A phylogenomic analysis of Culicomorpha (Diptera) resolves the relationships among the eight constituent families

Abstract

Culicomorpha is a particularly species‐rich clade within Diptera (true flies) that comprises c. 10% of the described diversity, including many medically important flies. Morphological studies – even when all life stages are included – yield relationships different from those derived from molecular data, notably with regard to the position of Chironomidae. Congruence amongst molecular studies has been weak due to limitations in gene‐ and family‐level taxon coverage. Here we use a whole‐transcriptome shotgun phylogenomic approach to clarify the relationships among all families of Culicomorpha. The dataset comprised 30 species (27 ingroup) and 364 888 amino acid residues for 1233 single‐copy protein‐encoding genes. Likelihood and parsimony analyses produce robust and highly congruent phylogenetic trees, with only one node in conflict. The superfamily Culicoidea is well supported and comprises Dixidae + [Corethrellidae + (Chaoboridae + Culicidae)]. As suggested previously, Chironomoidea is not monophyletic. The well supported Thaumaleidae + Simuliidae is sister group to Culicoidea, with the weakly supported Chironomidae + Ceratopogonidae probably being the sister group of all remaining Culicomorpha. We used random addition concatenation analysis (RADICAL) and four‐cluster likelihood mapping (FcLM) to assess the strengths of nodal support. The sister‐group relationship between Chironomidae + Ceratopogonidae is consistent with the FcLM results but support for this relationship emerges only when 1150 of the 1233 loci are analysed. We discuss briefly nodes that remain poorly supported even with thousands of genes and mention problems with vouchering in transcriptomic studies.

Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)

“…Studies of fly radiations at higher taxonomic levels are now able to process and analyse large amounts of molecular data (Kutty et al, 2010;Wiegmann et al, 2011;Marinho et al, 2012;Young et al, 2016;Gillung et al, 2018;Kutty et al, 2018;Kutty et al, 2019), but AHE and massive parallel sequencing have not yet been fully exploited. Previous attempts at reconstructing flesh fly phylogeny using molecular data (Kutty et al, 2010;Piwczyński et al, 2014Piwczyński et al, , 2017 had low support at the subfamily level, possibly due to insufficient taxon sampling, uninformative or conflicting data, or both.…”

Monophyletic blowflies revealed by phylogenomics

“…The data processing followed Misof et al [36], Kutty et al [19,55], and Yan et al [56]. We used orthograph [57] for reciprocal search to infer orthology for each target taxon following the workflow of Misof et al [36] and Kutty et al [55].…”

“…The data processing followed Misof et al [36], Kutty et al [19,55], and Yan et al [56]. We used orthograph [57] for reciprocal search to infer orthology for each target taxon following the workflow of Misof et al [36] and Kutty et al [55]. Orthograph (version 0.6.1) was run using reference ortholog sets [19,56] with the alignment-program set as mafft-linsi, hmmbuildprogram as hmmbuild, hmmsearch-program as hmmsearch, blast-program as blastp, exonerate-program as exonerate, blast-score-threshold as 10, and blast-evalue-threshold as 1e−05.…”

Mitochondrial Genomes Provide Insights into the Phylogeny of Culicomorpha (Insecta: Diptera)

“…More recent studies have clarified some of those conflicts by using more advanced analytical methods and more molecular markers. Kutty et al (2018) used whole-transcriptome shotgun phylogenomic approach to clarify the relationships among all families of Culicomorpha [17]. The transcriptomic data presented a well-supported monophyletic superfamily Culicoidea comprising Dixidae + (Corethrellidae + (Chaoboridae + Culicidae)).…”