Molecular phylogeny of the Byrrhoidea-Buprestoidea complex (Coleoptera, Elateriformia)

A Review of Araeopidius monachus (LeConte, 1874) (Coleoptera: Dryopoidea: Ptilodactylidae), with Main Emphasis on Its Biology and Ecology

Araeopidius monachus (LeConte, 1874) is the only species in the subfamily Araeopidiinae within the beetle family Ptilodactylidae. Its geographic distribution is mainly along the western coast of North America, where adults are uncommon. A diagnosis is provided along with detailed collection records highlighting its seasonality, elevational range, plant associations, and collection methods. Collection records from larvae and adults indicate a three-year life cycle. Digestive tract dissections show that the larvae consume woody material while the adults probably do not feed. Additionally, we briefly discuss the problems and prospects for research of this enigmatic species.

Rhagophthalmidae Olivier, 1907 (Coleoptera, Elateroidea): described genera and species, current problems, and prospects for the bioluminescent and paedomorphic beetle lineage

Rhagophthalmidae are a small beetle family known from the eastern Palaearctic and Oriental realms. Rhagophthalmidae are closely related to railroad worms (Phengodidae) and fireflies (Lampyridae) with which they share highly modified paedomorphic females and the ability to emit light. Currently, Rhagophthalmidae include 66 species classified in the following 12 genera: Bicladodrilus Pic, 1921 (two spp.), Bicladum Pic, 1921 (two spp.), Dioptoma Pascoe, 1860 (two spp.), Diplocladon Gorham, 1883 (two spp.), Dodecatoma Westwood, 1849 (eight spp.), Falsophrixothrix Pic, 1937 (six spp.), Haplocladon Gorham, 1883 (two spp.), Menghuoius Kawashima, 2000 (three spp.), Mimoochotyra Pic, 1937 (one sp.), Monodrilus Pic, 1921 (two spp. in two subgenera), Pseudothilmanus Pic, 1918 (two spp.), and Rhagophthalmus Motschulsky, 1854 (34 spp.). The replacement name Haplocladongorhami Kundrata, nom. nov. is proposed for Diplocladonhasseltii Gorham, 1883b (described in subgenus Haplocladon) which is preoccupied by Diplocladonhasseltii Gorham, 1883a. The genus Reductodrilus Pic, 1943 is tentatively placed in Lampyridae: Ototretinae. Lectotypes are designated for Pseudothilmanusalatus Pic, 1918 and P.marginalis Pic, 1918. Interestingly, in the eastern part of their distribution, Rhagophthalmidae have remained within the boundaries of the Sunda Shelf and the Philippines demarcated by the Wallace Line, which separates the Oriental and Australasian realms. This study is intended to be a first step towards a comprehensive revision of the group on both genus and species levels. Additionally, critical problems and prospects for rhagophthalmid research are briefly discussed.

The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications

Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebusdiminutus Gebhardt, 1928 (15,499 bp), Coraebuscloueti Théry, 1893 (15,514 bp), Meliboeussinae Obenberger, 1935 (16,108 bp), Agrilussichuanus Jendek, 2011 (16,521 bp), and Sambusfemoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A.sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

Two new species of Byrrhinus Motschulsky, 1858 (Coleoptera, Limnichidae, Limnichinae) from Negros, Philippines

Two new species of Limnichidae beetles, Byrrhinusnegrosensis sp. nov. and Byrrhinusvillarini sp. nov., are described from the Island of Negros in the Philippines. The adult specimens of the new species can be differentiated by patterns of body punctation, colour and orientation of elytral pubescence, posterolateral angle of pronotum, tarsomere length ratio and aedeagal form. Two clades, representing the two new species, were retrieved in the Maximum Likelihood gene tree using the 3'-end of the COI gene. Maximum genetic divergence within B.negrosensis sp. nov. and B.villarini sp. nov. were recorded to be 2.3% and 1.3%, respectively, while the mean interspecific divergence between the two new species was 19.7%. Morphological descriptions, digital photographs and COI sequences were provided for the two species. The state of knowledge of Byrrhinus is reviewed and an updated Philippine checklist is provided. By coupling morphological and molecular data, this paper provides the first additional new species of Philippine Byrrhinus in the last 28 years.

The First Ptilodactyla Illiger, 1807 (Coleoptera: Dryopoidea: Ptilodactylidae) Described from Eocene Baltic Amber

The beetle family Ptilodactylidae contains more than 500 extant species; however, its fossil record is scarce and remains understudied. In this study, we describe a new species of Ptilodactylidae, Ptilodactyla eocenica Kundrata, Bukejs and Blank, sp. nov., based on a relatively well-preserved specimen from Baltic amber. We use X-ray microcomputed tomography to reconstruct its morphology since some of the principal diagnostic characters have been obscured by opaque bubbles. It is the third ptilodactylid species described from Baltic amber, and the first one belonging to the subfamily Ptilodactylinae. Additionally, we summarize the classification, diversity, and distribution of both extinct and extant Ptilodactylidae.

