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Novel distances for Dollo data
Citation
Woodhams, M and Steane, DA and Jones, RC and Nicolle, D and Moulton, V and Holland, BR, Novel distances for Dollo data, Systematic Biology, 62, (1) pp. 62-77. ISSN 1063-5157 (2013) [Refereed Article]
Copyright Statement
Copyright 2013 Oxford University Press
Official URL: http://sysbio.oxfordjournals.org/content/62/1/62
DOI: doi:10.1093/sysbio/sys071
Abstract
We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), that applies to data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet/paralinear distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, a restriction-site-based distance, and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process, this may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyse gene family presence/absence data from bacterial genomes obtained from the COG database and compare the results to previous phylogenies estimated using the conditioned genome reconstruction approach. The results for these case studies are largely congruent with previous studies, in some cases giving more phylogenetic resolution.
Item Details
| Item Type: | Refereed Article |
|---|---|
| Keywords: | Additive Dollo Distance, Dollo process, LogDet/paralinear distances, diversity arrays technology, Eucalyptus phylogeny, Adnataria phylogeny, gene content phylogeny, conditioning genomes |
| Research Division: | Mathematical Sciences |
| Research Group: | Applied mathematics |
| Research Field: | Biological mathematics |
| Objective Division: | Expanding Knowledge |
| Objective Group: | Expanding knowledge |
| Objective Field: | Expanding knowledge in the mathematical sciences |
| UTAS Author: | Woodhams, M (Dr Michael Woodhams) |
| UTAS Author: | Steane, DA (Dr Dorothy Steane) |
| UTAS Author: | Jones, RC (Dr Rebecca Jones) |
| UTAS Author: | Holland, BR (Professor Barbara Holland) |
| ID Code: | 79953 |
| Year Published: | 2013 |
| Funding Support: | Australian Research Council (FT100100031) |
| Web of Science® Times Cited: | 24 |
| Deposited By: | Mathematics and Physics |
| Deposited On: | 2012-10-15 |
| Last Modified: | 2015-02-04 |
| Downloads: | 0 |
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