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

Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft-bodied elateroid lineage

This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Cantharidae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chauliognathinae is proposed as a sister to the remaining Cantharidae, followed by the redefined Malthininae (including Tytthonyxini), the paraphyletic "dysmorphocerine" lineages (Dysmorphocerinae sensu stricto and Heteromastiginae subfam. nov.), and Silinae + Cantharinae as a terminal clade. The present phylogeny supersedes earlier morphology and short-fragment molecular hypotheses that have not converged on a consensus. Few morphological characters corroborate the DNA-based relationships (see the adults and larval keys). However, morphology-based hypotheses have relied on a few informative characters, and no evidence strongly rejects the preferred molecular topology. The interpretation of morphological characters and uncertain polarity resulting from the high phenotypic disparity of Elateroidea are discussed in detail. The dated phylogeny hypothesizes the earliest split within the Cantharidae in the Berriasian stage (Early Cretaceous, ~141 Myr) and the diversification of most extant subfamilies and tribes already in the Late Cretaceous. The most diverse subfamily, Cantharinae, represents a delayed radiation that started during the Eocene climatic optimum, 55.5 Myr. The late origin of Cantharinae questions the classification of Cretaceous Cantharidae as members of Cantharinae. Instead, the results suggest their deeper rooting after separating from dysmorphocerine lineages and before the node between Cantharinae and Silinae.

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.

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.

New Genera and Species of the Family Throscidae (Coleoptera: Elateroidea) in Mid-Cretaceous Burmese Amber

Captopus depressiceps gen. et sp. nov., Electrothroscus yanpingae gen. et sp. nov. and Pseudopactopus robustus gen. et sp. nov. are reported from the mid-Cretaceous Burmese amber. These new findings greatly extend the Mesozoic diversity of Throscidae, which implies a high degree of morphological disparity for this family in the Cretaceous.

Click Beetle Mitogenomics with the Definition of a New Subfamily Hapatesinae from Australasia (Coleoptera: Elateridae)

Elateridae is a taxon with very unstable classification and a number of conflicting phylogenetic hypotheses have been based on morphology and molecular data. We assembled eight complete mitogenomes for seven elaterid subfamilies and merged these taxa with an additional 22 elaterids and an outgroup. The structure of the newly produced mitogenomes showed a very similar arrangement with regard to all earlier published mitogenomes for the Elateridae. The maximum likelihood and Bayesian analyses indicated that Hapatesus Candèze, 1863, is a sister of Parablacinae and Pityobiinae. Therefore, Hapatesinae, a new subfamily, is proposed for the Australian genera Hapatesus (21 spp.) and Toorongus Neboiss, 1957 (4 spp.). Parablacinae, Pityobiinae, and Hapatesinae have a putative Gondwanan origin as the constituent genera are known from the Australian region (9 genera) and Neotropical region (Tibionema Solier, 1851), and only Pityobius LeConte, 1853, occurs in the Nearctic region. Another putative Gondwanan lineage, the Afrotropical Morostomatinae, forms either a serial paraphylum with the clade of Parablacinae, Pityobiinae, and Hapatesinae or is rooted in a more terminal position, but always as an independent lineage. An Eudicronychinae lineage was either recovered as a sister to Melanotini or as a deep split inside Elaterinae and we herein transfer the group to Elaterinae as Eudicronychini, a new status. The mitochondrial genomes provide a sufficient signal for the placement of most lineages, but the deep bipartitions need to be compared with phylogenomic analyses.

The Clicking Elateroidea from Chinese Mesozoic Deposits (Insecta, Coleoptera)

Recent molecular studies have suggested that the clicking beetle families Elateridae, Eucnemidae, Throscidae, and Cerophytidae evolved in the Jurassic and diversified in the Cretaceous. These studies paid little attention to fossils, using them only as dating tools. The identification of Elateridae fossils is challenging, as external synapomorphies are not known for this family. Elateridae can be identified only as something not belonging to the other related families, all of which have diagnostic synapomorphies. Most subfamilies and tribes of Elateridae do possess definite diagnostic characters, however, making their identification feasible. We checked the 28 Elateridae described from Chinese Mesozoic deposits. Twelve were Elateridae, seven were Eucnemidae, and one was a Throscidae. Three species could be Eucnemidae, but showed aberrant characters. Five species could not be placed and may not belong to Elateroidea at all. On the basis of these results we suggest that all previously described Elateridae fossils should be re-checked. They should be searched for synapomorphies defining Eucnemidae, Throscidae, and Cerophytidae. If such characters are not present, a click beetle type of fossil can be placed in Elateroidae incertae sedis. The Mesozoic Chinese Elateridae fossils all belong to clades that do not exist today, whereas the Mesozoic Eucnemidae subfamilies are extant ones. This may be the source of the disagreement between Elateridae fossil age and datings based on molecular studies. One new combination was made: Desmatus ponomarenkoi (Chang, Kiretjshuk & Ren, 2009) NEW COMBINATION (= Paradesmatus ponomarenkoi Chang, Kirejtshuk & Ren, 2009).