Unlocking the mystery of the mid-Cretaceous Mysteriomorphidae (Coleoptera: Elateroidea) and modalities in transiting from gymnosperms to angiosperms

The monospecific family Mysteriomorphidae was recently described based on two fossil specimens from the Late Cretaceous Kachin amber of northern Myanmar. The family was placed in Elateriformia incertae sedis without a clear list of characters that define it either in Elateroidea or in Byrrhoidea. We report here four additional adult specimens of the same lineage, one of which was described using a successful reconstruction from a CT-scan analysis to better observe some characters. The new specimens enabled us to considerably improve the diagnosis of Mysteriomorphidae. The family is definitively placed in Elateroidea, and we hypothesize its close relationship with Elateridae. Similarly, there are other fossil families of beetles that are exclusively described from Cretaceous ambers. These lineages may have been evolutionarily replaced by the ecological revolution launched by angiosperms that introduced new co-associations with taxa. These data indicate a macroevolutionary pattern of replacement that could be extended to other insect groups.

The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga

In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.

Hidden diversity in the Brazilian Atlantic rainforest: the discovery of Jurasaidae, a new beetle family (Coleoptera, Elateroidea) with neotenic females

Beetles are the most species-rich animal radiation and are among the historically most intensively studied insect groups. Consequently, the vast majority of their higher-level taxa had already been described about a century ago. In the 21st century, thus far, only three beetle families have been described de novo based on newly collected material. Here, we report the discovery of a completely new lineage of soft-bodied neotenic beetles from the Brazilian Atlantic rainforest, which is one of the most diverse and also most endangered biomes on the planet. We identified three species in two genera, which differ in morphology of all life stages and exhibit different degrees of neoteny in females. We provide a formal description of this lineage for which we propose the new family Jurasaidae. Molecular phylogeny recovered Jurasaidae within the basal grade in Elateroidea, sister to the well-sclerotized rare click beetles, Cerophytidae. This placement is supported by several larval characters including the modified mouthparts. The discovery of a new beetle family, which is due to the limited dispersal capability and cryptic lifestyle of its wingless females bound to long-term stable habitats, highlights the importance of the Brazilian Atlantic rainforest as a top priority area for nature conservation.

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

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

One less mystery in Coleoptera systematics: the position of Cydistinae (Elateriformia incertae sedis) resolved by multigene phylogenetic analysis

Cydistinae are a rare monogeneric beetle lineage from Asia with a convoluted history of classification, historically placed in various groups within the series Elateriformia. However, their position has never been rigorously tested. To resolve this long-standing puzzle, we are the first to present sequences of two nuclear and two mitochondrial markers for four species of Cydistinae to determine their phylogenetic position. We included these sequences in two rounds of analyses: one including a broad Elateriformia dataset to test placement at the superfamily/family level, and a second, including a richer, targeted sampling of presumed close relatives. Our results strongly support Cydistinae as sister to Phengodidae in a clade with Rhagophthalmidae. Based on our molecular phylogenetic results and examination of morphological characters, we hereby transfer the formerly unplaced Cydistinae into Phengodidae and provide diagnoses for the newly circumscribed Phengodidae, Cydistinae and Cydistus. Since both Phengodidae and Rhagophthalmidae have bioluminescent larvae and strongly neotenic females, similar features can be hypothesized for Cydistinae. Additionally, Cydistus minor is transferred to the new genus Microcydistus.

The complete mitochondrial genome of the jewel beetle Trachys variolaris (Coleoptera: Buprestidae)

The complete mitochondrial genome (mitogenome) of the jewel beetle, Trachys variolaris, was sequenced and described. The mitogenome of T. variolaris is a typical circular DNA molecule with 16,771 bp in length. It contains the typical 37 mitochondrial genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and a long non-coding region called the control region. Twelve protein-coding genes initiate with ATN codons except ND1 uses TTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, ND4, and ND5 terminate with a single T-- or TA-. The length of the 22 tRNAs ranges from 61 to 70 bp and they all have the clover-leaf structure except for tRNASer(AGN) . The control region is 2155 bp long with the A + T content of 69.4%. The result of our phylogenetic analysis showed that Buprestoidea is monophyletic, and it is the sister group to (Byrrhoidea + Elateroidea).

The complete mitochondrial genome of the jewel beetle Coraebus cavifrons (Coleoptera: Buprestidae)

The complete mitochondrial genome (mitogenome) of the jewel beetle, Coraebus cavifrons, was sequenced and described in the present study. The mitogenome of Coraebus cavifrons is a typical circular DNA molecule of 15,686 bp. All of the 37 mitochondrial genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) were annotated and a putative control region with 1135 bp in length was found between tRNAIle and srRNA. Protein-coding genes all initiate with ATN codons except for COII uses GTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, and ND5 terminate with a single T. All tRNAs have the clover-leaf structure except for tRNASer(AGN) and the length of them range from 60 to 71 bp. Genome organization and nucleotide composition of the mitogenome were also noted. Our phylogenetic analysis of Elateriformia supported the monophyly of Buprestoidea and the sister relationship between Buprestoidea and (Byrrhoidea + Elateroidea).

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

Background

Rhinorhipidae 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.

Results

We 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.

Conclusions

Thus, Rhinorhipidae adds another example to several recently recognized ancient relict lineages which are interspersed within contemporaneous hugely species-rich lineages of Coleoptera.

Electronic supplementary material

The online version of this article (10.1186/s12983-018-0262-0) contains supplementary material, which is available to authorized users.