Novel distances for dollo data.
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 data sets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyze gene family presence/absence data from bacterial genomes obtained from the COG database and compare the results with 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.
School of Mathematics and Physics, CRC for Forestry, School of Plant Science, University of Tasmania, Private Bag 55, Hobart 7001, Australia.
Michael
M
Woodhams
Dorothy A
DA
Steane
Rebecca C
RC
Jones
Dean
D
Nicolle
Vincent
V
Moulton
Barbara R
BR
Holland
D001419:Bacteria / Q000145:classification / Q000235:genetics; D003198:Computer Simulation; D005052:Eucalyptus / Q000145:classification / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D015203:Reproducibility of Results; D013223:Statistics as Topic