Novel Distances for Dollo Data

M Woodhams; Dorothy A Steane; R C Jones; D Nicolle; V Moulton; B R Holland

doi:10.1093/sysbio/sys071

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Journal article

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Novel Distances for Dollo Data

M Woodhams, Dorothy A Steane, R C Jones, D Nicolle, V Moulton and B R Holland

Systematic Biology, Vol.62(1), pp.62-77

2013

DOI: https://doi.org/10.1093/sysbio/sys071

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Abstract

Additive Dollo Distance

Dollo process

LogDet/paralinear distances

Diversity Arrays Technology

Eucalyptus phylogeny

Adnataria phylogeny

gene content phylogeny

conditioning genomes

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.

Details

Title: Novel Distances for Dollo Data
Authors: M Woodhams (Author) - University of Tasmania
Dorothy A Steane (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
R C Jones (Author) - University of Tasmania
D Nicolle (Author) - Currency Creek Arboretum
V Moulton (Author) - University of East Anglia, United Kingdom
B R Holland (Author) - University of Tasmania
Publication details: Systematic Biology, Vol.62(1), pp.62-77
Publisher: Oxford University Press
Date published: 2013
DOI: 10.1093/sysbio/sys071
ISSN: 1063-5157
Copyright note: Copyright © 2013 The Authors. This is a pre-copyedited, author-produced PDF of an article accepted for publication in Systematic Biology following peer review. The definitive publisher-authenticated version is available online at: http://dx.doi.org/10.1093/sysbio/sys071
Organisation Unit: University of the Sunshine Coast, Queensland
Language: English
Record Identifier: 99450009902621
Output Type: Journal article

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Web Of Science research areas: Evolutionary Biology

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