Forbidden time travel: Characterization of time-consistent tree reconciliation maps

Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth

Publikation: Kapitel i bog/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review

72 Downloads (Pure)

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 eventlabeled 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. Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with horizontal 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.

OriginalsprogEngelsk
Titel17th International Workshop on Algorithms in Bioinformatics, WABI 2017
RedaktørerRussel Schwartz, Knut Reinert
UdgivelsesstedDagstuhl
ForlagSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Publikationsdato2017
Artikelnummer17
ISBN (Elektronisk)9783959770507
DOI
StatusUdgivet - 2017
Begivenhed17th International Workshop on Algorithms in Bioinformatics, WABI 2017 - Boston, USA
Varighed: 21. aug. 201723. aug. 2017

Konference

Konference17th International Workshop on Algorithms in Bioinformatics, WABI 2017
Land/OmrådeUSA
ByBoston
Periode21/08/201723/08/2017
NavnLeibniz International Proceedings in Informatics
Vol/bind88
ISSN1868-8969

Fingeraftryk

Dyk ned i forskningsemnerne om 'Forbidden time travel: Characterization of time-consistent tree reconciliation maps'. Sammen danner de et unikt fingeraftryk.

Citationsformater