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T. cruzi is a structured species

This means that its natural populations are divided into discrete and stable subdivisions between which the genetic distances convey reliable evolutionary information.39

The existence of such clusters was first postulated by the pioneering MLEE studies of Miles et al.61,68 It is interesting to note that, in spite of a lack of genetic interpretation of these data, the MLEE variants identified at that time (zymodemes I, II, and III) are still there, although the picture has of course been refined by further studies (Table 21.1). Again, the permanency of the multilocus genotypes to which these zymodemes correspond is in itself a strong indication of stable clonal propagation.

The discrete typing units or "near-clades"

The term “discrete typing units” was coined to overcome the difficulty that occasional hybridization events make it impossible to consider T. cruzi’s genetic

Table 21.1 Correspondence between the most recent nomenclature of Trypanosoma cruzi genetic variants and previously published nomenclatures

1

2

3

4

5

DTU I

DTU 1

1-25

ZI

X10 cl1, Cuica cl1

DTU II

DTU 2a

26-29

Z III

CAN III cl1

DTU III

DTU 2b

30-34

Z II

TU 18 cl2

DTU IV

DTU 2c

35-37

Z II

M5631, M6241

DTU V

DTU 2d

38, 39

Z II

MN cl2, SC43 cl1

DTU VI

DTU 2e

40, 43

Z II

CL Brenner, Tulahuen cl2

  • 1 = Ref. 69.
  • 2 5 Ref. 56.
  • 3 5 Ref. 1.
  • 4 5 Ref. 67.
  • 5 5 Representative stocks.

subdivisions as true clades. Indeed, (1) these subdivisions are not strictly separated from each other, as true clades should be, and (2) hybrid clones have two parental genotypes, while true clades should originate from one ancestral parent only. The concept of discrete typing units (DTUs) has therefore been proposed70: sets of stocks that are genetically closer to each other than to any other stock and are identifiable by common molecular, genetic, biochemical, or immunological markers called tags. The genetic subdivisions identified within T. cruzi fully match this definition, whereas they very imperfectly fit the definition of clades. More recently, we have proposed the term “near-clades” to design those stable genetic subdivisions within a given microbial species when discreteness is clouded by occasional recom- bination.2 Using the convergence criterion above exposed makes it possible to evidence the growing phylogenetic signal that is a typical feature of the near- clades. T. cruzi DTUs represent typical near-clades. The near-clade concept is more informative than the DTU concept, since it is based on a precise evolutionary definition. We have proposed that the very existence of near-clades was a typical signature and a main result of PCE in a given species.2 It has been asserted that the observation of such near-clades within a given species was “self-evident,” and therefore would be an artifactual evidence for PCE.22,42 It is true that, once the near-clades have been clearly evidenced, it is useless and redundant to perform on the whole species population genetic tests such as LD. However, (1) we have read nowhere but in our articles the proposal that near-clades, even considered as “selfevident,” were a typical manifestation of PCE; and (2) evidencing near-clades is all the less self-evident (except when arriving long after the battle) because their identification in T. cruzi took many years of in-depth population genetic analyses, and because their very numbering still is under dispute71. The near-clade concept has a clear evolutionary definition. It makes it possible to replace with a unique term the many, confusing, vague names used in the literature dealing with pathogen

population genetics to designate within-species genetic subdivisions (assemblages, clades, clusters, genogroups, lineages, genetic groups, among others).

Detailed analysis by MLEE,53 RAPD,56 and gene sequencing72,73 have congruently evidenced the existence of six DTUs within T. cruzi (Fig. 21.1). These DTUs have also been uncovered by RADES,58 which shows that this structuring persists when surveying coding expressed genes. PCR-RFLP typing74 and MLST49 have also corroborated this clustering into six DTUs.

The formerly proposed partition of T. cruzi into two major subdivisions,39,75 DTU 1 and 2,53,56 named TC I and TC II (TC = Trypanosoma cruzi76), is presently questioned, although possibly not ruled out. In a recent meeting, Chagas disease experts decided to retain the subdivision of T. cruzi into six DTUs as the official reference model for this parasite’s genetic variability. However, it was decided to renumber the DTUs into TC I—VI instead of DTUs 1, 2b, 2c, 2a, 2d, and 2e, respectively (Table 21.1), to take into account the present debate on the presence of two major subdivisions.69,77

It has proved to be impossible to reliably identify each DTU with unique markers. Instead, a convenient set of three markers has been proposed.78

Thus far the six DTUs have been upheld. The studies that have evidenced them have sometimes relied on impressively extensive samples, the most exhaustive of which is the MLEE study by Barnabe et al.53 which involved no less than 434 different stocks. It is possible that this classification will be slightly modulated by further samplings involving more sylvatic cycles. However, to date these studies have evidenced further variability within the DTUs and have revealed some very interesting new epidemiological features, but have corroborated the classification.60,79

A seventh near-clade, referred to as “Tc-Bat” (for it has been isolated only from bats) has been recently evidenced. , Tc-bat has been recorded years apart in Brazil, Colombia, Ecuador, and Panama, in different species of bats, which illustrates the stability in space and time of the near-clades. Lastly, the partitioning into seven near-clades has been recently challenged by Barnabe et al.71 on a broad sample of strains, but with a limited set of one nuclear gene and two mitochondrial genes. This proposal has obviously to be explored with a broader set of genetic markers. However, it illustrates the fact that even in the extremely well-studied species T. cruzi, evidencing near-clades is far from being “self-evident.”42

 
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