Find research datasets worth reusing

EOL Dynamic Hierarchy Trunk (trunk): EOL Dynamic Hierarchy Trunk Active Version

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.DH Trunk version that__s currently active on the EOL site. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 15 March 2017

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.Dynamic hierarchy trunk to family except for Birds (sourced from IOC Birdlist), several marine taxa (sourced from WoRMS), certain insect groups (sourced from Species File projects), and earthworms (sourced from EOL Earthworms patch). The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 24 April 2017

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.Updated dynamic hierarchy trunk. Removed additional taxa that are covered by subtrees from WoRMS, Species File Projects, IOC Birdlist, and other providers. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 26 April 2017

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.Gigaspermaceae added. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 14 June 2017

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.More minor tweaks to fix homonym problems. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 31 May 2017

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.Various improvements over previous version. Some genera added to anchor GBIF & WoRMS taxa in microbial eukaryotes and beetles. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk March 2019

This is the trunk for the EOL reference hierarchy. It determines the relationships among the higher taxa and adds a few taxa that are not covered by other resources. The EOL DH trunk is maintained in [TTT](http://ttt.biodinfo.org/) developed by Colin (Congtian Lin) and Jiangning Wang from Biodiversity Informatics Group of the Institute of Zoology, Chinese Academy of Sciences. ##References Adl, S. M., et al. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66, 4–119. https://doi.org/10.1111/jeu.12691 Aguiar, A.P., Deans, A.R., Engel, M.S., Forshage, M., Huber, J.T., Jennings, J.T., Johnson, N.F., Lelej, A.S., Longino, J.T., Lohrmann, V., Mikó, I., Ohl, M., Rasmussen, C., Taeger, A., Yu, D.S.K., 2013. Order Hymenoptera . In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 51–62. https://doi.org/10.11646/zootaxa.3703.1.12 Aspöck, U., Haring, E., Aspöck, H., 2012. The phylogeny of the Neuropterida: long lasting and current controversies and challenges (Insecta: Endopterygota). Arthropod Systematics & Phylogeny 70, 119–129. Benton, M., 2014. Vertebrate Palaeontology. John Wiley & Sons. Betancur-R, R., Wiley, E.O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., Ortí, G., 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162. https://doi.org/10.1186/s12862-017-0958-3 Bleidorn, Christoph. 2019. Recent Progress in Reconstructing Lophotrochozoan (Spiralian) Phylogeny." Organisms Diversity & Evolution 19, no. 4 (December 1, 2019): 557–66. https://doi.org/10.1007/s13127-019-00412-4. Bouchard, P., Bousquet, Y., Davies, A., Alonso-Zarazaga, M., Lawrence, J., Lyal, C., Newton, A., Reid, C., Schmitt, M., Slipinski, A., Smith, A., 2011. Family-Group Names In Coleoptera (Insecta). ZooKeys 88, 1–972. https://doi.org/10.3897/zookeys.88.807 Cannon, Johanna Taylor, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius, and Andreas Hejnol. 2016. Xenacoelomorpha Is the Sister Group to Nephrozoa. Nature 530(7588):89–93. https://doi.org/10.1038/nature16520. Davis, R.B., Baldauf, S.L., Mayhew, P.J., 2010. The origins of species richness in the Hymenoptera: insights from a family-level supertree. BMC Evolutionary Biology 10, 109. https://doi.org/10.1186/1471-2148-10-109 Dunlop, J. A., Penney, D. & Jekel, D. 2015. A summary list of fossil spiders and their relatives. In World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annu. Rev. Ecol. Evol. Syst. 45, 371–395. https://doi.org/10.1146/annurev-ecolsys-120213-091627 Foottit, R. G., Adler, P. H., eds. 2017. Insect Biodiversity: Science and Society, Volume 1 & 2. 2nd Edition. Wiley-Blackwell. Fritz, U., Havaš, P., 2013. Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013). Zootaxa 3703, 12–14. https://doi.org/10.11646/zootaxa.3703.1.4 Giribet, Gonzalo. 2016. New Animal Phylogeny: Future Challenges for Animal Phylogeny in the Age of Phylogenomics. Organisms Diversity & Evolution 16 (2):419–26. https://doi.org/10.1007/s13127-015-0236-4. Giribet, Gonzalo, and Gregory D. Edgecombe. 2020. The Invertebrate Tree of Life. Princeton, United States: Princeton University Press, 2020. Guy, L., Ettema, T.J.G., 2011. The archaeal __TACK__ superphylum and the origin of eukaryotes. Trends in Microbiology 19, 580–587. https://doi.org/10.1016/j.tim.2011.09.002 Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R., Gude, K., Hibbett, D.S., Katz, L.A., Laughinghouse, H.D., McTavish, E.J., Midford, P.E., Owen, C.L., Ree, R.H., Rees, J.A., Soltis, D.E., Williams, T., Cranston, K.A., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112, 12764–12769. https://doi.org/10.1073/pnas.1423041112 Holzenthal, R.W., Morse, J.C., Kjer, K.M., 2011. Order Trichoptera Kirby, 1813. