In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.

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.

The first thorough molecular phylogeny of the superfamily Cleroidea, represented by 377 taxa, and the first with an emphasis on Trogossitidae, was undertaken. Maximum likelihood and Bayesian analyses were performed on a four-gene dataset (18S, 28S, cox1, cytb) of 395 taxa (along with 18 outgroups), including all 16 currently recognized families of Cleroidea and all current and formerly recognized tribes of Trogossitidae. The superfamily as a whole received strong support in Bayesian analyses. On the basis of phylogenetic results, 18 families in Cleroidea are recognized, including three taxa elevated to family for the first time and two reinstated families. The former tribe Rentoniini (Trogossitidae: Peltinae) was strongly supported as a monophyletic group apart from the remainder of Trogossitidae, and is herein elevated to family status, Rentoniidae stat.n. Protopeltis was also found to be an isolated lineage and becomes Protopeltidae stat.n. Peltini + Larinotini were recovered as a weakly supported sister grouping; Peltini (including only Peltis) becomes Peltidae stat.rest. The trogossitid subfamily Lophocaterinae, to the exclusion of Decamerini, formed a clade which is here designated Lophocateridae stat.rest. and sensu n. The Trogossitinae tribes Calityini, Egoliini (represented by Egolia) and Larinotini were recovered apart from core Trogossitidae but showed no strong affinities to other taxa or congruence between analyses; they are here conservatively retained in Trogossitidae as Calityinae stat.rest., Egoliinae stat.rest. and Larinotinae stat.rest. The genus Thymalus of the peltine tribe Thymalini was indicated with moderate to strong support as the sister group of the Decamerini (Trogossitidae: Lophocaterinae); together these represent Thymalidae stat.n. and sensu n. with subfamilies Decamerinae stat.rest. (new placement) and Thymalinae stat.n. The remainder of Trogossitinae, the tribes Trogossitini and Gymnochilini, formed a well-supported clade which comprises the Trogossitidae: Trogossitinae sensu n. The tribe Gymnochilini syn.n. is synonymized with Trogossitini. The monotypic family Phloiophilidae was recovered, contradicting a recent placement within Trogossitidae. The melyrid lineage was recovered with moderate (maximum likelihood) to strong (Bayesian analyses) support and includes the families Phycosecidae, Rhadalidae, Mauroniscidae, Prionoceridae and Melyridae (including Dasytidae and Malachiidae). The genus Dasyrhadus is tentatively transferred from Rhadalidae to Mauroniscidae. The genus Gietella, once proposed as a distinct family but recently placed within Dasytidae, was recovered as strongly sister to Rhadalidae sensu n., and we transfer it to that family as Gietellinae new placement. Attalomiminae (formerly Attalomimidae) syn.n. is synonymized with Melyridae: Malachiinae: Lemphini sensu n. Melyridae sensu n. includes only Dasytinae, Malachiinae and Melyrinae. Metaxina

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.

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A pre-phylogenetic revision of the family Phalacridae at the genus level is presented. Twenty-eight new generic synonymies are established as follows: Acylomus Sharp 1888 (=Liophalacrus Sharp 1888, syn. nov.; Ganyrus Guillebeau 1894, syn. nov.; Podocesus Guillebeau 1894, syn. nov.; Tinodemus Guillebeau 1894, syn. nov.; Ledorus Guillebeau 1895, syn. nov.; Astenulus Guillebeau 1896, syn. nov.; Afronyrus Švec 2006, syn. nov.), Apallodes Reitter 1873 (=Litolibrus Sharp 1889, syn. nov.; Sphaeropsis Guillebeau 1893, syn. nov.; Gyromorphus Guillebeau 1894, syn. nov.), Augasmus Motschulsky 1858 (=Megischius Guillebeau 1896, syn. nov.; Nematolibrus Sahlberg 1913, syn. nov.), Entomocnemus Guillebeau 1894 (=Stilbomimus Champion 1924, syn. nov.), Grouvelleus Guillebeau 1892 (=Ochrolitoides Champion 1924, syn. nov.; Litotarsus Champion 1925, syn. nov.), Litochrus Erichson 1845 (=Merobrachys Guillebeau 1895, syn. nov.), Litostilbus Guillebeau 1894 (=Pseudolitochrus Liubarsky 1993, syn. nov.), Ochrolitus Sharp 1889 (=Gorginus Guillebeau 1894, syn. nov.), Olibroporus Casey 1890 (=Parasemus Guillebeau 1894, syn. nov.), Olibrosoma Tournier 1889 (=Lichrotus Lyubarsky 1993, syn. nov.), Phaenocephalus Wollaston 1873 (=Phalacratomus Scott 1922, syn. nov.; Heterostilbus Champion 1924, syn. nov.), Phalacrinus Blackburn 1891 (=Sphaerostilbus Champion 1924, syn. nov.), Pseudolibrus Flach 1889 (=Biophytus Guillebeau 1894, syn. nov.; Polyaloxus Guillebeau 1894, syn. nov.), Pycinus Guillebeau 1893 (=Ochrodemus Guillebeau 1893, syn. nov.; Radinus Guillebeau 1893, syn. nov.; Euphalacrus Champion 1925, syn. nov.). Ten new genera and seven new species are described: Antennogasmus, gen. nov. (type species: A. cordatus, sp. nov.), Austroporus, gen. nov. (type species: A. victoriensis (Blackburn)), Malagasmus Gimmel, gen. nov. (type species: M. thalesi, sp. nov.), Malagophytus, gen. nov. (type species: M. steineri, sp. nov.), Neolitochrus, gen. nov. (type species: N. pulchellus (LeConte)), Paracylomus, gen. nov. (type species: P. asiaticus (Champion)), Platyphalacrus, gen. nov. (type species: P. lawrencei, sp. nov.), Ranomafanacrinus, gen. nov. (type species: R. nigrinus, sp. nov.), Steinerlitrus, gen. nov. (type species: S. warreni, sp. nov.), Sveculus, gen. nov. (type species: S. lewisi, sp. nov.). Generic reassignments resulted in 194 new combinations. Nine new names have been established for junior primary and secondary homonyms: Acylomus bicoloratus nom. nov. for Tinodemus bicolor Švec 2002; Acylomus lyubarskyi nom. nov. for Olibrus capriviensis Lyubarsky 1998; Acylomus sveci nom. nov. for Tinodemus reticulatus Švec 2002; Acylomus orientalis nom. nov. for Stilbus similis Švec 1992; Acylomus zdeneki nom. nov. for Afronyrus snizeki Švec 2006; Apallodes championi nom. nov. for Litolibrus ocellatus Champion 1925; Olibrus peringueyi nom. nov. for Olibrus consanguineus Péringuey 1892; Augasmus exquisitus nom. nov. for Litochrus pulchellus Blackburn 1895; Litochrus pronotalis nom. nov. for Augasmus bimaculatus Lyubarsky 1996. A type species is design...

With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. 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 genes sampling 129 out of the 194 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., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic 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, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.

No abstract