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317 results for “hierarchy”
Dataset: An Analytic Hierarchy Process-Based Multicriteria Model for Component Selection in a Computational Numerical Control (CNC) Machine
<p><i><strong>"An Analytic Hierarchy Process-Based Multicriteria Model for Component Selection in a Computational Numerical Control (CNC) Machine"</strong></i></p><p><i>CHILECON 2023 - </i><a href="https://site.ieee.org/chilesur/ieee-chilecon-2023/"><i>https://site.ieee.org/chilesur/ieee-chilecon-2023/</i></a><i> </i></p><p>---</p><p>En el marco del trabajo de referencia, los autores ponemos a disposición de los lectores la base de datos utilizada para el proceso de toma de decisión multicriterio para la selección del software y del MCU de una maquina CNC. </p><p>En el repositorio podrán encontrar los datos referentes a los criterios, subcriterios, indicadores, datos, fuentes de los datos extraídos, política de decisión, cálculos de las evaluaciones de los modelos AHP aplicados y el análisis de sensibilidad de estos. Además, podrán encontrar las gráficas utilizadas en el estudio en la mejor calidad posible. </p><p>El material fue puesto a disposición de todos los interesados para fines académicos y científicos. </p><p>Atte. </p><p>Los autores. </p><p>---</p>
Mapping of FoodEx2 Exposure Hierarchy with the food categories of Annex II (part D) of Regulation (EC) No 1333/2008 on food additives
<p>FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains. All foods, including beverages and food supplements reported in the EFSA Comprehensive Food Consumption Database are coded with the FoodEx2 Exposure Hierarchy. EFSA developed a mapping of all FoodEx2 basic terms reported in the Comprehensive Database with the food categories of Annex II (part D) of Regulation (EC) No 1333/2008 on food additives in order to facilitate the assessment of exposure to food additives. In particular, this mapping has been used in the Food Additives Intake Model 2.0 (FAIM), which allows the estimation of chronic dietary exposure to food additives based on use levels proposed for food categories as presented in Annex II (part D) of Regulation (EC) No 1333/2008 on food additives.</p> <p>Some of the food categories, restrictions and/or exceptions presented in the Regulation could have not been mapped with FoodEx2 basic terms and the original food descriptors and/or FoodEx2 facets might have been used to correctly map all eating events. This information might not be available in this table.</p>
Insights in the structural hierarchy of statically crystallized palm oil
<p>This dataset contains all data obtained on palm oil samples and used in the publication "Insights in the structural hierarchy of statically crystallized palm oil". See paper for more information on the methods for obtaining the data.</p> <p> </p> <p>Abbreviations used:</p> <p>PO = palm oil</p> <p>PPP = tripalmitin</p> <p>I = intensity (in X-ray scattering)</p> <p>q = scattering vector (in X-ray scattering)</p> <p>SEM = Scanning Electron Microscopy</p> <p>DSC = Differential Scanning Calorimetry</p> <p>WAXS = Wide Angle X-ray Scattering</p> <p>SAXS = Small Angle X-ray Scattering</p> <p>USAXS = Ultra Small Angle X-ray Scattering</p> <p>PLM = Polarized Light Microscopy</p> <p>FC = fast cooling = 20°C/min</p> <p>SC = slow cooling = 1°C/min</p> <p>TAG = triglyceride</p> <p>FA = fatty acid</p>
A cellular hierarchy in melanoma uncouples growth and metastasis
<p>Although melanoma is notorious for its high degree of heterogeneity and plasticity<sup>1,2</sup>, the origin and magnitude of cell state diversity remains poorly understood. Equally, it is not known whether melanoma growth and metastatic dissemination are supported by overlapping or distinct melanoma subpopulations. By combining mouse genetics, unbiased lineage tracing and quantitative modelling, single-cell and spatial transcriptomics, we provide evidence of a hierarchical model of tumour growth that mirrors the cellular and molecular logic underlying embryonic neural crest cell fate specification and differentiation. Our findings indicate that tumorigenic competence is associated with a spatially localized perivascular niche environment, a phenotype acquired through a NOTCH3-dependent intercellular communication pathway established by endothelial cells. Consistent with a model in which only a fraction of melanoma cells is fated to fuel growth, temporal single-cell tracing of a population of melanoma cells harbouring a mesenchymal-like state revealed that these cells do not contribute to primary tumour growth but, instead, constitutes a pool of metastatic-initiating cells that can switch cell identity while disseminating to secondary organs. Our data provide a spatially and temporally resolved map of the diversity and trajectories of cancer cell states within the evolving melanoma ecosystem and suggest that the ability to support growth and metastasis are limited to distinct pools of melanoma cells. The observation that these phenotypic competencies can be dynamically acquired upon exposure to specific niche signals warrant the development of therapeutic strategies that interfere with the cancer cell reprogramming activity of such microenvironmental cues.</p>
EOL Dynamic Hierarchy Trunk (trunk): EOL Dynamic Hierarchy Trunk January 2021
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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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 <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>https://eol.org/docs/eol-dynamic-hierarchy)
EOL Dynamic Hierarchy Trunk (trunk): Dynamic Hierarchy Trunk 25 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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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 <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>https://eol.org/docs/eol-dynamic-hierarchy)
EOL Dynamic Hierarchy Trunk (trunk): EOL Dynamic Hierarchy Trunk 12 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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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 <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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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](<p></p>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](<p></p>https://eol.org/docs/eol-dynamic-hierarchy)
