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Wu, Taoyang 
ORCID: https://orcid.org/0000-0002-2663-2001 and Zhang, Louxin
(2011)
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree.
BMC Bioinformatics, 12 (Suppl 9).
ISSN 1471-2105
Abstract
Introduction: A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur. Hence, it is of great challenge to infer the containing species tree from a set of gene trees. One common approach to this inference problem is through gene tree and species tree reconciliation. Results: In this paper, we generalize the traditional least common ancestor (LCA) reconciliation to define a reconciliation between a gene tree and species tree under the tree homomorphism framework. We then study the structural properties of the space of all reconciliations between a gene tree and a species tree in terms of the gene duplication, gene loss or deep coalescence costs. As application, we show that the LCA reconciliation is the unique one that has the minimum deep coalescence cost, provide a novel characterization of the reconciliations with the optimal duplication cost, and present efficient algorithms for enumerating (nearly-)optimal reconciliations with respect to each cost. Conclusions: This work provides a new graph-theoretic framework for studying gene tree and species tree reconciliations.
| Item Type: | Article |
|---|---|
| Faculty \ School: | Faculty of Science > School of Computing Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Data Science and AI |
| Related URLs: | |
| Depositing User: | Users 2731 not found. |
| Date Deposited: | 03 Apr 2013 21:04 |
| Last Modified: | 10 Dec 2024 01:18 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/42067 |
| DOI: | 10.1186/1471-2105-12-S9-S7 |
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