The Euro-American lineage of the Mycobacterium tuberculosis complex consists of 
10 sublineages, each defined by a deletion of a large genomic region (RD, region 
of difference); by spoligotyping, that probes the polymorphism of the Direct 
Repeat (DR) locus, the Euro-American strains are classified into 5 lineages (T, 
Haarlem, LAM, S and X) and 34 sublineages, but the relationships between the 
RD-defined sublineages and the spoligotype groupings are largely unclear. By 
testing a global sample of 158 Euro-American strains, mutually exclusive 
deletions of RD115, RD122, RD174, RD182, RD183, RD193, RD219, RD726 or RD761 
were found in 122 strains; deletion of RD724, typical of strains from Central 
Africa, was not found. The RD-defined sublineages, tested for katG463/gyrA95 
polymorphism, belonged to Principal Genotypic Group (PGG) 2, with the exception 
of RD219 sublineage belonging to PGG3; the 36 strains with no deletion were of 
either PGG2 or 3. Based on these polymorphisms, a phylogenetic reconstruction of 
the Euro-American lineage, that integrates the previously reported phylogeny, is 
proposed. Although certain deletions were found to be associated to certain 
spoligotype lineages (i.e., deletion RD115 to T and LAM, RD174 to LAM, RD182 to 
Haarlem, RD219 to T), our analysis indicates a general lack of concordance 
between RD-defined sublineages and spoligotype groupings. Moreover, of the 42 
spoligotypes detected among the study strains, sixteen were shared by strains 
belonging to different RD sublineages. IS6110-RFLP analysis of strains sharing 
spoligotypes confirmed a poor genetic relatedness between strains of different 
RD sublineages. These findings provide evidence for the occurrence of a high 
degree of homoplasy in the DR locus leading to convergent evolution to identical 
spoligotypes. The incongruence between Large Sequence Polymorphism and 
spoligotype polymorphism argues against the use of spoligotyping for 
establishing phylogenetic relationships within the Euro-American lineage.