• This record comes from PubMed

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

. 2018 ; 15 () : 21. [epub] 20180502

Status PubMed-not-MEDLINE Language English Country England, Great Britain Media electronic-ecollection

Document type Journal Article

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.

See more in PubMed

Bocak L, Barton C, Crampton-Platt A, Chesters D, Ahrens D, Vogler AP. Building the Coleoptera tree-of-life for >8000 species: composition of public DNA data and fit with Linnaean classification. Syst Entomol. 2014;39:97–110. doi: 10.1111/syen.12037. DOI

Hunt T, Bergsten J, Levkanicova Z, Papadopoulou A, John OS, Wild R, et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science. 2007;318:1913–1916. doi: 10.1126/science.1146954. PubMed DOI

McKenna DD, Wild AL, Kanda K, Bellamy CL, Beutel RG, Caterino MS, et al. The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the cretaceous terrestrial revolution. Syst Entomol. 2015;40:835–880. doi: 10.1111/syen.12132. DOI

Zhang SQ, Che LH, Li Y, Dan L, Pang H, Ślipiński A, Zhang P. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species. Nat Commun. 2018;205:2041–1723. PubMed PMC

Nikitsky NB, Lawrence JF, Kirejtshuk AG, Gratshev VGA. New beetle family, Decliniidae fam. N., from the Russian far east and its taxonomic relationships (Coleoptera, Polyphaga) Russ Entomol J. 1993;2:3–10.

Lawrence JF, Nikitsky NB, Kirejtshuk AB. Phylogenetic position of Decliniidae (Coleoptera: Scirtoidea) and comments on the classification of Elateriformia (sensu lato) In: Pakaluk J, Ślipiński SA, editors. Biology, phylogeny, and classification of Coleoptera: papers celebrating the 80th birthday of Roy a. Crowson. Warszawa: Muzeum i Instytut Zoologii PAN; 1995. pp. 373–410.

Ribera I, Beutel RG, Balke M, Vogler AP. Discovery of Aspidytidae, a new family of aquatic Coleoptera. Proc Biol Sci. 2002;269:2351–2356. doi: 10.1098/rspb.2002.2157. PubMed DOI PMC

Spangler PJ, Steiner WE., Jr A new aquatic beetle family, Meruidae, from Venezuela (Coleoptera: Adephaga) Syst Entomol. 2005;30:339–357. doi: 10.1111/j.1365-3113.2005.00288.x. DOI

Bocak L, Kundrata R, Andújar CF, Vogler AP. The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing. Proc Biol Sci. 2016;283:20152350. doi: 10.1098/rspb.2015.2350. PubMed DOI PMC

Lawrence JF. Rhinorhipidae, a new beetle family from Australia, with comments on the phylogeny of the Elateriformia. Invertebr Taxon. 1988;2:1–53. doi: 10.1071/IT9880001. DOI

Lawrence JF, Newton AF. Families and subfamilies of Coleoptera (with selected genera, notes, references and data on family-group names) In: Pakaluk J, Ślipiński SA, editors. Biology, phylogeny, and classification of Coleoptera: papers celebrating the 80th birthday of Roy a. Crowson. Warszawa: Muzeum i Instytut Zoologii PAN; 1995. pp. 779–1006.

Leschen RAB, Beutel RG, Lawrence JF. Handbook of zoology, Arthropoda: Insecta. Coleoptera, beetles; volume 2: morphology and systematics (Elateroidea, Bostrichiformia, Cucujiformia partim) In: Kristensen NP, Beutel RG, editors. Handbook of zoology, Arthropoda: Insecta. Berlin and New York: Walter de Gruyter GmbH & Co. KG; 2010.

