{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T04:41:58Z","timestamp":1791866518383,"version":"4.3.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1916558"],"award-info":[{"award-number":["DEB-1916558"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-2331644"],"award-info":[{"award-number":["DEB-2331644"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1916539"],"award-info":[{"award-number":["DEB-1916539"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Large phylogenetic trees are often unbalanced near the root, with a species-depauperate lineage sister to a far more species-rich clade. The species-poor branches, sometimes referred to as \u201cearly diverging,\u201d are often viewed as key sources of information about deep evolutionary history. As a result, these lineages occupy a central role in debates about ancestral states. Using simulations and likelihood-based models of trait evolution, we show that the information contributed by species-depauperate lineages to ancestral state reconstructions is surprisingly limited. Instead, in unbalanced phylogenetic trees, the accuracy of ancestral state reconstructions at the root node is determined primarily by the species-rich clade and, more specifically, the evolutionary distance separating that clade from the root, rather than by the character state or evolutionary rate of the \u201cearly-diverging\u201d sister lineage. This pattern reflects a general property of how phylogenetic inference aggregates information across descendant lineages: ancestral state reconstructions combine evidence from both descendant lineages rather than applying disproportionate weight to one of the descendants simply because fewer branching events separate it from the ancestral node. Our results highlight the limits of using extant, species-depauperate lineages to infer deep ancestors and the importance of fossils and other evidence that more directly sample early evolutionary history.<\/jats:p>","DOI":"10.1093\/sysbio\/syag074","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T11:16:14Z","timestamp":1790334974000},"source":"Crossref","is-referenced-by-count":1,"title":["\"Early-Diverging\" Lineages Provide Little Information about Ancestors"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5953-1701","authenticated-orcid":false,"given":"Jeremy M","family":"Beaulieu","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Arkansas , Fayetteville, AR 72701 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1241-2654","authenticated-orcid":false,"given":"Andrew J","family":"Alverson","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Arkansas , Fayetteville, AR 72701 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0337-5997","authenticated-orcid":false,"given":"Brian C","family":"O\u2019Meara","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, TN 37996 ,","place":["USA"]},{"name":"National Institute for Modeling Biological Systems, University of Tennessee , Knoxville, TN 37996 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"2026100510520849600_bib1","first-page":"2729","article-title":"Are rates of species diversification correlated with rates of morphological evolution?","volume":"276","author":"Adams","year":"2009","journal-title":"Proc. Biol. Sci."},{"key":"2026100510520849600_bib2","volume-title":"Tree thinking: an introduction to phylogenetic biology","author":"Baum","year":"2013"},{"issue":"5","key":"2026100510520849600_bib3","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/sysbio\/syt034","article-title":"Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms","volume":"62","author":"Beaulieu","year":"2013","journal-title":"Syst. Biol."},{"key":"2026100510520849600_bib4","doi-asserted-by":"crossref","unstructured":"Boyko J.D., Beaulieu J.M. \u00a02021. Generalized hidden Markov models for phylogenetic comparative datasets. Methods Ecol. Evol. \u00a012 (3):468\u2013478.","DOI":"10.1111\/2041-210X.13534"},{"issue":"51","key":"2026100510520849600_bib5","doi-asserted-by":"crossref","first-page":"e2517741122","DOI":"10.1073\/pnas.2517741122","article-title":"Cilia-driven epithelial folding and unfolding in an early diverging animal","volume":"122","author":"Brannon","year":"2025","journal-title":"Proc. Natl Acad. Sci. USA"},{"issue":"8099","key":"2026100510520849600_bib6","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1038\/d41586-026-00238-z","article-title":"What were the first animals? The fierce sponge-jelly battle that just won\u2019t end","volume":"649","author":"Callaway","year":"2026","journal-title":"Nature"},{"key":"2026100510520849600_bib7","doi-asserted-by":"crossref","first-page":"99514","DOI":"10.3389\/fevo.2014.00049","article-title":"Coelacanths as almost living fossils","volume":"2","author":"Cavin","year":"2014","journal-title":"Front. Ecol. Evol."