dc.contributor.author |
Bryant, C |
en |
dc.contributor.author |
Fischer, M |
en |
dc.contributor.author |
Linz, Simone |
en |
dc.contributor.author |
Semple, Charles |
en |
dc.date.accessioned |
2017-05-22T21:54:32Z |
en |
dc.date.issued |
2017-03-21 |
en |
dc.identifier.citation |
Journal of Theoretical Biology 417:100-108 21 Mar 2017 |
en |
dc.identifier.issn |
0022-5193 |
en |
dc.identifier.uri |
http://hdl.handle.net/2292/32995 |
en |
dc.description.abstract |
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks |
en |
dc.publisher |
Academic Press |
en |
dc.relation.ispartofseries |
Journal of Theoretical Biology |
en |
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from http://www.sherpa.ac.uk/romeo/issn/0022-5193/ |
en |
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
en |
dc.rights.uri |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
en |
dc.title |
On the quirks of maximum parsimony and likelihood on phylogenetic networks |
en |
dc.type |
Journal Article |
en |
dc.identifier.doi |
10.1016/j.jtbi.2017.01.013 |
en |
pubs.begin-page |
100 |
en |
pubs.volume |
417 |
en |
dc.description.version |
AM - Accepted Manuscript |
en |
dc.rights.holder |
Copyright: Academic Press |
en |
dc.identifier.pmid |
28087420 |
en |
pubs.end-page |
108 |
en |
pubs.publication-status |
Published |
en |
dc.rights.accessrights |
http://purl.org/eprint/accessRights/OpenAccess |
en |
pubs.subtype |
Article |
en |
pubs.elements-id |
606785 |
en |
pubs.org-id |
Science |
en |
pubs.org-id |
School of Computer Science |
en |
dc.identifier.eissn |
1095-8541 |
en |
pubs.record-created-at-source-date |
2017-05-23 |
en |
pubs.dimensions-id |
28087420 |
en |