Bouchard P, Bousquet Y, Davies AE, Alonso-Zarazaga MA, Lawrence JF, Lyal CHC, et al. Family-group names in Coleoptera (Insecta) ZooKeys. 2011;88:1–972. doi: 10.3897/zookeys.88.807. PubMed DOI PMC

Lawrence JF, Ślipiński SA, Seago AE, Thayer MK, Newton AF, Marvaldi AE. Phylogeny of the Coleoptera based on morphological characters of adults and larvae. Annal Zool. 2011;61:1–217. doi: 10.3161/000345411X576725. DOI

Beutel RG, Leschen RAB. Coleoptera, beetles; volume 1: morphology and systematics (Archostemata, Adephaga, Myxophaga, Polyphaga partim) In: Kristensen NP, Beutel RG, editors. Handbook of zoology, Arthropoda: Insecta. 2. Berlin and Boston: Walter de Gruyter GmbH & Co. KG; 2016.

Timmermans MJTN, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DTJ, et al. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res. 2010;38(21):e197. doi: 10.1093/nar/gkq807. PubMed DOI PMC

Timmermans MJTN, Barton C, Haran J, Ahrens D, Ollikainen A, Culverwell L, et al. Family-level sampling of mitochondrial genomes in Coleoptera: compositional heterogeneity and Phylogenetics. Genome Biol Evol. 2016;8:161–175. doi: 10.1093/gbe/evv241. PubMed DOI PMC

Bocakova M, Bocak L, Hunt T, Teravainen M, Vogler AP. Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny. Cladistics. 2007;23:477–496. doi: 10.1111/j.1096-0031.2007.00164.x. DOI

Kundrata R, Bocakova M, Bocak L. The comprehensive phylogeny of the superfamily Elateroidea (Coleoptera: Elateriformia) Mol Phylogenet Evol. 2014;76:162–171. doi: 10.1016/j.ympev.2014.03.012. PubMed DOI

Kundrata R, Jäch M, Bocak L. Molecular phylogeny of the Byrrhoidea-Buprestoidea complex (Coleoptera, Elateriformia) Zool Scr. 2017;46(2):150–164. doi: 10.1111/zsc.12196. DOI

Sharkey CR, Fujimoto MS, Lord NPSS, Mckenna DD, Suvorov A, et al. Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles. Sci Rep. 2017;7:8. doi: 10.1038/s41598-017-00061-7. PubMed DOI PMC

Wang K, Hong W, Jiao H, Zhao H. Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles. Sci Rep. 2017;7:1814. doi: 10.1038/s41598-017-01835-9. PubMed DOI PMC

Parker DJ, Cunningham CB, Walling CA, Stamper CE, Head ML, Roy-Zokan EM, et al. Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle. Nat Commun. 2015;6:8449. doi: 10.1038/ncomms9449. PubMed DOI PMC

Fallon TR, Li FS, Vicent MA, Weng JK. Sulfoluciferin is biosynthesized by a specialized luciferin sulfotransferase in fireflies. Biochemistry. 2016;55(24):3341–3344. doi: 10.1021/acs.biochem.6b00402. PubMed DOI

Peters RS, Meusemann K, Petersen M, Mayer C, Wilbrandt J, Ziesmann T, et al. The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol. 2014;14(1):52. doi: 10.1186/1471-2148-14-52. PubMed DOI PMC

Poelchau M, Childers C, Moore G, Tsavatapalli V, Evans J, Lee CY, et al. The i5k workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Res. 2014;43:(D1) 10.1093/nar/gku983. PubMed PMC

McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, et al. Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface. Genome Biol. 2017;17(1):227. doi: 10.1186/s13059-016-1088-8. PubMed DOI PMC

Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, et al. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol. 2013;14(3) 10.1186/gb-2013-14-3-r27. PubMed PMC

Richards S, et al. (Tribolium genome sequencing consortium). The genome of the model beetle and pest Tribolium castaneum. Nature. 2008;452(7190):949–955. doi: 10.1038/nature06784. PubMed DOI

Toussaint E, Seidel M, Arriaga-Varela E, Hájek J, Král D, Sekerka L, et al. The peril of dating beetles. Syst Entomol. 2017;42:1–10. doi: 10.1111/syen.12198. DOI