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 209. https://doi.org/10.11646/zootaxa.3148.1.40 Hormiga, G., Griswold, C.E., 2014. Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders. Annu. Rev. Entomol. 59, 487–512. https://doi.org/10.1146/annurev-ento-011613-162046 James, S.W., Davidson, S.K., 2012. Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences. Invertebrate Systematics 26, 213. https://doi.org/10.1071/IS11012 Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y.W., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Fonseca, R.R. da, Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P.C., Prosdocimi, F., Samaniego, J.A., Velazquez, A.M.V., Alfaro-Núñez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jønsson, K.A., Johnson, W., Koepfli, K.-P., O__Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T.P., Zhang, G., 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. https://doi.org/10.1126/science.1253451 Kathirithamby, J., Engel, M.S., 2014. A Revised Key to the Living and Fossil Families of Strepsiptera, with the Description of a New Family, Cretostylopidae. Journal of the Kansas Entomological Society 87, 385–388. https://doi.org/10.2317/JKES140407.1 Kjer, K.M., Simon, C., Yavorskaya, M., Beutel, R.G., 2016. Progress, pitfalls and parallel universes: a history of insect phylogenetics. Journal of The Royal Society Interface 13, 20160363. https://doi.org/10.1098/rsif.2016.0363 Klopfstein, S., Vilhelmsen, L., Heraty, J.M., Sharkey, M., Ronquist, F., 2013. The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data. PLoS ONE 8, e69344. https://doi.org/10.1371/journal.pone.0069344 Kocot, Kevin M., Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. https://doi.org/10.1093/sysbio/syw079. Laumer, Christopher E., Rosa Fernández, Sarah Lemer, David Combosch, Kevin M. Kocot, Ana Riesgo, Sónia C. S. Andrade, Wolfgang Sterrer, Martin V. Sørensen, and Gonzalo Giribet. 2019. Revisiting Metazoan Phylogeny with Genomic Sampling of All Phyla. Proceedings of the Royal Society B: Biological Sciences 286 (1906): 20190831. https://doi.org/10.1098/rspb.2019.0831. Laumer, Christopher E., Nicolas Bekkouche, Alexandra Kerbl, Freya Goetz, Ricardo C. Neves, Martin V. Sørensen, Reinhardt M. Kristensen, et al. 2015. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology 25(15): 2000–2006. https://doi.org/10.1016/j.cub.2015.06.068. Leschen, R.A.B., Beutel, R.G., 2014. Morphology and Systematics: Phytophaga. Walter de Gruyter. Li, H., Shao, R., Song, N., Song, F., Jiang, P., Li, Z., Cai, W., 2015. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Scientific Reports 5. https://doi.org/10.1038/srep08527 Lozano-Fernandez, J., Tanner, A.R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G.D., Pisani, D., 2019. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nature Communications 10, 2295. https://doi.org/10.1038/s41467-019-10244-7 Malm, T., Nyman, T., 2015. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 31, 1–17. https://doi.org/10.1111/cla.12069 Marlétaz, Ferdinand, Katja T. C. A. Peijnenburg, Taichiro Goto, Noriyuki Satoh, and Daniel S. Rokhsar. 2019. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology 29(2):312-318.e3. https://doi.org/10.1016/j.cub.2018.11.042. Nakano, T., Ramlah, Z., Hikida, T., 2012. Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella. Zoologica Scripta 41, 177–185. https://doi.org/10.1111/j.1463-6409.2011.00506.x Naylor, G.J.P., Caira, J.N., Jensen, K.R.E., Rosana, K.M., Straube, N., Lakner, C., 2012. Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species. In J.C. Carrier, J.A. Musick and M.R. Heithaus (editors), The Biology of Sharks and Their Relatives. 31-56. CRC Press, Taylor & Francis Group. Nesbitt, S.J., 2011. The Early Evolution of Archosaurs: Relationships and the Origin of Major Clades. Bulletin of the American Museum of Natural History, 2011(352):1-292. https://doi.org/10.1206/352.1 Nesnidal, Maximilian P., Martin Helmkampf, Achim Meyer, Alexander Witek, Iris Bruchhaus, Ingo Ebersberger, Thomas Hankeln, Bernhard Lieb, Torsten H. Struck, and Bernhard Hausdorf. 2013. New Phylogenomic Data Support the Monophyly of Lophophorata and an Ectoproct-Phoronid Clade and Indicate That Polyzoa and Kryptrochozoa Are Caused by Systematic Bias. BMC Evolutionary Biology 13(1): 253. https://doi.org/10.1186/1471-2148-13-253. Oaks, J.R., 2011. A Time-Calibrated Species Tree of Crocodylia Reveals a Recent Radiation of the True Crocodiles. Evolution 65, 3285–3297. https://doi.org/10.1111/j.1558-5646.2011.01373.x Okamura, B., Gruhl, A., Reft, A.J., 2015. Cnidarian Origins of the Myxozoa, in: Okamura, B., Gruhl, A., Bartholomew, J.L. (Eds.), Myxozoan Evolution, Ecology and Development. Springer International Publishing, Cham, pp. 45–68. https://doi.org/10.1007/978-3-319-14753-6_3 Pyron, R.A., Burbrink, F.T., Wiens, J.J., 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93. https://doi.org/10.1186/1471-2148-13-93 Robertson, J.A., Ślipiński, A., Moulton, M., Shockley, F.W., Giorgi, A., Lord, N.P., Mckenna, D.D., Tomaszewska, W., Forrester, J., Miller, K.B., Whiting, M.F., Mchugh, J.V., 2015. Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia): Systematics of Cucujoidea and Coccinelloidea. Systematic Entomology 40, 745–778. https://doi.org/10.1111/syen.12138 Rouse, Greg W., Nerida G. Wilson, Jose I. Carvajal, and Robert C. Vrijenhoek. 2016. New Deep-Sea Species of Xenoturbella and the Position of Xenacoelomorpha. Nature 530(7588):94–97. https://doi.org/10.1038/nature16545. Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., Burleigh, J.G., 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14, 23. https://doi.org/10.1186/1471-2148-14-23 Schiffer, Philipp H., Helen E. Robertson, and Maximilian J. Telford. 2018. Orthonectids Are Highly Degenerate Annelid Worms. Current Biology 28(12):1970-1974.e3. https://doi.org/10.1016/j.cub.2018.04.088. The Angiosperm Phylogeny Group, 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20. https://doi.org/10.1111/boj.12385 Van Nieukerken, E.J., Kaila, L., Kitching, I.J., Kristensen, N.P., Lees, D.C., Minet, J., Mitter, C., Mutanen, M., Regier, J.C., Simonsen, T.J., Wahlberg, N., Yen, S.-H., Zahiri, R., Adamski, D., Baixeras, J., Bartsch, D., Bengtsson, B.Å., Brown, J.W., Bucheli, S.R., Davis, D.R., Prins, J.D., Prins, W.D., Epstein, M.E., Gentili-Poole, P., Gielis, C., Hättenschwiler, P., Hausmann, A., Holloway, J.D., Kallies, A., Karsholt, O., Kawahara, A.Y., Koster, S.J.C., Kozlov, M.V., Lafontaine, J.D., Lamas, G., Landry, J.-F., Lee, S., Nuss, M., Park, K.-T., Penz, C., Rota, J., Schintlmeister, A., Schmidt, B.C., Sohn, J.-C., Solis, M.A., Tarmann, G.M., Warren, A.D., Weller, S., Yakovlev, R.V., Zolotuhin, V.V., Zwick, A., 2011. Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148, 212. https://doi.org/10.11646/zootaxa.3148.1.41 Vea, I.M., Grimaldi, D.A., 2015. Diverse New Scale Insects (Hemiptera: Coccoidea) in Amber from the Cretaceous and Eocene with a Phylogenetic Framework for Fossil Coccoidea. novi 2015, 1–15. https://doi.org/10.1206/3823.1 Vélez-Zuazo, X., Agnarsson, I., 2011. Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Molecular Phylogenetics and Evolution 58, 207–217. https://doi.org/10.1016/j.ympev.2010.11.018 Weigert, A., Bleidorn, C., 2016. Current status of annelid phylogeny. Org Divers Evol 16, 345–362. https://doi.org/10.1007/s13127-016-0265-7 Weirauch, C., Schuh, R.T., 2011. Systematics and Evolution of Heteroptera: 25 Years of Progress. Annu. Rev. Entomol. 56, 487–510. https://doi.org/10.1146/annurev-ento-120709-144833 Wiegmann, B.M., Trautwein, M.D., Winkler, I.S., Barr, N.B., Kim, J.-W., Lambkin, C., Bertone, M.A., Cassel, B.K., Bayless, K.M., Heimberg, A.M., Wheeler, B.M., Peterson, K.J., Pape, T., Sinclair, B.J., Skevington, J.H., Blagoderov, V., Caravas, J., Kutty, S.N., Schmidt-Ott, U., Kampmeier, G.E., Thompson, F.C., Grimaldi, D.A., Beckenbach, A.T., Courtney, G.W., Friedrich, M., Meier, R., Yeates, D.K., 2011. Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences 108, 5690–5695. https://doi.org/10.1073/pnas.1012675108 Winterton, S.L., Hardy, N.B., Wiegmann, B.M., 2010. On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data. Systematic Entomology 35, 349–378. https://doi.org/10.1111/j.1365-3113.2010.00521.x Yuri, T., Kimball, R.T., Harshman, J., Bowie, R.C.K., Braun, M.J., Chojnowski, J.L., Han, K.-L., Hackett, S.J., Huddleston, C.J., Moore, W.S., Reddy, S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Braun, E.L., 2013. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2, 419–444. https://doi.org/10.3390/biology2010419 Zverkov, Oleg A., Kirill V. Mikhailov, Sergey V. Isaev, Leonid Y. Rusin, Olga V. Popova, Maria D. Logacheva, Alexey A. Penin, et al. 2019. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Frontiers in Genetics 10. https://doi.org/10.3389/fgene.2019.00443.Trunk designed to work with DH 1.1 based on Catalogue of Life, NCBI, WoRMS, and other branch contributors. The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented (Patterson et al., 2016). Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy ([see current version here](https://opendata.eol.org/dataset/tram-807-808-809-810-dh-v1-1/resource/00adb47b-57ed-4f6b-8f66-83bfdb5120e8)) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see [EOL Dynamic Hierarchy](https://eol.org/docs/eol-dynamic-hierarchy)

EOL Dynamic Hierarchy, digest form, January 2019: Dynamic hierarchy digest January 2019

__Digest__ of the EOL dynamic hierarchy prepared by querying the online traits database. Unlike the full DH files, this file provides only the bare minimum information for each taxon: page id, parent page id, canonical name.Zip file containing a README and a three-column CSV (pages.csv) with header row

opencc-by-4.0Aug 2024View details →

Revealing real-time 3D in vivo pathogen dynamics in plants by label-free optical coherence tomography

This repository contains all data and code underlying the publication: J. de Wit et al. "Revealing real-time 3D in vivo pathogen dynamics in plants by label-free optical coherence tomography" in Nature Communications (2024) (https://doi.org/10.1038/s41467-024-52594-x) --------------Code description------------------ The set of scripts is largely organized around the figures. For each (sub)figure, also from supplementary materials, that involves data and plotting, there is a script that generates the plot from data that can be found in the different zip files that are present in the Zenodo repository under https://doi.org/10.5281/zenodo.11428245. The scripts use the data that is contained in the ZIP folders. The ZIP folders are organized by experiment (Experiment 1, including contrast optimization; Experiment 2), one for the other data (OtherData, the validation for with Trypan blue, and the Arabidopsis, Radish and nematode) and one as a smaller dataset to explain the method on a single B-scan (Example_Bscan_dynamicOCT). IMPORTANT: The folder where the ZIP files are unzipped should be put in the file 'basepath.txt', such that the data can be automatically loaded. Besides the figures that mention 'MakeFig...' there are a few more scripts: <ul> <li>pointcloud_generation_experiment1.py: this file makes the point clouds from the dynamic OCT images as described in Fig 2b. The resulting data is saved as maximum intensity projections and axial sums(forming the basis for Fig S4, S6 and S7) and as voxel counts (forming the basis of Fig.2c and Fig S5)</li> <li>pointcloud_generation_timelapses.py: this file does the segmentation for experiment 2 and saves the maximum intensity projections and axial sums of the different stages in the segmentation (forming the basis of Fig3a,d,e and FigS9a,b), and saves the point clouds of the data. These point clouds were refined manually in CloudCompare as described in methods. These segmented point clouds are contained in the data zip folder of experiment 2.</li> <li>StatisticalTests.R: This R file calculates the statistical tests for Fig.2cd and Fig.S5d. Here the path is not automatically updated, and should be manually set. The input file is contained in "Experiment1/SegmentationData/segmentationdata_samples.csv" and the output of the file is "D:/DataZenodo/Experiment1/SegmentationData/data_combined_Rstats_output.csv"</li> <li>example_dynamic_Bscan.py: This script gives an example of the dynamic OCT processing as proposed in this paper. First it shows the process from an OCT interference spectrum to a B-scan. Then it loads 100 B-scans and applies dynamic OCT, including normalization with histograms. Finally it gives a dynamic B-scan and plots this against the average normal OCT image. This script can be used with only the zip folder "Example_Bscan_dynamicOCT", which reduces the amount of data needed to download/unzip.</li> </ul> The list of other script files to load the data and generate the figures (guiding to the path of uncropped figures) is: <ul> <li>MakeFig1bce_Fig2e.py</li> <li>MakeFig1d.py</li> <li>MakeFig1agraphs_FigureS1.py</li> <li>MakeFig3acde_S9ab.py</li> <li>MakeFigS2_determine_dynamic_range_experiment1.py</li> <li>MakeFigS8.py</li> <li>MakeFigureS4-S6-S7.py</li> <li>MakeFigureS5.py</li> <li>MakeHistFig2b_makeFigS3b-e.py</li> <li>MakePlotsFig2ab.py</li> <li>MakePlotsFig2cd.py</li> </ul> Code was all run in Python 3 using Anaconda Spyder. Moreover, the zip file with the code contains the folder 'figures' with all subfigures. Some of them are automatically saved from the scripts, others (like photos, icons, but also the Trypan blue microscopy figure) are added in the respective folder. The are logically organized by figure number. --------------Dataset Description----------------- As mentioned above, the data is organized in four zip folders for both experiments, the other data (validation with Trypan blue, other plant-pathogens) and one for the dynamic OCT B-scan example. The data contain the following: Experiment 1:  <ul> <li>DynamicOCTimages whose subfolders (organized by date) contain a folder per volume dataset in experiment 1 with a z-stack of .tif files that form the imaged volume. The lateral sampling is 3 um and the axial sampling is 1.37 um. </li> <li>ContrastOptimization: This folder contains  <ul> <li>Bscans_with_segmentation: segmented B-scans for contrast optimization (Fig S3)</li> <li>Bscan_figS1_fig1: The B-scans and segementation for Figure S1.</li> <li>histogramdata_dynamicrange: The histograms, bins and deducted reference data for determining the dynamic range per color channel for experiment 1 (Fig S2)</li> <li>logcompressed_3value_dOCT_example: An example data stack for obtaining histograms (see script MakeFigS2_determine_dynamic_range_experiment1.py)</li> <li>overlaps_threshold-100-98-95-92-90-85-80-75-70-65-60-55-50-45perc_red-1_2_blue_-3_0_green1_filt.npy: A file with intermediate data for the contrast optimization, which can also be generated with the script "MakeHistFig2b_makeFigS3b-e.py"</li> </ul> </li> <li>SegmentationData: This folder contains  <ul> <li>MIP_segmentation_stages: maximum intensityp projections and axial sums for all images at different stages in the segmentation (basis for Fig S4,6,7)</li> <li>processed_masks and StackMasks: the manually obtained masks (segmented in StackMasks, made into masks in the folder 'processed_masks') for filtering out stomata, veins and artefacts.</li> <li>Unmasked_axialsum_th34_formanualsegmentation: This folder contains the images of Fig.S4 and were used for the segmentation (we addes a small offset, such that the in segmentation we could set it to 0 and have a unique mask). </li> <li>overview_samples_bremiayn.csv: A dataframe with the data for all the samples in experiment 1 that is used as input for the segmentation. It also contains the result of the manual check whether it has infection (Fig2c, left).</li> <li>segmentationdata_samples.csv: This supplements the file of overview_samples_bremiayn.csv with the results from the segmentation and is output to script "pointcloud_generation_experiment1.py". It forms the basis of Fig.2a-c, and FigS5, as well as for the R-script to do the statistical testing.</li> <li>qPCR_dOCT.csv: This script contains the qPCR data and is input to Fig2d. </li> </ul> </li> </ul> Experiment 2: <ul> <li>DynamicOCTimages: This contains the z-stacks of .tif files of the volumes for experiment 2 (and one extra, where a z-slice is used in Fig.1b, bottom). Sampling step size is here again 3 um in lateral direction and 1.37 um in axial direction.</li> <li>.npy files with the histograms (with same bins as Experiment 1), maxvalues and reference values for the dynamic range calculation.</li> <li>segmentation_data: this folder contains: <ul> <li>quantification_volume_disc160_33_10.csv and quantification_volume_disc160_33_10.xlsx: data from the manually segmented point clouds that form the basis of Fig.3c.</li> <li>timelapse_sampleoverview.csv: overview of the samples that is used as input in the file "pointcloud_generation_timelapses.py"</li> <li>pointclouds: Folder with segmented point clouds for the three leaf discs. These files could  be loaded in CloudCompare.</li> <li>overviewMIPs: folder with overview maximum intensity projections for the different steps in segmentation, which also forms the input of Fig.3a, FigS9ab.</li> <li>rawpointclouds: folder with the automatically generated point clouds from file pointcloud_generation_timelapses.py which were imported into CloudCompare as the basis for the segmented point clouds.</li> </ul> </li> </ul> OtherData: This folder contains the z-stacks of dynamic OCT tif images for Arabidopsis (here both a normal contrast and one that has been increased to only contain the original 0-180 range); nematodes, radish (called radijs_test_PP_py_0002), spores for Fig1c (SporesImaging) and the dynamic OCT image of Fig1d.  example_Bscan_dynamicOCT: This folder contains data to run the script example_dynamic_Bscan.py to show the dynamic OCT imaging process from raw OCT spectra. <ul> <li>raw_spectra_exampleframe: contains interference spectra, a reference spectrum and interpolation grid to show how to get from a raw OCT spectrum to a normal single B-scan.</li> <li>abs_images: contains 100 subsequent B-scans that can be used to generate a dynamic OCT image as done in example_dynamic_Bscan.py</li> </ul>

opencc-by-4.0Sep 2024View details →

Evaluating Changes in the Local Protein Physicochemical En-vironment induced by Molecular Dynamics Simulation

Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated physicochemical variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.

opencc-by-4.0Sep 2024View details →

Experimental data for nonlinear dynamics and energy harvesting of bistable cantilever shells (grant 2021/41/B/ST8/03190 from the National Science Centre, Poland)

An experimental tests on a cantilever composite bistable shell with a piezoelectric patch is reported. The shell is characterized by two stable configurations. Periodic force is applied at the shell’s clamped side through an electrodynamic shaker and the dynamic response is measured through an embedded strain gauge. Selected dynamic regimes are recorded by performing excitation frequency and amplitude sweeps. The resonance scenarios around the two natural frequencies corresponding to the stable configurations show different softening behavior. The excitation amplitude threshold level for snap-through motion is identified. The thested thin-walled pseudo-conical shell has been made of carbon-epoxy composite prepreg tape (AS4-GP-12K_40gsm- 300mm-ThinPreg135EP). The composite single layer is characterized by unidirectional reinforcement, thickness 0.04 mm. The manufacturing standard samples for strength tests in the autoclave process reduces to about 0.038 mm.

opencc-by-4.0Jan 2024View details →

The conception of a solvated electron: X-ray-induced attosecond electron dynamics of aqueous ions - data

Data set pertaining to the article "Attosecond formation of charge-transfer-to-solvent states of aqueous ions probed using the core-hole-clock technique", published in <a href="https://doi.org/10.1038/s41467-024-52740-5" target="_blank" rel="noopener">Nature Communications</a>. Here we describe the time-evolution of core level excited electronic states of metal ions in aqueous solution on an ultrashort time scale. Extensive simulations towards this project were carried out. Simulated data include geometries for solvated metal ion complexes and their X-Ray absorption spectra. Experimental data were recorded by photoemission spectroscopy from a liquid jet source using synchrotron radiation.  Files with extension .h5 are hdf5-files structured according to the NeXus standard v2022.07, see https://www.nexusformat.org/ https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format: * nexpy (distributed with python) * https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium) In each NeXus file-entry, two types of spectra are shown: 1. Sweep-averaged spectra, integrated over the non-dispersive coordinate of our detector ('data') if applicable. 2. As-measured data ('raw'). Files with extension .csv or .txt are comma-separated ascii-files, designed to be opened with a spreadsheet programme. The following files are provided: <table> <tbody> <tr> <td>Filename</td> <td>Content</td> </tr> <tr> <td> </td> <td>Experimental Data:</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/na_mg_al_1s-resonance_cfs.h5/content" target="_blank" rel="noopener noreferrer">na_mg_al_1s-resonance_cfs.h5</a></td> <td>Series of experimental photoemission spectra recorded over the 1s - val resonances, for NaCl, MgCl2 andAlCl3 metallic salt solutions</td> </tr> <tr> <td><a href="https://zenodo.org/api/records/13862194/draft/files/SI-Fig6.zip/content" target="_blank" rel="noopener noreferrer">SI-Fig6.zip</a></td> <td>Ascii representation of the data and fit curves used to determine in 1s lifetime broadening, shown in Fig. 6 of the Supplementary Information.</td> </tr> <tr> <td> </td> <td>Theoretical Data:</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.geometries.zip/content" target="_blank" rel="noopener noreferrer">th.geometries.zip</a></td> <td>Cartesian coordinates of the constituents of metal-water clusters containing 6 water molecules and containing 18 water molecules. Unit of length is Ångström.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.excitation_energy.zip/content" target="_blank" rel="noopener noreferrer">th.excitation_energy.zip</a></td> <td>Excitation energies for metal-water clusters containing 6 water molecules and containing 18 water molecule, at various levels of approximation. tddft-src2: at the SRC2-R2 level with a cc-pCVTZ basis set on the cations and a cc-pVTZ basis set on the water molecules in a polarizable continuum; eomccsd: at the EOM-EE-CCSD level with a cc-pCVTZ basis set on the cations and a cc-pVTZ basis set on the water molecules. For the purpose of spectra construction in Figure 1, each calculated spectral point was broadened by a phenomenological value of 0.2 eV. Energies are in eV, transition dipole moment components in e*bohr.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.spektrum.pade.zip/content" target="_blank" rel="noopener noreferrer">th.spektrum.pade.zip</a></td> <td>Excitation energies for metal-water clusters containing 6 water molecules calculated at the RT-TDDFT level with a cc-pVTZ basis set. For each cation, 3 trajectories were run. Energies are in eV.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.excitation_energy.zip/content" target="_blank" rel="noopener noreferrer">th.excitation_energy.zip</a></td> <td>Exciton analysis of the wave function (RMS electron size) for a set of 50 geometries of clusters containing 6 water molecules (small) or 18 water molecules (large) calculated at the SRC2-R2/cc-pVTZ level. The oscillator strengths are in a.u., the size of the electron is in Ångström.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/description_zenodo.pdf/content" target="_blank" rel="noopener noreferrer">description_zenodo.pdf</a></td> <td>More detailed description of the theoretical data sets.</td> </tr> </tbody> </table>   Version history v2: fixed incorrect choice of data file for Na scan. Data for lifetime-figure in SI added. v1: initial upload If you use part or all of these data in your scientific work we kindly ask you to provide us a copy. Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .

Active Foam Dynamics of Tissue Spheroid Fusion (Datasets and scripts)

The file attached supporting information for the paper "Active Foam Dynamics of Tissue Spheroid Fusion". Included are data from experiments, data from simulations, and a singularity image to execute a demo simulation similarly to the ones of the paper.

restrictedcc-by-4.0Jul 2024View details →

Data and code from: "Building multidimensional tolerance landscapes to predict the population dynamics of bacteria exposed to antibiotics in urban sewers"

City sewers harbor diverse bacterial communities exposed to various antibiotic residues resulting from human consumption and excretion. Although these residues typically occur at sub-inhibitory concentrations, they can still impact the growth rate and yield of susceptible wastewater bacteria. Many bacteria exhibit antibiotic tolerance through transient phenotypic changes. Antibiotic residues, combined with complex environmental factors like temperature and salinity, especially in coastal cities, contribute to non-additive interactions that modulate antibiotic tolerance and affect population dynamics. To better understand these interactions, we developed continuous multivariate tolerance landscapes for three bacterial species: Escherichia coli, the emerging pathogen Streptococcus suis, and the sewer-inhabiting Arcobacter cryaerophilus. We modeled their intrinsic growth rates and carrying capacities across complex environments, incorporating temperature, salinity, and concentrations of two antibiotics (ciprofloxacin and azithromycin). Using these multivariate tolerance curves, we predicted microbial population dynamics in two sewers of Barcelona, highlighting the importance of environmental complexity in shaping microbial responses to antibiotic stressors.   Usage Users can perform the analysis by running the R script (TC3D.R) after the installation of all package mentioned in the preamble,  This folder contains: - 3 datasets with OD measures for the 3 species:               * data_acrya.xlsx               * data_ecoli.xlsx               * data_ssuis.xlsx - 1 excel files with metadata (plate, well, species, environmental conditions)               * map_plate_all.xlsx - 4 datasets giving time series of the flow and several measures including  conductivity and   temperaturefor 2 sewers of Barcelona obtained from sample cabines  set during the implementation of SCOREWATER (ID:820751)               * carmel_flow.csv               * carmel_quality.csv               * poblenou_flow.csv               * poblenou_quality.csv - 1 C++ script compiled and run with the R TMB package:               * fit_growth_r_K_SS_treatment.cpp : computes the negative loglikelihood for r and K, and state DOs, given the observed DO, for the populations under one same environmental treatment (salinity * temperature * antibiotic), and computes the density-dependence parameter alpha from r and K using the Delta Method.

Data from "Resource pulses drive spatio-temporal dynamics of non-native bark beetles and wood borers"