X-ray micro-computed tomography reveals a unique morphology in a new click-beetle (Coleoptera, Elateridae) from the Eocene Baltic amber

Beetle fossils are a rich source of information about the palaeodiversity and evolutionary history of the order Coleoptera. Despite the increasing rate of fossil research on click-beetles (Coleoptera: Elateridae), the most diverse group in the superfamily Elateroidea, their fossil record has remained largely unstudied. This may be caused by the combination of their rather uniform external morphology and the suboptimal state of preservation and visibility in most fossil specimens. Here, we used X-ray micro-computed tomography to reconstruct the morphology of an interesting click-beetle from Eocene Baltic amber, which had some principal diagnostic characters obscured by opaque bubbles and body position. Our results suggest that the newly described Baltelater bipectinatus gen. et sp. nov. belongs to tribe Protelaterini within subfamily Lissominae. Since Protelaterini have a predominantly Gondwanan distribution, our discovery is of a great importance for the historical biogeography of the group. Very distinctive are the bipectinate antennae with 11 antennomeres and with rami beginning on antennomere IV, which are not found in any recent Elateridae. The discovery of a new click-beetle lineage from European Eocene amber sheds further light on the palaeodiversity and historical diversification of the family as well as on the composition of the extinct amber forest ecosystem.

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.

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.

Basal polyphagan beetles in mid-Cretaceous amber from Myanmar: biogeographic implications and long-term morphological stasis

The origin and early evolutionary history of polyphagan beetles have been largely based on evidence from the derived and diverse 'core Polyphaga', whereas little is known about the species-poor basal polyphagan lineages, which include Scirtoidea (Clambidae, Decliniidae, Eucinetidae, and Scirtidae) and Derodontidae. Here, we report two new species Acalyptomerus thayerae sp. nov. and Sphaerothorax uenoi sp. nov., both belonging to extant genera of Clambidae, from mid-Cretaceous Burmese amber. Acalyptomerus thayerae has a close affinity to A. herbertfranzi, a species currently occurring in Mesoamerica and northern South America. Sphaerothorax uenoi is closely related to extant species of Sphaerothorax, which are usually collected in forests of Nothofagus of Australia, Chile, and New Zealand. The discovery of two Cretaceous species from northern Myanmar indicates that both genera had lengthy evolutionary histories, originated at least by the earliest Cenomanian, and were probably more widespread than at present. Remarkable morphological similarities between fossil and living species suggest that both genera changed little over long periods of geological time. The long-term persistence of similar mesic microhabitats such as leaf litter may account for the 99 Myr morphological stasis in Acalyptomerus and Sphaerothorax. Additionally, the extinct staphylinoid family Ptismidae is proposed as a new synonym of Clambidae, and its only included species Ptisma zasukhae is placed as incertae sedis within Clambidae.

The evolution and genomic basis of beetle diversity

The order Coleoptera (beetles) is arguably the most speciose group of animals, but the evolutionary history of beetles, including the impacts of plant feeding (herbivory) on beetle diversification, remain poorly understood. We inferred the phylogeny of beetles using 4,818 genes for 146 species, estimated timing and rates of beetle diversification using 89 genes for 521 species representing all major lineages and traced the evolution of beetle genes enabling symbiont-independent digestion of lignocellulose using 154 genomes or transcriptomes. Phylogenomic analyses of these uniquely comprehensive datasets resolved previously controversial beetle relationships, dated the origin of Coleoptera to the Carboniferous, and supported the codiversification of beetles and angiosperms. Moreover, plant cell wall-degrading enzymes (PCWDEs) obtained from bacteria and fungi via horizontal gene transfers may have been key to the Mesozoic diversification of herbivorous beetles-remarkably, both major independent origins of specialized herbivory in beetles coincide with the first appearances of an arsenal of PCWDEs encoded in their genomes. Furthermore, corresponding (Jurassic) diversification rate increases suggest that these novel genes triggered adaptive radiations that resulted in nearly half of all living beetle species. We propose that PCWDEs enabled efficient digestion of plant tissues, including lignocellulose in cell walls, facilitating the evolution of uniquely specialized plant-feeding habits, such as leaf mining and stem and wood boring. Beetle diversity thus appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.

