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Assassin bugs (Hemiptera: Reduviidae Latreille) comprise not only one of the largest radiations of predatory animals (22 subfamilies; >6,800 spp.) but also include the medically important kissing bugs (Triatominae Jeannel). Reduviidae are morphologically diverse, engage in an astounding array of predatory strategies and have evolved some of the most unique anti‐predator and stealth techniques in the animal kingdom. While significant progress has been made to reveal the evolutionary history of assassin bugs and revise their taxonomy, the non‐monophyly of the second largest assassin bug subfamily, Reduviinae Latreille, remains to be addressed. Leveraging phylogenomic data (2,291 loci) and 112 morphological characters, we performed the first data‐ and taxon‐rich (195 reduvioid taxa) combined phylogenetic analysis across Reduvioidea and reconstructed morphological diagnostic features for major lineages. We corroborated the rampant polyphyly of Reduviinae that demands substantial revisions to the subfamilial and tribal classification of assassin bugs. Our new classification for Reduviidae reduces the number of subfamilies to 19 and recognizes 40 tribes. We describe three new subfamilies to accommodate distantly related taxa previously classified as Reduviinae (Heteropinae subfam. nov., Nanokeralinae subfam. nov., and Pasirinae subfam. nov.). Triatominae sensu nov. are expanded to include closely related predatory reduviine genera. Cetherinae Jeannel, Chryxinae Champion, Pseudocetherinae Villiers, Salyavatinae Amyot & Serville and Sphaeridopinae Amyot & Serville are treated as junior synonyms of Reduviinae sensu nov. Epiroderinae Distant are synonymized with Phimophorinae Handlirsch sensu nov. and Bactrodini Stål stat. nov. are reclassified as a tribe of Harpactorinae Amyot & Serville. Psophidinae Distant is treated as a valid subfamily. This new classification represents a robust framework for future taxonomic and evolutionary research on assassin bugs.Zoobank Registration: http://zoobank.org/urn:lsid:zoobank.org:pub:2310C9AA-0D53-4EF6-9E75-C2B3A98CE096 [ABSTRACT FROM AUTHOR]

Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g. nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade. [ABSTRACT FROM AUTHOR]