AUTHOR=Filée Jonathan , Merle Marie , Bastide Héloïse , Mougel Florence , Bérenger Jean-Michel , Folly-Ramos Elaine , Almeida Carlos Eduardo , Harry Myriam 

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

JOURNAL=Frontiers in Ecology and Evolution

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2021.750317

DOI=10.3389/fevo.2021.750317

ISSN=2296-701X

ABSTRACT=<p>We provide in this study a very large DNA dataset on <italic>Rhodnius</italic> species including 36 samples representing 16 valid species of the three <italic>Rhodnius</italic> groups, <italic>pictipes, prolixus</italic> and <italic>pallescens.</italic> 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 <italic>Rhodnius</italic> phylogeny. At the species level, we confirmed the species-specific status of <italic>R. montenegrensis</italic> and <italic>R. marabaensis</italic> and we agree with the synonymy of <italic>R. taquarussuensis</italic> with <italic>R. neglectus.</italic> We also invite to revisit the species-specific status of <italic>R. milesi</italic> that is more likely <italic>R. nasutus</italic>. We proposed to define a <italic>robustus</italic> species complex that comprises the four close relative species: <italic>R. marabaensis, R. montenegrensis, R. prolixus</italic> and <italic>R. robustus.</italic> As <italic>Psammolestes tertius</italic> was included in the <italic>Rhodnius</italic> clade, we strongly recommend reclassifying this species as <italic>R. tertius</italic>. At the <italic>Rhodnius</italic> group level, molecular data consistently supports the clustering of the <italic>pictipes</italic> and <italic>pallescens</italic> groups, more related to each other than they are to the <italic>prolixus</italic> group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three <italic>Rhodnius</italic> groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the <italic>prolixus</italic> group, involving the related species of the <italic>robustus</italic> complex but also the pairwise <italic>R. nasutus</italic> and <italic>R. neglectus</italic>. A genome wide analysis highlighted an introgression event in the <italic>pictipes</italic> group between <italic>R. stali</italic> and <italic>R. brethesi</italic> and suggested a complex gene flow between the three species of the <italic>pallescens</italic> group, <italic>R. colombiensis, R. pallescens</italic> and <italic>R. ecuadoriensis</italic>. The molecular data supports also a sylvatic distribution of <italic>R. prolixus</italic> in Brazil (Pará state) and the monophyly of <italic>R. robustus</italic>. 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.</p>