This is a compilation of datasets that were used for the publication entitled "Resource pulses drive spatio-temporal dynamics of non-native bark beetles and wood borers" by Eckehard G. BROCKERHOFF, Stephanie L. SOPOW, and Martin K.-F. BADER, published in the Journal of Applied Ecology, 'in press' in October 2024. Note: The date format is either (i) season (spring/summer/autumn/winter) plus a two-figure short form for the year (e.g., "autumn08" stands for autumn 2008), or (ii) just the year for an annual total in either four- or two-figure form in the file name (e.g., "reg2010sums.csv" or "reg10sums.csv" for the year 2010). 1. File "mean_trap_catches.csv" = Data used for Fig. 1 - Mean trap catch data of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus over time in Kaingaroa forest stands 378 ("F2006"), 377 ("F2009"), and 383 ("F2010"). For further explanations see methods of Brockerhoff et al. (2024). 2. File "reg2010sums.csv" = Data used for Fig. 2 - Year 2010, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 2 in Brockerhoff et al. (2024). 3. File "reg2010sums.csv" = Data used for Fig. 2 - Year 2011, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 2 in Brockerhoff et al. (2024). 4. File "reg2010sums.csv" = Data used for Fig. 2 - Year 2012, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 2 in Brockerhoff et al. (2024). 5. File "reg10sums.csv" = Data used for Fig. 3 - Year 2010, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 3 in Brockerhoff et al. (2024). 6. File "reg11sums.csv" = Data used for Fig. 3 - Year 2011, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 3 in Brockerhoff et al. (2024). 7. File "reg12sums.csv" = Data used for Fig. 3 - Year 2012, annual trap catches of Hylastes ater, Hylurgus ligniperda and Arhopalus ferus indicating approximate dispersal distances between Pinus radiata stands. For details see caption of Fig. 3 in Brockerhoff et al. (2024). 8. File "hylu2010-fitted_dispersal_to_5km-Version_23May2024.csv" = Data shown in Fig. 4 - Extension of the prediction range to 5 km of Hylurgus ligniperda dispersal data, using a generalised additive mixed model (GAMM) with beta distributed errors and the default logarithmic link. For details see caption of Fig. 4 and methods in Brockerhoff et al. (2024).

Dynamic load model for passenger trains based on dynamic train signature

20 conventional load model trains based on dynamic signature envelope of 3,140 operating passenger trains in Europe <ul> <li>axle distances in m and axle loads in kN for all model trains as txt-files</li> </ul>

'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer

Additional data to report <a href="https://doi.org/10.1002/anie.202414069">https://doi.org/10.1002/anie.202414069</a>: <a name="_Hlk172654864"></a>Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis-PBI 1) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol–1), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.

opencc-by-4.0Apr 2021View details →

Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains

Provided are reduced trajectories (.dcd) of the MD simulations -- each trajectory has 100 ps/frame with only protein and ion atoms remaining. Each set of trajectories are accompanied by a protein structure file (.psf) which is required to visualize the trajectories in VMD. Additionally, the z-trajectories of each intracellular ion (2 ps/frame) are provided in zipped files. To re-create the potentials of mean force (PMF) in Yue & Haddad et al., use the scripts provided with the paper (https://github.com/reichow-lab/Yue-Haddad_et-al.JPhysiol2021):   <pre><code class="language-bash">python3 GapJ_Analysis.py "Cx46_Ace_Produc-1_POT_*"</code></pre> <ul> <li>Choose a bin size in Å (3)</li> <li>Choose an output name (Cx46_Ace)</li> <li>Choose option (M)</li> <li>Choose time (ps) / frame (2)</li> <li>Choose column from file (1)</li> <li>Choose binmin/binmax (auto)</li> </ul>

opengpl-2.0Jun 2021View details →

Benchmarking (multi)wavelet-based dynamic and static non-uniform grid solvers for flood inundation modelling (Simulation results)

Simulation result data for Environment Agency benchmark test 5, Thamesmead hypothetical flood, and Carlisle 2005 case studies, using uniform DG2, adaptive MWDG2, adaptive HWFV1, non-uniform DG2, non-uniform FV1 and non-uniform ACC solvers.  Model results are archived in 3 zip files: <ul> <li>EA5.zip contains results of Environment Agency test 5 (Néelz and Pender, 2013)</li> <li>Thamesmead.zip contains results of Thamesmead hypothetical flood (Liang et al., 2008)</li> <li>Carlisle.zip contains results of Carlisle 2005 flooding (Neal et al., 2009)</li> </ul> The results are stored with the following file extensions: <ul> <li>".wd" for 2D flood inundation maps in ESRI ASCII format</li> <li>".stage" for water depth or water level time-series at staging points in tabulated text format</li> <li>".velocity" for velocity time-series at staging points in tabulated text format</li> </ul> Model outputs are stored under directories named for each solver. References Néelz, S., & Pender, G. (2013). Benchmarking the latest generation of 2D hydraulic modelling packages. Environment Agency: Bristol, UK. Liang, Q., Du, G., Hall, J. W., & Borthwick, A. G. (2008). Flood Inundation Modeling with an Adaptive Quadtree Grid Shallow Water Equation Solver. Journal of Hydraulic Engineering, 134(11), 1603–1610. https://doi.org/10.1061/(ASCE)0733-9429(2008)134:11(1603) Neal, J. C., Bates, P. D., Fewtrell, T. J., Hunter, N. M., Wilson, M. D., & Horritt, M. S. (2009). Distributed whole city water level measurements from the Carlisle 2005 urban flood event and comparison with hydraulic model simulations. Journal of Hydrology, 368(1–4), 42–55. https://doi.org/10.1016/j.jhydrol.2009.01.026