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We provide in this study a very large DNA dataset on  Rhodnius  species including 36 samples representing 16 valid species of the three  Rhodnius  groups,  pictipes, prolixus  and  pallescens.  Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the  Rhodnius  phylogeny. At the species level, we confirmed the species-specific status of  R. montenegrensis  and  R. marabaensis  and we agree with the synonymy of  R. taquarussuensis  with  R. neglectus.  We also invite to revisit the species-specific status of  R. milesi  that is more likely  R. nasutus . We proposed to define a  robustus  species complex that comprises the four close relative species:  R. marabaensis, R. montenegrensis, R. prolixus  and  R. robustus.  As  Psammolestes tertius  was included in the  Rhodnius  clade, we strongly recommend reclassifying this species as  R. tertius . At the  Rhodnius  group level, molecular data consistently supports the clustering of the  pictipes  and  pallescens  groups, more related to each other than they are to the  prolixus  group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three  Rhodnius  groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the  prolixus  group, involving the related species of the  robustus  complex but also the pairwise  R. nasutus  and  R. neglectus . A genome wide analysis highlighted an introgression event in the  pictipes  group between  R. stali  and  R. brethesi  and suggested a complex gene flow between the three species of the  pallescens  group,  R. colombiensis, R. pallescens  and  R. ecuadoriensis . The molecular data supports also a sylvatic distribution of  R. prolixus  in Brazil (Pará state) and the monophyly of  R. robustus . As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.

Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations