dc.contributor.author |
Drummond, Alexei |
en |
dc.contributor.author |
Ho, SY |
en |
dc.contributor.author |
Phillips, MJ |
en |
dc.contributor.author |
Rambaut, A |
en |
dc.date.accessioned |
2012-04-02T22:58:54Z |
en |
dc.date.issued |
2006 |
en |
dc.identifier.citation |
PLoS Biology 4(5):699-710 2006 |
en |
dc.identifier.issn |
1544-9173 |
en |
dc.identifier.uri |
http://hdl.handle.net/2292/16484 |
en |
dc.description.abstract |
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution. |
en |
dc.publisher |
PLOS |
en |
dc.relation.ispartofseries |
PLOS 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/1544-9173/ |
en |
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
en |
dc.title |
Relaxed phylogenetics and dating with confidence |
en |
dc.type |
Journal Article |
en |
dc.identifier.doi |
10.1371/journal.pbio.0040088 |
en |
pubs.issue |
5 |
en |
pubs.begin-page |
699 |
en |
pubs.volume |
4 |
en |
dc.rights.holder |
Copyright: PLOS |
en |
dc.identifier.pmid |
16683862 |
en |
pubs.end-page |
710 |
en |
dc.rights.accessrights |
http://purl.org/eprint/accessRights/RestrictedAccess |
en |
pubs.subtype |
Article |
en |
pubs.elements-id |
94384 |
en |
pubs.org-id |
Science |
en |
pubs.org-id |
Biological Sciences |
en |
pubs.number |
e88 |
en |
pubs.record-created-at-source-date |
2010-09-01 |
en |
pubs.dimensions-id |
16683862 |
en |