Abstract
Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or “near-clades”. The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main “near-clades”, and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades (“Russian doll pattern”), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.
Highlights
At odds with theoretical predictions about their considerable cost, sexuality and recombination are ubiquitous, at least in metazoa
Standardized between 0 and 1 resulted in a network where nodes represent Multilocus Genotyping (MLG) and links among them depend on the strength of their pairwise Shared Allele Distance (SAD)
The networks are scanned for successive thresholds called Dp that can be understood as an estimate of the percentage of shared markers among the stocks and near-clades
Summary
At odds with theoretical predictions about their considerable cost, sexuality and recombination are ubiquitous, at least in metazoa. Recombination may be positively selected by breaking down the negative associations generated by random drift [4], and may allow the emergence of unique multilocus genotypes gathering advantageous alleles that arose in different individuals at the same locus [5] or at other loci [6]. It may be noted, that several authors do not consider that generation of new, better-adapted multilocus associations is the main reason for maintenance of genetic recombination in micropathogens, be they viruses [7] or bacteria [8]. They have rather proposed that recombination is a side effect of other evolutionary mechanisms, such as DNA repair for example [9]
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