Abstract
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model of speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model of speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call “beaded trees”. However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have some restricted form. We discuss several possibilities to overcome this problem.
Original language | English |
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Title of host publication | Algorithms for Computational Biology - 5th International Conference, AlCoB 2018, Proceedings |
Editors | Jesper Jansson, Carlos Martin-Vide, Miguel A. Vega-Rodriguez |
Place of Publication | Cham |
Publisher | Springer |
Pages | 37-49 |
Number of pages | 13 |
ISBN (Electronic) | 978-3-319-91938-6 |
ISBN (Print) | 978-3-319-91937-9 |
DOIs | |
Publication status | Published - 2018 |
Event | 5th International Conference on Algorithms for Computational Biology, AlCoB 2018 - Hong Kong, China Duration: 25 Jun 2018 → 26 Jun 2018 Conference number: 5 http://grammars.grlmc.com/AlCoB2018/ |
Publication series
Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 10849 LNBI |
ISSN (Print) | 0302-9743 |
ISSN (Electronic) | 1611-3349 |
Conference
Conference | 5th International Conference on Algorithms for Computational Biology, AlCoB 2018 |
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Abbreviated title | AlCoB 2018 |
Country/Territory | China |
City | Hong Kong |
Period | 25/06/18 → 26/06/18 |
Internet address |
Bibliographical note
Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-careOtherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.
Keywords
- Phylogenetic inference problems
- Polynomial-time algorithms