Reconciling event-labeled gene trees with MUL-trees and species networks

Hellmuth, Marc, Huber, Katharina and Moulton, Vincent (2019) Reconciling event-labeled gene trees with MUL-trees and species networks. Journal of Mathematical Biology, 79 (5). pp. 1885-1925. ISSN 0303-6812

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Abstract

Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by speciation or gene duplication events), and to then look for a species tree which can be reconciled with this tree through a reconciliation map between the trees. In practice, however, it can happen that there is no such map from a given event-labeled tree to any species tree. An important situation where this might arise is where the species evolution is better represented by a network instead of a tree. In this paper, we therefore consider the problem of reconciling event-labeled trees with species networks. In particular, we prove that any event-labeled gene tree can be reconciled with some network and that, under certain mild assumptions on the gene tree, the network can even be assumed to be multi-arc free. To prove this result, we show that we can always reconcile the gene tree with some multi-labeled (MUL-)tree, which can then be “folded up” to produce the desired reconciliation and network. In addition, we study the interplay between reconciliation maps from event-labeled gene trees to MUL-trees and networks. Our results could be useful for understanding how genomes have evolved after undergoing complex evolutionary events such as polyploidy.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: LivePure Connector
Date Deposited: 29 Jul 2019 08:30
Last Modified: 11 Jun 2020 01:12
URI: https://ueaeprints.uea.ac.uk/id/eprint/71822
DOI: 10.1007/s00285-019-01414-8

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