An evaluation of DNA pairing in bacterial systematics.

The main aim of this work was to evaluate the use of DNA-DNA pairing techniques in bacterial systematics. The genus Listeria was chosen for the study because of the small number of biochemical differences between the seven species. Also there has been a limited amount of nucleic acid studies carried out on the group using an endonuclease technique (Rocourt et al., 1982), therefore some comparisons of the two techniques were possible. Using optical DNA-DNA reassociation on a spectrophotometer with 23 Listeria strains from the seven species, a complete matrix of DNA-DNA homology values was produced. The data were analysed for reproducibility and second order kinetics. Possible distortion of the derived taxonomic structure due to choice of reference strains was investigated by analysing the structure obtained from the complete matrix and comparing it to results obtained from incomplete 'strip' matrices. An analysis was made on a published matrix of complete DNA relationships (Nakamura and Swezey, 1983a; Hartford and Sneath, 1988) as well as on the data from Listeria species produced in this study. Great distortion in apparent taxonomic structure can result unless reference strains are widely spaced and representative of the clusters present. Problems caused by the choice of reference strains and the use of incomplete matrices was also explored by generating a random normal swarm of OTUs and illustrating the often bizarre effects obtained by using incomplete data sets in bacterial systematics. DNA-DNA pairing data from a selection of published work were examined for experimental error. The average error from replications lay between 3 and 8.6 %, but the data were very limited.