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Dave J. Clarke

Bio: Dave J. Clarke is an academic researcher from University of Memphis. The author has contributed to research in topics: Steninae & Stenus. The author has an hindex of 9, co-authored 18 publications receiving 603 citations. Previous affiliations of Dave J. Clarke include University of Illinois at Chicago & Field Museum of Natural History.
Topics: Steninae, Stenus, Weevil, Nemonychidae, Anoplophora

Papers
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TL;DR: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle and to a lesser degree, other phytophagous insects.
Abstract: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.

166 citations

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TL;DR: Beetles diversity 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.
Abstract: 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.

157 citations

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TL;DR: A reconstructed timetree for weevils is consistent with a Mesozoic radiation of gymnosperm‐associated taxa to form most extant families and diversification of Curculionidae alongside flowering plants—first monocots, then other groups—beginning in the Cretaceous.
Abstract: The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50,000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein-coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in previous studies, but with some interesting exceptions. Notably, the backbone relationships of the weevil phylogeny were consistently strongly supported, and the former Nemonychidae (pine flower snout beetles) were polyphyletic, with the subfamily Cimberidinae (here elevated to Cimberididae) placed as sister group of all other weevils. The clade comprising the sister families Brentidae (straight-snouted weevils) and Curculionidae was maximally supported and the composition of both families was firmly established. The contributions of substitution modeling, codon usage and/or mutational bias to differences between trees reconstructed from amino acid and nucleotide sequences were explored. A reconstructed timetree for weevils is consistent with a Mesozoic radiation of gymnosperm-associated taxa to form most extant families and diversification of Curculionidae alongside flowering plants-first monocots, then other groups-beginning in the Cretaceous.

58 citations

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TL;DR: The geniculate antennae and long rostrum with exodont mandibles of most Mesophyletidae indicate that they were highly specialised phytophages of early angiosperms preserved in the amber, likely ovipositing in flowers or seeds.
Abstract: Only a few weevils have been described from Burmese amber, and although most have been misclassified, they show unusual and specialised characters unknown in extant weevils. In this paper, we present the results of a study of a much larger and more diverse selection of Burmese amber weevils. We prepared all amber blocks to maximise visibility of structures and examined these with high-magnification light microscopy as well as CT scanning (selected specimens). We redescribe most previously described taxa and describe 52 new species in 26 new genera, accompanied by photographs. We compare critical characters of these weevils with those of extant taxa and outline the effects of distortion on their preservation and interpretation. We conclude that only two weevil families are thus far represented in Burmese amber, Nemonychidae and a newly recognised family, Mesophyletidae, which appears closely related to Attelabidae but cannot be accommodated in this family. The geniculate antennae and long rostrum with exodont mandibles of most Mesophyletidae indicate that they were highly specialised phytophages of early angiosperms preserved in the amber, likely ovipositing in flowers or seeds. This weevil fauna appears to represent an extinct mid-Cretaceous ecosystem and fills a critical gap in the fossil record of weevils.

54 citations

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TL;DR: It is suggested that the continuous presence of mesic habitats may have buffered these lineages from strong selection for morphological change and originated in the Late Jurassic– Early Cretaceous and the Staphylinine group in the Early Jurassic.
Abstract: The Staphylinine group of rove beetle subfamilies is a significant animal radiation, and one subordinate monophyletic clade – the ‘Euaesthetine subgroup’ – includes around 3000 species in subfamilies Euaesthetinae and Steninae and has a fossil record dating to the Early Cretaceous. Detailed morphological study of a new well-preserved Cretaceous Burmese amber fossil revealed strong evidence consistent with its taxonomic placement in the euaesthetine genus Octavius . We thus describe Octavius electrospinosus sp. nov., the first Cretaceous record of the genus and of the tribe Euaesthetini. Previously, the oldest records of Octavius and Euaesthetini were from the Eocene (Baltic amber) and discovery of O. electrospinosus sp. nov. therefore nearly doubles the minimum lineage age of Octavius , increasing it by ∼50 million years. We also briefly review the known Euaesthetine subgroup fossil record and tabulate summary data for all previously described fossils. All are placed in extant genera, and have visible diagnostic generic-level characters including some putative synapomorphies as judged by recent phylogenetic work. Including O. electrospinosus sp. nov., there are now four known Cretaceous species, all of which belong to either Octavius , Nordenskioldia , or Stenus . To explain the long-term morphological stasis in this group of rove beetles, we suggest that the continuous presence of mesic habitats may have buffered these lineages from strong selection for morphological change. Considering the fossils along with phylogenetic hypotheses we suggest the Euaesthetine subgroup originated in the Late Jurassic– Early Cretaceous and the Staphylinine group in the Early Jurassic. We emphasize the derived status of Cretaceous fossils in assessing possible divergence times and the significance of the pre-Cretaceous taphonomic bias for restricting more robust estimates. Further detailed morphological study of available fossils in a phylogenetic framework is badly needed to clarify the phylogenetic positions of these taxa.

