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T. cruzi undergoes some genetic exchange

In an organism such as T. cruzi, in which some recombination is occurring (see Introduction section and further), phylogenetic analysis should be understood in a specific manner. Indeed, by definition, phylogenetic analysis surveys the evolution of discrete lines that are genetically strictly separated from each other (clades). When some genetic exchange occurs between these lines, it clouds the phylogenetic picture of the species under study.215 The observed departures from an ideal phylogenetic reconstruction are in themselves useful information on how and how much occasional recombination is operating. On the other hand, the cleaner the phylogenetic reconstruction is, the stronger the evidence is that recombination is exceptional or absent. Pathogenic microorganisms that are strictly clonal are probably the exception rather than the rule. It would be the case of the African trypanosome Trypanosoma brucei gambiense “group I.”41 It is for this reason that we have stated2 that a strict cladistic approach is not adequate in the case of micropathogens. We have rather recommended a flexible phylogenetic approach based on a congruence criterion inspired by the principle of genealogical concordance between independent genes proposed for the recognition of biological taxa.9 According to this congruence criterion, adding more relevant data (e.g., more loci, or more molecular markers, or data obtained from different phylogenetic approaches), will reveal a growing phylogenetic signal in the sample under study. We have proposed that such a growing phylogenetic signal is the signature of the “clonality threshold,” beyond which the impact of clonal evolution definitely overcomes that of genetic recombination.7 This clonality threshold concept is neither “pseudoquantitative” nor “vague.”42 Moreover, “predominant” clonal evolution is not open to “wide interpre- tation.”42 The growing phylogenetic signal, on which the clonality threshold concept is based, is easy to observe with appropriate data (see: T. cruzi is a structured species). The clonality threshold concept makes it possible to dismiss vague, subjective terms, such as “gross” incongruences (between phylogenetic trees),43 “widespread genetic exchange,”22 and “intense lateral exchange of genetic information,”42 and to rather rely on a clear-cut parameter that identifies the “clonality border.”

Gene trees and species trees are not the same44

The evolutionary history of a given gene often does not reflect the general evolution of the species under study. The gene could undergo strong selective pressures or have a specific evolutionary rapidity (molecular clock). The general, most welcome, tendency is now to base phylogenetic reconstruction of species on a broad range of genes. Although gene sequencing conveys a great deal of information, the use of classical markers such as multilocus enzyme electrophoresis (MLEE) or random amplified polymorphic DNA (RAPD), if it is based on a broad range of loci, could be more reliable than the analysis of the sequence of only one gene or a few genes to reconstruct the evolution of a species. Many studies on T. cruzi have relied on the analysis of only one gene or a few genes.45-47 These studies convey useful information on the precise genes they investigate. However, extrapolation to the entire species should be done with caution. The ideal approach is of course to combine the power of (1) gene sequencing and (2) multilocus analysis. This is done by multilocus sequence typing (MLST48), which has been now widely used for T. cruzi.49,50 The last step is accomplished by population genomics, relying on the whole genome analysis of various strains. Such an approach tends to become routine in viruses51 and bacteria.52 This has not been done until now in the case of T. cruzi.

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