A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identifywhether substitution takes place under a covariotide model in sequencesused for phylogenetic inference and (2) to determine the influence ofcovariotide substitution on phylogenetic trees inferred for photosyntheticand other organisms. (Covariotide and covarion models are ones in whichsites that are variable in some parts of the underlying tree are invariablein others and vice versa.) Two tests were developed. The first was acontingency test, and the second was an inequality test comparing theexpected number of variable sites in two groups with the observed number.Application of these tests to 16S rDNA and tufA sequences from a range ofnonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes andeukaryotes suggests the occurrence of a covariotide mechanism. The degreeof support for partitioning of taxa in reconstructed trees involving theseorganisms was determined in the presence or absence of sites showingparticular substitution patterns. This analysis showed that the support forsplits between (1) photosynthetic eukaryotes and prokaryotes and (2)photosynthetic and nonphotosynthetic organisms could be accounted for bypatterns arising from covariotide substitution. We show that the additionalproblem of compositional bias in sequence data needs to be considered inthe context of patterns of covariotide/covarion substitution. We argue thatwhile covariotide or covarion substitution may give rise tophylogenetically informative patterns in sequence data, this may not alwaysbe so.