49 citations


Cited by
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23 Nov 1935-Nature
TL;DR: The Principles of Insect Morphology by R. E. Snodgrass as discussed by the authors is one of the most important works in the field of insect morphology, and it has been widely used in the literature.
Abstract: THE author of this book ranks as the foremost American worker on insect morphology. His contributions on the subject are notable for their clarity and originality of thought, and the appearance of a volume, embodying his ideas in comprehensive form, is sure of a hearty welcome. In its preparation, Mr. Snodgrass has incorporated the results of much first-hand study with those of many recent investigators in the same field. He has produced an outstanding book wherein knowledge of facts is combined with that of function and, at the same time, theoretical conceptions of the origins and relationships of organs and parts are not overlooked. Principles of Insect Morphology By R. E. Snodgrass. (McGraw-Hill Publications in the Zoological Sciences.) Pp. ix + 667. (New York and London: McGraw-Hill Book Co., Inc., 1935.) 36s. net.

770 citations

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224 citations

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206 citations

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TL;DR: Beetles diversity 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.
Abstract: 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.

157 citations

Journal ArticleDOI

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TL;DR: The results strongly suggest that ant-like stone beetles do not form an independent family, but are morphologically modified members of Staphylinidae and, consequently, should be treated as a 32nd recent subfamily within the megadiverse Staphyllinidae sensu latissimo.
Abstract: Ant-like stone beetles (Coleoptera: Scydmaenidae) include more than 4,850 described species in about 90 genera main- tained as a separate cosmopolitan family since 1815. Recent authors have hypothesised that Scydmaenidae might be rooted deep inside rove-beetles (Staphylinidae). To test this hypothesis we analysed 206 parsimoniously informative larval and adult morpho- logical characters scored for 38 taxa. Strict consensus topologies from the shortest trees in all 12 analyses consistently placed Scyd- maenidae as sister to (Steninae + Euaesthetinae) in a monophyletic Staphylinine Group (with or without Oxyporinae). The single fully resolved and most consistently supported topology maintains a monophyletic Staphylinine Group consisting of Oxyporinae + (Megalopsidiinae + (("Scydmaenidae" + (Steninae + Euaesthetinae)) + (Leptotyphlinae + (Pseudopsinae + (Paederinae + Staphylini- nae))))); Solierius lacks larval data and is ambiguously placed within the Group. Eight analyses of variably aligned 18S rDNA data for 93 members of Staphylinoidea under parsimony, neighbour-joining and Bayesian approaches were markedly inconsistent, although partly congruent with the Scydmaenidae + (Steninae + Euaesthetinae) hypothesis. Our results strongly suggest that ant-like stone beetles do not form an independent family, but are morphologically modified members of Staphylinidae and, consequently, should be treated as a 32nd recent subfamily within the megadiverse Staphylinidae sensu latissimo. Formal taxonomic acts are: Scydmaeninae Leach, 1815, status novus (= Scydmaenidae Leach, 1815); Scydmaenitae Leach, 1815, status novus (= Scydmaeninae Leach, 1815); Mastigitae Fleming, 1821, status novus (= Mastiginae Fleming, 1821); Hapsomelitae Poinar & Brown, 2004, status novus (= Hapsomelinae Poinar & Brown, 2004). The family Staphylinidae sensu latissimo becomes the largest in Coleoptera and in the whole of the Animal Kingdom, with 55,440 described species (extant plus extinct), thus surpassing Curculionidae with an esti- mated 51,000 described species.

157 citations