests. We expect that these results will be useful in developing new methods for representing introgression histories, a growing area of interest in phylogenetics.

Recommendations

• Forest-based networks
• \(D_{\text{GEN}}\): a test statistic for detection of general introgression scenarios
• Computational Science – ICCS 2005
• Identifying a species tree subject to random lateral gene transfer
• Modelling reticulate evolution

Cites work

• scientific article; zbMATH DE number 1865935 (Why is no real title available?)
• Folding and unfolding phylogenetic trees and networks
• On the computational complexity of the rooted subtree prune and regraft distance
• On the maximum parsimony distance between phylogenetic trees
• Phylogenetic networks from multi-labelled trees

Cited in

(4)

• Forest-based networks
• Is this network proper forest-based?
• \(D_{\text{GEN}}\): a test statistic for detection of general introgression scenarios
• Path partitions of phylogenetic networks

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