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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
Author:Woodhams, M (Dr Michael Woodhams)
Author:Steane, DA (Dr Dorothy Steane)
Author:Jones, RC (Dr Rebecca Jones)
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:79953
Year Published:2013
Funding Support:Australian Research Council (FT100100031)
Web of Science® Times Cited:12
Deposited By:Mathematics and Physics
Deposited On:2012-10-15
Last Modified:2015-02-04
Downloads:0

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