},{"issue":"1","key":"2026100510520849600_bib8","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/s42003-023-04498-7","article-title":"First monotreme from the Late Cretaceous of South America","volume":"6","author":"Chimento","year":"2023","journal-title":"Commun. Biol."},{"issue":"3","key":"2026100510520849600_bib9","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.tree.2004.11.010","article-title":"Do early branching lineages signify ancestral traits?","volume":"20","author":"Crisp","year":"2005","journal-title":"Trends Ecol. Evol."},{"issue":"4","key":"2026100510520849600_bib10","doi-asserted-by":"crossref","first-page":"E78","DOI":"10.1086\/701630","article-title":"Speciation rate is independent of the rate of evolution of morphological size, shape, and absolute morphological specialization in a large clade of birds","volume":"193","author":"Crouch","year":"2019","journal-title":"Am. Nat."},{"issue":"2","key":"2026100510520849600_bib11","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1111\/nph.13367","article-title":"Confluence, synnovation, and depauperons in plant diversification","volume":"207","author":"Donoghue","year":"2015","journal-title":"New Phytol."},{"issue":"3","key":"2026100510520849600_bib12","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1111\/faf.12136","article-title":"Fishes that rule the world: circumtropical distributions revisited","volume":"17","author":"Gaither","year":"2016","journal-title":"Fish Fish"},{"issue":"1","key":"2026100510520849600_bib13","doi-asserted-by":"crossref","first-page":"4039","DOI":"10.1038\/s41467-025-59343-8","article-title":"Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis","volume":"16","author":"Hu","year":"2025","journal-title":"Nat. Commun."},{"issue":"2","key":"2026100510520849600_bib14","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1080\/00275514.2025.2460003","article-title":"Use their names: there are no basal, lower, or early diverging fungi","volume":"117","author":"James","year":"2025","journal-title":"Mycologia"},{"issue":"3","key":"2026100510520849600_bib15","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1111\/j.0307-6970.2004.00262.x","article-title":"Which side of the tree is more basal?","volume":"29","author":"Krell","year":"2004","journal-title":"Syst. Entomol."},{"issue":"10","key":"2026100510520849600_bib16","doi-asserted-by":"crossref","first-page":"4322","DOI":"10.1093\/molbev\/msab170","article-title":"Rooting the animal tree of life","volume":"38","author":"Li","year":"2021","journal-title":"Mol. Biol. Evol."},{"issue":"33","key":"2026100510520849600_bib17","doi-asserted-by":"crossref","first-page":"eadw0486","DOI":"10.1126\/sciadv.adw0486","article-title":"Insights into angiosperm evolution and lineage-specialized lignan biosynthesis from the early-diverging Schisandra genome","volume":"11","author":"Liu","year":"2025","journal-title":"Sci. Adv."},{"issue":"4","key":"2026100510520849600_bib18","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1093\/sysbio\/42.4.576","article-title":"Missing data versus missing characters in phylogenetic analysis","volume":"42","author":"Maddison","year":"1993","journal-title":"Syst. Biol."},{"issue":"3794","key":"2026100510520849600_bib19","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1126\/science.157.3794.1270","article-title":"The ginkgo, the most ancient living tree","volume":"157","author":"Major","year":"1967","journal-title":"Science"},{"issue":"5","key":"2026100510520849600_bib20","doi-asserted-by":"crossref","first-page":"e15104","DOI":"10.1111\/jbi.15104","article-title":"Recent long-distance-dispersal explains the range disjunction of the old-word cockleburs (Xanthium strumarium)","volume":"52","author":"Manzo","year":"2025","journal-title":"J. Biogeogr."