Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

Abstract

BackgroundRhinorhipidae Lawrence, 1988 is an enigmatic beetle family represented by a single species, Rhinorhipus tamborinensis Lawrence, 1988, from Australia, with poorly established affinities near the superfamily Elateroidea (click beetles, soldier beetles and fireflies) or the more inclusive series (infraorder) Elateriformia. Its evolutionary position may inform the basal relationships of the suborder Polyphaga, the largest clade of Coleoptera.ResultsWe analyzed four densely sampled DNA datasets of major coleopteran lineages for mitogenomes, rRNA genes and single copy nuclear genes. Additionally, genome sequencing was used for incorporation of R. tamborinensis into a set of 4220 orthologs for 24 terminals representing 12 polyphagan superfamilies. Topologies differed to various degrees, but all consistently refute the proposed placement of Rhinorhipidae in Elateroidea and instead indicate either sister relationships with other Elateriformia, frequently together with Nosodendridae, another divergent small family hitherto placed in Derodontoidea, or in an isolated position among the deepest lineages of Polyphaga. The phylogenomic analyses recovered Rhinorhipus in a sister position to all other Elateriformia composed of five superfamilies. Therefore, we erect the new superfamily Rhinorhipoidea Lawrence, 1988, stat. Nov., with the type-family Rhinorhipidae. The origins of the Rhinorhipidae were dated to the Upper Triassic/Lower Jurassic at the very early phase of polyphagan diversification.ConclusionsThus, Rhinorhipidae adds another example to several recently recognized ancient relict lineages which are interspersed within contemporaneous hugely species-rich lineages of Coleoptera.Electronic supplementary materialThe online version of this article (10.1186/s12983-018-0262-0) contains supplementary material, which is available to authorized users.

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

“…Both trees show that Buprestoidea (Buprestidae only, without Schizopodidae) and Byrrhoidea (excluding Psephenidae) are reciprocally monophyletic groups; Elateroidea clusters as a sister to a clade of Byrrhoidea and Buprestoidea, but Psephenidae (of Byrrhoidea) is located within the Scirtoidea group. Our phylogenetic results support that Buprestoidea is a monophylum that is close to Byrrhoidea [12,14,16,19,21,22,30]; Buprestoidea and Byrrhoidea cluster within a clade sister to Elateroidea [16,28,29,31], and the position of Psephenidae is undetermined [30].…”

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

“…The predicted species‐specific gene models were then used for ab initio gene predictions in augustus , and predicted protein coding sequences were used in Orthograph v. 0.6.1 (Petersen et al , ). Outgroup data were assembled as described in previous studies (Kusy et al , ,b). The completeness of transcriptomes, genomes and predicted protein‐coding gene sets were evaluated with busco using Endopterygota single‐copy orthologs as targets.…”

“…By contrast, molecular phylogenies suggest that neoteny has multiple origins and neotenics occur in limited ranges (Bocak et al , ; Masek et al , ). Therefore, we aimed to test whether neotenic taxa evolved repeatedly in Lycidae, in congruence with evolutionary trends for soft‐bodiedness and neoteny in Elateroidea (Kundrata & Bocak, ; Kundrata et al , ; Bocak et al , ; Kusy et al , ,b). We used genomic data, as these can provide independent and decisive phylogenetic information to analyse the distribution of homoplasy in the morphological phylogeny (Misof et al , ; Peters et al , ).…”

Early evolution of Cupedidae revealed by a mid‐Cretaceous reticulated beetle from Myanmar (Coleoptera: Archostemata)

“…However, our Bayesian analysis (using the discrete Marcov k model) of the same dataset strongly supported the monophyly of the two families (C. Cai, unpublished data). The molecular-based phylogenetic studies are promising for elucidating the interrelationships in Archostemata, but published results appear limited by insufficient taxon and gene sampling, and the effects of missing data (Bocak et al, 2014;McKenna et al, 2015;Kusy et al, 2018;Linard et al, 2018). One of the challenges we face is that Crowsoniella relicta Pace (Crowsoniellidae) has not been sequenced because so far only three specimens are known.…”