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Adv."],"published-print":{"date-parts":[[2026,10,16]]},"abstract":"<jats:p>Brachiopods appeared early in the Cambrian radiation and represent an important clade for understanding the origin of animal body plans and the evolution of biomineralized structures. A robust phylogenetic framework of the living representatives is needed to answer persistent questions about the evolution of brachiopod mineralogy, shell morphology, and identification of the brachiopod sister group among Lophotrochozoa. To the best of our knowledge, we present the first phylogenomic analysis of Brachiopoda and related lophotrochozoan lineages using a comprehensive dataset encompassing all five extant brachiopod orders and using a custom-developed data-refining strategy, compositionally heterogeneous substitution models, and a novel implementation of the parametric-bootstrap likelihood ratio test. We recover monophyly of Lophophorata, with strong support for Brachiopoda as sister to Bryozoa plus Phoronida. Within Brachiopoda, we recover the clade of inarticulated phosphatic Linguliformea sister to the inarticulated calcitic Craniiformea, with both sister to the articulated calcitic Rhynchonellata, with miniaturized Thecideida unexpectedly nested within Terebratulida. Our phylogeny implies that at least one evolutionary transition in primary mineralogy occurred in Brachiopoda, a phenomenon not recognized in any other metazoan group.<\/jats:p>","DOI":"10.1126\/sciadv.aeh5363","type":"journal-article","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T17:58:53Z","timestamp":1792173533000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":0,"title":["A comprehensive phylogenomic framework for brachiopod evolution among lophotrochozoans"],"prefix":"10.1126","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-9123-6493","authenticated-orcid":true,"given":"Mingzhu","family":"Yang","sequence":"first","affiliation":[{"name":"Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1906-0009","authenticated-orcid":true,"given":"Aodh\u00e1n","family":"Butler","sequence":"additional","affiliation":[{"name":"Department of Earth and Planetary Sciences, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1393-2902","authenticated-orcid":true,"given":"Natalia","family":"L\u00f3pez Carranza","sequence":"additional","affiliation":[{"name":"Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616-8605, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3584-9616","authenticated-orcid":true,"given":"Jakob","family":"Vinther","sequence":"additional","affiliation":[{"name":"Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6953-5829","authenticated-orcid":true,"given":"Rowan","family":"Whittle","sequence":"additional","affiliation":[{"name":"British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6814-0198","authenticated-orcid":true,"given":"Daniela","family":"Henkel","sequence":"additional","affiliation":[{"name":"Marine Biogeochemistry\/ Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hana","family":"Jurikova","sequence":"additional","affiliation":[{"name":"School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9TS, UK."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gert","family":"W\u00f6rheide","sequence":"additional","affiliation":[{"name":"Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universit\u00e4t, 80333 M\u00fcnchen, Germany."},{"name":"GeoBio-Center, Ludwig-Maximilians-Universit\u00e4t, 80333 Munich, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mattia","family":"Giacomelli","sequence":"additional","affiliation":[{"name":"Department of Genetics, Microbiology and Statistics, and Biodiversity Research Institute, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3116-7463","authenticated-orcid":true,"given":"Philip C. 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