Resumé
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.
| Originalsprog | Engelsk |
|---|---|
| Titel | 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 |
| Redaktører | Russel Schwartz, Knut Reinert |
| Udgivelses sted | Dagstuhl |
| Forlag | Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing |
| Publikationsdato | 2017 |
| Artikelnummer | 17 |
| ISBN (Elektronisk) | 9783959770507 |
| DOI | |
| Status | Udgivet - 2017 |
| Begivenhed | 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 - Boston, USA Varighed: 21. aug. 2017 → 23. aug. 2017 |
Konference
| Konference | 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 |
|---|---|
| Land | USA |
| By | Boston |
| Periode | 21/08/2017 → 23/08/2017 |
| Navn | Leibniz International Proceedings in Informatics |
|---|---|
| Vol/bind | 88 |
| ISSN | 1868-8969 |
Fingeraftryk
Citer dette
}
Forbidden time travel : Characterization of time-consistent tree reconciliation maps. / Nøjgaard, Nikolai; Geiß, Manuela; Merkle, Daniel; Stadler, Peter F.; Wieseke, Nicolas; Hellmuth, Marc.
17th International Workshop on Algorithms in Bioinformatics, WABI 2017. red. / Russel Schwartz; Knut Reinert. Dagstuhl : Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2017. 17 (Leibniz International Proceedings in Informatics, Bind 88).Publikation: Bidrag til bog/antologi/rapport/konference-proceeding › Konferencebidrag i proceedings › Forskning › peer review
TY - GEN
T1 - Forbidden time travel
T2 - Characterization of time-consistent tree reconciliation maps
AU - Nøjgaard, Nikolai
AU - Geiß, Manuela
AU - Merkle, Daniel
AU - Stadler, Peter F.
AU - Wieseke, Nicolas
AU - Hellmuth, Marc
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - History of gene families
KW - Horizontal Gene Transfer
KW - Reconciliation Map
KW - Time- Consistency
KW - Tree Reconciliation
U2 - 10.4230/LIPIcs.WABI.2017.17
DO - 10.4230/LIPIcs.WABI.2017.17
M3 - Article in proceedings
BT - 17th International Workshop on Algorithms in Bioinformatics, WABI 2017
A2 - Schwartz, Russel
A2 - Reinert, Knut
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
CY - Dagstuhl
ER -