Slowinski JB, Guyer C. Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction. Am Nat. 1993;142:1019–1024. doi: 10.1086/285586. PubMed DOI

Rabosky DL, Grundler M, Anderson C, Title P, Shi JJ, Brown JW, et al. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol Evol. 2014;5(7):701–707. doi: 10.1111/2041-210X.12199. DOI

Wolfe JM, Daley AC, Legg D, Edgecombe GD. Fossil calibrations for the arthropod tree of life. Earth Sci Rev. 2016;160:43–110. doi: 10.1016/j.earscirev.2016.06.008. DOI

Labandeira CC, Eble GJ. The fossil record of insect diversity and disparity. In: Anderson J, Thackeray F, Van Wyk B, De Wit M, editors. Gondwana alive: biodiversity and the evolving biosphere. Johannesburg: Witwatersrand University Press; 2000.

Kirejtshuk AG, Poschmann M, Prokop J, Garrouste R, Nel A. Evolution of the elytral venation and structural adaptations in the oldest Palaeozoic beetles (Insecta: Coleoptera: Tshekardocoleidae) J Syst Palaeontol. 2014;12(5):575–600. doi: 10.1080/14772019.2013.821530. DOI

Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, et al. HybPiper: extracting coding sequence and introns for Phylogenetics from high-throughput sequencing reads using target enrichment. Appl Plant Sci. 2016;4(7):1600016. doi: 10.3732/apps.1600016. PubMed DOI PMC

Allen JM, Boyd B, Nguyen NP, Vachaspati P, Warnow T, Huang D, et al. Phylogenomics from whole genome sequences using aTRAM. Syst Biol. 2017;66:786–798. PubMed

Gould SJ. A special fondness for beetles. Nat Hist. 1993;102:4–6.

Holz M. Mesozoic paleogeography and paleoclimates – a discussion of the diverse greenhouse and hothouse conditions of an alien world. J S Am Earth Sci. 2015;61:91–107. doi: 10.1016/j.jsames.2015.01.001. DOI

Andújar C, Arribas P, Ruzicka F, Crampton-Platt A, Timmermans MJTN, Vogler AP. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol Ecol. 2015;24(14):3603–3617. doi: 10.1111/mec.13195. PubMed DOI

Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Mol Biol Evol. 2015;32(9):2302–2316. doi: 10.1093/molbev/msv111. PubMed DOI PMC

Andújar C, Arribas P, Linard B, Kundrata R, Bocak L, Vogler AP. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles. Mitochondrial DNA A DNA Mapp Seq Anal. 2017;28(2):156–158. PubMed

Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, et al. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–319. doi: 10.1016/j.ympev.2012.08.023. PubMed DOI

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Katoh K, Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics. 2008;9:212. doi: 10.1186/1471-2105-9-212. PubMed DOI PMC

Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, et al. SOAPdenovo-trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30(12):1660–1666. doi: 10.1093/bioinformatics/btu077. PubMed DOI

Amaral DT, Silva JR, Viviani VR. Transcriptional comparison of the photogenic and non-photogenic tissues of Phrixothrix hirtus (Coleoptera: Phengodidae) and non-luminescent Chauliognathus flavipes (Coleoptera: Cantharidae) give insights on the origin of lanterns in railroad worms. Gene Rep. 2017;7:78–86. doi: 10.1016/j.genrep.2017.02.004. DOI

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, et al. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res. 2016;45:(D1) 10.1093/nar/gkw1119. PubMed PMC

Petersen M, Meusemann K, Donath A, Dowling D, Liu S, Peters RS, et al. Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics. 2017;18(1) 10.1186/s12859-017-1529-8. PubMed PMC

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. doi: 10.1186/1471-2105-10-421. PubMed DOI PMC

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi: 10.1089/cmb.2012.0021. PubMed DOI PMC

Slater G, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6(1):31. doi: 10.1186/1471-2105-6-31. PubMed DOI PMC

Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992;89(22):10915–10919. doi: 10.1073/pnas.89.22.10915. PubMed DOI PMC

Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, et al. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014;346:763. doi: 10.1126/science.1257570. PubMed DOI

Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34(Web Server 10.1093/nar/gkl315. PubMed PMC

Misof B, Misof KA. Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst Biol. 2009;58(1):21–34. doi: 10.1093/sysbio/syp006. PubMed DOI

Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, Wägele JW, Misof B. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Front Zool. 2010;7(1):10. doi: 10.1186/1742-9994-7-10. PubMed DOI PMC

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–2690. doi: 10.1093/bioinformatics/btl446. PubMed DOI

Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44(W1):W232–W235. doi: 10.1093/nar/gkw256. PubMed DOI PMC

Kalyaanamoorthy S, Minh BQ, Wong TK, Haeseler AV, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Chernomor O, von Haeseler A, Minh BQ. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 2016;65:997–1008. doi: 10.1093/sysbio/syw037. PubMed DOI PMC

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518–522. doi: 10.1093/molbev/msx281. PubMed DOI PMC

Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004;21(6):1095–1109. doi: 10.1093/molbev/msh112. PubMed DOI

Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: 2010 gateway computing environments workshop, GCE, vol. 2010. 10.1109/GCE.2010.5676129.

Grunewald S, Spillner A, Bastkowski S, Bogershausen A, Moulton V. SuperQ: computing Supernetworks from quartets. IEEE/ACM Trans Comput Biol Bioinform. 2013;10(1):151–160. doi: 10.1109/TCBB.2013.8. PubMed DOI

Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V, SPECTRE. A suite of PhylogEnetiC tools for reticulate evolution. 2017; 10.1101/169177. PubMed PMC

Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2005;23(2):254–267. doi: 10.1093/molbev/msj030. PubMed DOI

Rasnitsyn AP, Quicke DLJ. History of insects. Dordrecht, The Netherlands: Kluwer Academic Publisher; 2002.

Behrensmeyer AK, Turner A. Taxonomic occurrences of Elateriformia and Scarabaeiformia recorded in the Paleobiology database Fossilworks. 2015. See. http://fossilworks.org

Whalley PES. The systematics and palaeogeography of the lower Jurassic insects of Dorset, England. Bull Br Mus Nat Hist. 1985;39:107–189.

Heer O. Die Urwelt der Schweiz. Friedrich Schulthess: Zürich; 1865.

Prokin AA, Makarov KV, Ponomarenko AG, Bashkuev AS. New beetle larvae (Coleoptera: Coptoclavidae, Caraboidea, Polyphaga) from the upper Triassic of Germany. Russ Entomol J. 2013;22(4):259–274.

Ho SYW, Phillips MJ. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol. 2009;58(3):367–380. doi: 10.1093/sysbio/syp035. PubMed DOI

Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29(8):1969–1973. doi: 10.1093/molbev/mss075. PubMed DOI PMC

Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2017;34:772–773. PubMed

Newest 20 citations...

See more in
Medvik | PubMed

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

. 2022 ; 1126 () : 55-130. [epub] 20221101

Integrated phylogenomics and fossil data illuminate the evolution of beetles

. 2022 Mar ; 9 (3) : 211771. [epub] 20220323

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

. 2020 Dec 29 ; 12 (1) : . [epub] 20201229

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

. 2020 Nov 19 ; 10 (1) : 20158. [epub] 20201119

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

. 2020 Oct 08 ; 10 (1) : 16854. [epub] 20201008

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

. 2020 Jan 31 ; 10 (1) : 1544. [epub] 20200131

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

. 2019 ; 7 () : e6511. [epub] 20190305

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

. 2018 Nov 20 ; 8 (1) : 17084. [epub] 20181120

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

. 2018 Nov 01 ; 9 (4) : . [epub] 20181101

Find record

Citation metrics

Loading data ...

Archiving options

Loading data ...