Phylogenetic analyses of surface antigens and other chlamydial proteins were used to reconstruct the evolution of the Chlamydiaceae. Trees for all five coding genes [the major outer-membrane protein (MOMP), GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine-rich protein] supported the current organization of the family Chlamydiaceae, which is based on ribosomal, biochemical, serological, ecological and DNA-DNA hybridization data. Genetic distances between some species were quite large, so phylogenies were evaluated for robustness by comparing analyses of both nucleotide and protein sequences using a variety of algorithms (neighbour-joining, maximum-likelihood, maximum-parsimony with bootstrapping, and quartet puzzling). Saturation plots identified areas of the trees in which factors other than relatedness may have determined branch attachments. All nine species were clearly differentiated by distinctness ratios calculated for each gene. The distribution of virulence traits such as host and tissue tropism were mapped onto the consensus phylogeny. Closely related species were no more likely to share virulence characters than were more distantly related species. This phylogenetically disjunct distribution of virulence traits could not be explained by lateral transfer of the genes we studied, since we found no evidence for lateral gene transfer above the species level. One interpretation of this observation is that when chlamydiae gain access to a new niche, such as a new host or tissue, significant adaptation ensues and the virulence phenotype of the new species reflects adaptation to its environment more strongly than it reflects its ancestry.Keywords : Chlamydia, Chlamydophila, Chlamydiales, phylogeny, intracellular bacteria
INTRODUCTIONBacteria in the family Chlamydiaceae are obligately intracellular parasites that infect a diverse array of vertebrates. Chlamydiae cause a wide variety of health problems, including spontaneous abortion in livestock, systemic disease in birds and both endemic and zoonotic infection of humans (Herring, 1993 ; Everett & Andersen, 1997 This paper is dedicated to the late Jan Ursing, Associate Editor of IJSB, who was extraordinarily helpful with our paper on reclassification of Chlamydiales.
Abbreviations : INDELs, insertions and deletions ;LGT, lateral gene transfer ; ML, maximum-likelihood ; MOMP, major outer-membrane protein ; MP, maximum-parsimony ; NJ, neighbour-joining ; QP, quartet puzzling.The GenBank accession numbers for the scanned and new data produced in this study are AF269256-AF269282 and AF240773.leading cause of preventable blindness and sexually transmitted disease and have suspected links to cardiovascular disease (Campbell et al., 1998 ;Schachter, 1999). The evolutionary processes responsible for this diverse array of virulence phenotypes have long been of interest. Previous evolutionary studies of the Chlamydiaceae involved phylogenetic reconstruction using rRNA genes ( Fig. 1a) (Everett et al., 1999a) and the gene for the maj...