},{"issue":"4","key":"2026100510520849600_bib21","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1111\/nph.17241","article-title":"Bryophytes are not early diverging land plants","volume":"230","author":"McDaniel","year":"2021","journal-title":"New Phytol."},{"issue":"1","key":"2026100510520849600_bib22","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1038\/s42003-025-08654-z","article-title":"Digging into the evolutionary history of the fungus-growing-ant symbiont, Escovopsis (Hypocreaceae)","volume":"8","author":"Montoya","year":"2025","journal-title":"Commun. Biol."},{"key":"2026100510520849600_bib23","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1146\/annurev-ecolsys-110411-160331","article-title":"Evolutionary inferences from phylogenies: a review of methods","volume":"43","author":"O\u2019Meara","year":"2012","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"issue":"26","key":"2026100510520849600_bib24","doi-asserted-by":"crossref","first-page":"790","DOI":"10.21105\/joss.00790","article-title":"phylogram: an R package for phylogenetic analysis with nested lists","volume":"3","author":"P.\u00a0Wilkinson","year":"2018","journal-title":"J. Open Source Softw."},{"issue":"3","key":"2026100510520849600_bib25","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1080\/106351599260184","article-title":"The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies","volume":"48","author":"Pagel","year":"1999","journal-title":"Syst. Biol."},{"issue":"3","key":"2026100510520849600_bib26","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"2026100510520849600_bib27","first-page":"1","article-title":"Amborella\u2014bearing witness to the past?","volume":"2","author":"Poncet","year":"2019","journal-title":"Annu. Plant Rev. Online."},{"issue":"11","key":"2026100510520849600_bib28","doi-asserted-by":"crossref","first-page":"R491","DOI":"10.1016\/j.cub.2026.03.011","article-title":"Amborella","volume":"36","author":"Renner","year":"2026","journal-title":"Curr. Biol."},{"key":"2026100510520849600_bib29","article-title":"The ancestors are not among us","author":"Smith","year":"2016"},{"issue":"6","key":"2026100510520849600_bib30","doi-asserted-by":"crossref","first-page":"997","DOI":"10.3732\/ajb.91.6.997","article-title":"Amborella not a \u201cbasal angiosperm\u201d? Not so fast","volume":"91","author":"Soltis","year":"2004","journal-title":"Am. J. Bot."},{"issue":"6774","key":"2026100510520849600_bib31","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.adw9456","article-title":"RETRACTED: integrative phylogenomics positions sponges at the root of the animal tree","volume":"390","author":"Steenwyk","year":"2025","journal-title":"Science"},{"issue":"2","key":"2026100510520849600_bib32","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1093\/botlinnean\/boaf005","article-title":"Fruit structure and development in representatives of Iriarteeae (Arecaceae\u2013Arecoideae)","volume":"209","author":"Timchenko","year":"2025","journal-title":"Bot. J. Linn. Soc."},{"issue":"1","key":"2026100510520849600_bib33","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/j.cub.2024.10.075","article-title":"Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life","volume":"35","author":"Torruella","year":"2025","journal-title":"Curr. Biol."},{"issue":"2","key":"2026100510520849600_bib34","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.mambio.2015.10.002","article-title":"Tree thinking and species delimitation: guidelines for taxonomy and phylogenetic terminology","volume":"81","author":"Zachos","year":"2016","journal-title":"Mamm. Biol."}],"container-title":["Systematic Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/sysbio\/advance-article-pdf\/doi\/10.1093\/sysbio\/syag074\/71402599\/syag074.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/sysbio\/advance-article-pdf\/doi\/10.1093\/sysbio\/syag074\/71402599\/syag074.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T14:52:19Z","timestamp":1791211939000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sysbio\/advance-article\/doi\/10.1093\/sysbio\/syag074\/8836570"}},"subtitle":[],"editor":[{"given":"Stacey","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,26]]},"references-count":34,"URL":"https:\/\/doi.org\/10.1093\/sysbio\/syag074","relation":{},"ISSN":["1063-5157","1076-836X"],"issn-type":[{"value":"1063-5157","type":"print"},{"value":"1076-836X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,26]]},"article-number":"syag074"}}