DOI: 10.5281/zenodo.13239345
title: EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 25 April 2017

description: 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.
description: Updated dynamic hierarchy trunk.  Ready for second Smasher run.
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)