University of Tasmania

File(s) under permanent embargo

Novel distances for Dollo data

journal contribution
posted on 2023-05-17, 13:33 authored by Woodhams, M, Dorothy SteaneDorothy Steane, Rebecca JonesRebecca Jones, Nicolle, D, Moulton, V, Barbara HollandBarbara Holland
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.


Australian Research Council


Publication title

Systematic Biology








School of Natural Sciences


Oxford University Press

Place of publication

Oxford, UK

Rights statement

Copyright 2013 Oxford University Press

Repository Status

  • Restricted

Socio-economic Objectives

Expanding knowledge in the mathematical sciences