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Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2017.17
URN: urn:nbn:de:0030-drops-76362
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2017/7636/
Nojgaard, Nikolai ;
Geiß, Manuela ;
Merkle, Daniel ;
Stadler, Peter F. ;
Wieseke, Nicolas ;
Hellmuth, Marc
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps
Abstract
Motivation: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer.
Results: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an O(|V(T)|log(|V(S)|))-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. The algorithms are implemented in C++ using the boost graph library and are freely available at https://github.com/Nojgaard/tc-recon.
Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with hor- izontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems.
BibTeX - Entry
@InProceedings{nojgaard_et_al:LIPIcs:2017:7636,
author = {Nikolai Nojgaard and Manuela Gei{\ss} and Daniel Merkle and Peter F. Stadler and Nicolas Wieseke and Marc Hellmuth},
title = {{Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps}},
booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
pages = {17:1--17:12},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-050-7},
ISSN = {1868-8969},
year = {2017},
volume = {88},
editor = {Russell Schwartz and Knut Reinert},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address = {Dagstuhl, Germany},
URL = {http://drops.dagstuhl.de/opus/volltexte/2017/7636},
URN = {urn:nbn:de:0030-drops-76362},
doi = {10.4230/LIPIcs.WABI.2017.17},
annote = {Keywords: Tree Reconciliation, Horizontal Gene Transfer, Reconciliation Map, Time-Consistency, History of gene families}
}
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Keywords: |
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Tree Reconciliation, Horizontal Gene Transfer, Reconciliation Map, Time-Consistency, History of gene families |
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Collection: |
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17th International Workshop on Algorithms in Bioinformatics (WABI 2017) |
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Issue Date: |
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2017 |
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Date of publication: |
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11.08.2017 |
