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Background   Giardia duodenalis  is a common protozoan parasite of humans and animals. Genetic characterization of single loci indicates the existence of eight groups called assemblages, which differ in their host distribution. Molecular analyses challenged the idea that  G. duodenalis  is a strictly clonal diplomonad by providing evidence of recombination within and between assemblages. Particularly, inter-assemblage recombination events would complicate the interpretation of multi-locus genotyping data from field isolates: where is a host infected with multiple  Giardia  genotypes or with a single, recombined  Giardia  genotype.    Methods  Population genetic analyses on the single and multiple-locus level on an extensive dataset of  G. duodenalis  isolates from humans and animals were performed.    Results  Our analyses indicate that recombination between isolates from different assemblages are apparently very rare or absent in the natural population of  Giardia duodenalis.  At the multi-locus level, our statistical analyses are more congruent with clonal reproduction and can equally well be explained with the presence of multiple  G. duodenalis  genotypes within one field isolate.    Conclusions  We conclude that recombination between  G. duodenalis  assemblages is either very rare or absent. Recombination between genotypes from the same assemblage and genetic exchange between the nuclei of a single cyst needs further investigation.

Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure