Borrelia burgdorferi is one of the bacterial species responsible for the most prevalent vector-borne disease in the temperate zone of the northern hemisphere, Lyme borreliosis [1]. Phylogenetic analyses of B. burgdorferi are now based on a concatenation of several housekeeping genes that are assumed to evolve according to one evolutionary pattern.

This is a strong assumption and, when untrue, inferences are a compromise between different phylogenetic signals., We have designed a Bayesian mixture model under a missing data formulation to automatically recover the evolutionary pattern of each site in a DNA alignment. Evolutionary consistency among a set of genes can be argued whenever most of the sites are allocated to the same evolutionary class.

Only in this case will a concatenation of genes produce valid inferences., In this study we demonstrate consistency in the evolution of eight housekeeping genes and evolutionary inconsistency between these housekeeping genes and the gene encoding the immunodominant outer surface protein C. Our method is a suitable indicator of evolutionary agreement or disagreement when employing large-scale gene concatenations, not only in B. burgdorferi, but for any phylogenetic analysis.,

[1] Margos, G. et al., 2008. Proceedings of the National Academy of Sciences of the USA, 105(25): 8730 - 8735.