A COVARIOTIDE MODEL EXPLAINS APPARENT PHYLOGENETIC STRUCTURE OF OXYGENIC PHOTOSYNTHETIC LINEAGES

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequenc es used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosy nthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. T he first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with th e observed number. Application of these tests to 16S rDNA and tufA seq uences from a range of nonphotosynthetic prokaryotes and oxygenic phot osynthetic prokaryotes and eukaryotes suggests the occurrence of a cov ariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the pr esence or absence of sites showing particular substitution patterns. T his analysis showed that the support for splits between (1) photosynth etic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosyn thetic organisms could be accounted for by patterns arising from covar iotide substitution. We show that the additional problem of compositio nal bias in sequence data needs to be considered in the context of pat terns of covariotide/covarion substitution. We argue that while covari otide or covarion substitution may give rise to phylogenetically infor mative patterns in sequence data, this may not always be so.