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](<p></p>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. <p></p>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). 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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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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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](<p></p>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](<p></p>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](<p></p>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. <p></p>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). 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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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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Frontiers in Genetics 10. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>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](<p></p>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. <p></p>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). 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BMC Evolutionary Biology 14, 23. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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). 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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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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Brannock, David A. Weese, et al. 2016. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Systematic Biology, syw079. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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 <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>https://doi.org/10.3389/fgene.2019.00443.<p></p>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](<p></p>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](<p></p>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](<p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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 <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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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](<p></p>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](<p></p>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](<p></p>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. <p></p>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). 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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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. <p></p>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. 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Entomol. 56, 487–510. <p></p>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. <p></p>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. 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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](<p></p>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](<p></p>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.<p></p>Zip file containing a README and a three-column CSV (pages.csv) with header row
EOL Hierarchy Entries April 2017: Hierarchy Entries April 2017
This is a file listing all EOL hierarchy entries along with associated name strings, mapped taxon concept (EOL page ID), richness score of mapped page, and source hierarchy. Columns in the file: EOL_ID (taxon concept/page ID)|richness score|scientificName|hierarchy entry ID| source hierarchy
Research Data/Code for "Scale-bridging within a complex model hierarchy for investigation of a metal-fueled circular energy economy by use of Bayesian model calibration with model error quantification"
<p>This repository contains research data and code for supplementing the manuscript <br>"Scale-bridging within a complex model hierarchy for investigation of a metal-fueled circular energy economy by use of Bayesian model calibration with model error quantification" <br>by L. Gossel, E. Corbean, S. Dübal, P. Brand, M. Fricke, H. Nicolai, C. Hasse, S. Hartl, S. Ulbrich, and D. Bothe. </p> <p>There is a corresponding preprint available on Arxiv: https://doi.org/10.48550/arXiv.2404.13092</p> <p><br>Users are referred to the manuscript for background information. This repository shall enable reproduction of the reported results and does not stand alone. </p> <p>Please read important information in the README in the top-level directory. </p> <p>Funded by the Hessian Ministry of Higher Education, Research, Science and the Arts - cluster project Clean Circles. </p>
Quantifying Hierarchy and Prestige in US Ballet Academies as Social Predictors of Career Success
<p>This data contains aggregated competition outcomes from 6,363 ballet students affiliated with 1,603 schools in the United States, who participated in the Youth America Grand Prix (YAGP) between 2000 and 2021.</p> <p>We adopt a network science and <em>science of science</em> approach that empowers logistic regression models and matching experiments to quantify social prestige and its influence on dancers' careers. The analysis of career success in the performing arts, like ballet, in the context of a competition setting offers a unique opportunity to investigate the social influences on success while controlling for competition performance.</p> <p>Our work reveals the importance of institutional prestige on career success in ballet and showcases the potential of network science approaches to provide quantitative viewpoints for the professional development of careers beyond science.</p>
Multi-scale sea ice kinematics modeling dataset with a tripolar grid hierarchy (TS grids) in CESM
<p>1. We design a new tripolar grid generation method for global ocean-sea ice modeling. The generated grid is orthogonal and compatible with ocean and sea ice models. A hierarchy of ocean-sea ice model grid is constructed and incorporated in CESM by using the grid generation method. The generated tripolar grids are regarded as TS045, TS015 and TS005, with the nominal resolution of 0.45<sup>o </sup>(800x560), 0.15<sup>o</sup> (2400x1680) and 0.05<sup>o </sup>(7200x5040), respectively. The resolution range for the grid hierarchy covers climate modeling to sub-mesoscale capable for ocean modeling.</p> <p>2. Atmosphere forced simulations based on CESM D-type experiments are carried out for TS grid. Both TS045 and TS015 experiments start with no sea ice, integrate for 42 years. TS005 starts from the equilibrium state of TS015 result (36 year), runs for another 7 years.</p> <p>3. TS0*.grid files include necessary grid information, such as grid latitude, longitude, etc. TS0*.kmt files denote the deepest level at each grid location. Bilinear interpolators from TS grid to atmosphere T62 grid are provided with map*.nc files. The model outputs at year 42 are provided with T*.nc files. The last two kinds of netcdf files are compressed with Linux command "gzip".</p>
Time-implicit Hierarchies in Different Languages
<p>These datasets are used for the study named "Learning Temporal Hierarchies with Synchronic Word Embeddings"</p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.