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.

Molecular phylogeny reveals the gradual evolutionary transition to soft-bodiedness in click-beetles and identifies sub-Saharan Africa as a cradle of diversity for Drilini (Coleoptera: Elateridae)

Drilini are soft-bodied predatory click-beetles (Elateridae: Agrypninae) with incompletely metamorphosed females. Due to divergent morphology, their classification has been contentious. We present the first densely sampled molecular phylogeny of Drilini based on nuclear and mitochondrial markers. Altogether, 44 species, representing all genera, were analysed using maximum likelihood and the Bayesian approach. Molecular analyses recovered five major clades that were also well supported by morphology. Afrotropical lineages mark deep splits. Most Palearctic species belong to a terminal clade. A few species of the predominantly Afrotropical Selasia are distributed from Arabia up to the Himalayas and Thailand. The origin of Drilini is dated to the Late Eocene (~35.5 Mya) and rapid radiation is identified from the Eocene/Oligocene to the Middle Miocene. We describe the gradual transformation of male morphological traits, e.g. the level of sclerotization, structure of mouthparts, loss of the thoracic interlocking mechanism, shortened elytra and expanded larviform abdomen. Five new genera, Austroselasia, Habeshaselasia, Illubaboria, Malacodrilus and Mashaselasia are proposed. Latoselasia, previously a subgenus of Wittmerselasia, is elevated to the genus rank. Five new species, Habeshaselasia nekemtensis, H. illubaborensis, Illubaboria bicolor, Malacodrilus hajeki and Mashaselasia aethiopica are described.

The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles

We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.

Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)

Plastoceridae Crowson, 1972, Drilidae Blanchard, 1845 and Omalisidae Lacordaire, 1857 (Elateroidea) are families of the Coleoptera with obscure phylogenetic relationships and modified morphology showing neotenic traits such as soft bodies, reduced wing cases and larviform females. We shotgun sequenced genomes of Plastocerus, Drilus and Omalisus and incorporated them into data matrices of 66 and 4202 single-copy nuclear genes representing Elateroidea. Phylogenetic analyses indicate their terminal positions within the broadly defined well-sclerotized and fully metamorphosed Elateridae and thus Omalisidae should now be considered as Omalisinae stat. nov. in Elateridae Leach, 1815. The results support multiple independent origins of incomplete metamorphosis in Elateridae and indicate the parallel evolution of morphological and ecological traits. Unlike other neotenic elateroids derived from the supposedly pre-adapted aposematically coloured and unpalatable soft-bodied elateroids, such as fireflies (Lampyridae) and net-winged beetles (Lycidae), omalisids and drilids evolved from well-sclerotized click beetles. These findings suggest sudden morphological shifts through incomplete metamorphosis, with important implications for macroevolution, including reduced speciation rate and high extinction risk in unstable habitats. Precise phylogenetic placement is necessary for studies of the molecular mechanisms of ontogenetic shifts leading to profoundly changed morphology.

Molecular Phylogeny, Diversity and Zoogeography of Net-Winged Beetles (Coleoptera: Lycidae)

We synthesize the evidence from molecular phylogenetics, extant distribution, and plate tectonics to present an insight in ancestral areas, dispersal routes and the effectiveness of geographic barriers for net-winged beetle tribes (Coleoptera: Lycidae). Samples from all zoogeographical realms were assembled and phylogenetic relationships for ~550 species and 25 tribes were inferred using nuclear rRNA and mtDNA markers. The analyses revealed well-supported clades at the rank of tribes as they have been defined using morphology, but a low support for relationships among them. Most tribes started their diversification in Southeast and East Asia or are endemic to this region. Slipinskiini and Dexorini are Afrotropical endemics and Calopterini, Eurrhacini, Thonalmini, and Leptolycini remained isolated in South America and the Caribbean after their separation from northern continents. Lycini, Calochromini, and Erotini support relationships between the Nearctic and eastern Palearctic faunas; Calochromini colonized the Afrotropical realm from East Asia and Metriorrhynchini Afrotropical and Oriental realms from the drifting Indian subcontinent. Most tribes occur in the Oriental and Sino-Japanese realms, the highest alpha-taxonomic diversity was identified in Malesian tropical rainforests. The turn-over at zoogeographical boundaries is discussed when only short distance over-sea colonization events were inferred. The lycid phylogeny shows that poor dispersers can be used for reconstruction of dispersal and vicariance history over a long time-span, but the current data are insufficient for reconstruction of the early phase of their diversification.