Overlaid species forests

Huber, Katharina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Scholz, Guillaume (2022) Overlaid species forests. Discrete Applied Mathematics, 309. pp. 110-122. ISSN 0166-218X

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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 (OSF) was introduced as a discrete way to model introgression. Basically, an OSF consists of a gene history in the form of a phylogenetic tree, a collection of lineage trees or forest for some species of interest, and a map that overlays the gene tree onto the forest. In this paper we shall study mathematical properties of OSFs and their relationship with other structures in phylogenetics, such as lateral gene transfer models, subtree prune and regraft operations, and phylogenetic networks. In particular, we show that a certain algorithm called \textsc{OSF-Builder} for constructing an OSF is guaranteed to produce a special type of OSF with a minimum number of introgressions, as well as providing some characterizations for networks that can arise from OSFs. We also give bounds on how much an OSF can change when the underlying gene tree or forest is perturbed. We expect that these results will be useful in developing new algorithms for deriving introgression histories, a rapidly growing area of interest in phylogenomics.

Item Type: Article
Uncontrolled Keywords: phylogenetic network,introgression model,overlaid species forest (osf),unfolding,phylogenetic network,introgression model,unfolding,overlaid species forest (osf),applied mathematics,discrete mathematics and combinatorics ,/dk/atira/pure/subjectarea/asjc/2600/2604
Faculty \ School: Faculty of Science > School of Computing Sciences
UEA Research Groups: Faculty of Science > Research Groups > Computational Biology
Faculty of Science > Research Groups > Norwich Epidemiology Centre
Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
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Depositing User: LivePure Connector
Date Deposited: 13 Nov 2021 01:51
Last Modified: 21 Apr 2023 01:13
URI: https://ueaeprints.uea.ac.uk/id/eprint/82087
DOI: 10.1016/j.dam.2021.11.005


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