{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T08:52:48Z","timestamp":1791190368041,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,29]]},"group-title":"Evolutionary Biology","reference-count":38,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["DEB-2040347"],"award-info":[{"award-number":["DEB-2040347"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01 TW012704"],"award-info":[{"award-number":["R01 TW012704"]}],"id":[{"id":"https:\/\/ror.org\/02xey9a22","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Washington University Incubator for Transdisciplinary Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Biologists often wish to explain why one trait is more common than its alternatives among species in a clade: is it due to asymmetries in diversification or character evolution processes? State-dependent speciation\u2013extinction (SSE) models provide a flexible framework for jointly modeling such processes. Here, we derive mathematical results that define functional relationships (\u201crulesets\u201d) among rate parameters, establish a mapping between rulesets and evolutionary scenarios, and characterize how these scenarios give rise to different long-term tip state distributions. In particular, we show that multiple evolutionary scenarios can produce identical stationary distributions of tip state frequencies. Performing inference on simulated data from extant-only trees, we find that not all scenarios are equally favored for explaining datasets constructed solely from extant species. This bias could arise from the interplay between mixing rates, elapsed time, and the conditioning inherent in tree likelihoods. As a proof of concept, we apply our framework to the binary SSE (BiSSE) model across multiple Squamate clades and conduct a literature survey of previous BiSSE analyses on Angiosperm phylogeny. We show that, to some extent, the preference for certain scenarios observed in simulations is also reflected in analyses of empirical trees. This study provides a theoretical ground to directly link data-generating process and observed tip state frequencies under an SSE framework.<\/jats:p>","DOI":"10.64898\/2026.09.24.754193","type":"posted-content","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:45:14Z","timestamp":1790750714000},"source":"Crossref","is-referenced-by-count":0,"title":["On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2527-4361","authenticated-orcid":false,"given":"Albert C.","family":"Soewongsono","sequence":"first","affiliation":[{"name":"Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130-4899, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8672-6966","authenticated-orcid":false,"given":"Michael J.","family":"Landis","sequence":"additional","affiliation":[{"name":"Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130-4899, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100501100940000_2026.09.24.754193v1.1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syw022"},{"key":"2026100501100940000_2026.09.24.754193v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syt010"},{"key":"2026100501100940000_2026.09.24.754193v1.3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-13-38"},{"key":"2026100501100940000_2026.09.24.754193v1.4","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2022.0330"},{"key":"2026100501100940000_2026.09.24.754193v1.5","doi-asserted-by":"publisher","DOI":"10.2307\/2408678"},{"key":"2026100501100940000_2026.09.24.754193v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syq053"},{"issue":"6","key":"2026100501100940000_2026.09.24.754193v1.7","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1111\/j.2041-210X.2012.00234.x","article-title":"Diversitree: comparative phylogenetic analyses of diversification in R","volume":"3","year":"2012","journal-title":"Methods in Ecology and Evolution"},{"key":"2026100501100940000_2026.09.24.754193v1.8","doi-asserted-by":"crossref","unstructured":"Gamisch A (2016) Notes on the statistical power of the binary state speciation and extinction (BiSSE) model. Evolutionary Bioinformatics 12:EBO\u2013S39732","DOI":"10.4137\/EBO.S39732"},{"key":"2026100501100940000_2026.09.24.754193v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/35012228"},{"key":"2026100501100940000_2026.09.24.754193v1.10","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.2012.01730.x"},{"key":"2026100501100940000_2026.09.24.754193v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syr046"},{"key":"2026100501100940000_2026.09.24.754193v1.12","doi-asserted-by":"publisher","DOI":"10.1111\/ele.14170"},{"key":"2026100501100940000_2026.09.24.754193v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2176-1"},{"key":"2026100501100940000_2026.09.24.754193v1.14","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-185X.1965.tb00815.x"},{"key":"2026100501100940000_2026.09.24.754193v1.15","doi-asserted-by":"publisher","DOI":"10.1080\/10635150701607033"},{"key":"2026100501100940000_2026.09.24.754193v1.16","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201500149"},{"key":"2026100501100940000_2026.09.24.754193v1.17","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adk7623"},{"issue":"4","key":"2026100501100940000_2026.09.24.754193v1.18","doi-asserted-by":"crossref","first-page":"e13812","DOI":"10.1111\/geb.13812","article-title":"Squambase\u2014a database of Squamate (reptilia: Squamata) traits","volume":"33","year":"2024","journal-title":"Global Ecology and Biogeography"},{"key":"2026100501100940000_2026.09.24.754193v1.19","doi-asserted-by":"publisher","DOI":"10.1111\/j.1461-0248.2007.01020.x"},{"key":"2026100501100940000_2026.09.24.754193v1.20","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-ecolsys-102722-020508"},{"key":"2026100501100940000_2026.09.24.754193v1.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.17.8322"},{"key":"2026100501100940000_2026.09.24.754193v1.22","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.1994.0068"},{"key":"2026100501100940000_2026.09.24.754193v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2018.11.009"},{"key":"2026100501100940000_2026.09.24.754193v1.24","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-001-0034-9"},{"key":"2026100501100940000_2026.09.24.754193v1.25","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syu131"},{"key":"2026100501100940000_2026.09.24.754193v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/nature02053"},{"key":"2026100501100940000_2026.09.24.754193v1.27","doi-asserted-by":"crossref","unstructured":"do Rosario Petrucci B , May MR , Heath TA (2025) Fossils improve extinction-rate estimates under state-dependent diversification models. Philos Trans R Soc, B 380(1919)","DOI":"10.1098\/rstb.2023.0313"},{"key":"2026100501100940000_2026.09.24.754193v1.28","doi-asserted-by":"crossref","unstructured":"Soewongsono AC , Landis MJ (2024) A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics. arXiv preprint arXiv:240200246","DOI":"10.1007\/s11538-024-01337-6"},{"key":"2026100501100940000_2026.09.24.754193v1.29","doi-asserted-by":"crossref","unstructured":"Soewongsono AC , Landis MJ (2026) Phylogenetic estimation of diversity-dependent biogeographic rates using deep learning. bioRxiv","DOI":"10.64898\/2026.02.17.706216"},{"key":"2026100501100940000_2026.09.24.754193v1.30","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/sys073"},{"key":"2026100501100940000_2026.09.24.754193v1.31","unstructured":"Tarasov S , Uyeda J (2024) Nonidentifiability of state-dependent diversification models (SSEs) is ubiquitous but not problematic for phylogenetics. bioRxiv"},{"key":"2026100501100940000_2026.09.24.754193v1.32","doi-asserted-by":"publisher","DOI":"10.1126\/science.adh2449"},{"issue":"1","key":"2026100501100940000_2026.09.24.754193v1.33","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1093\/sysbio\/syae058","article-title":"The fossilized birth\u2013death model is identifiable","volume":"74","year":"2025","journal-title":"Syst Biol"},{"key":"2026100501100940000_2026.09.24.754193v1.34","unstructured":"Wolfram Research, Inc. (2023) Mathematica. URL https:\/\/www.wolfram.com\/mathematica"},{"key":"2026100501100940000_2026.09.24.754193v1.35","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025811"},{"key":"2026100501100940000_2026.09.24.754193v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syr046"},{"key":"2026100501100940000_2026.09.24.754193v1.37","doi-asserted-by":"crossref","unstructured":"Soewongsono AC , Landis MJ (2024) A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics. arXiv preprint arXiv:240200246","DOI":"10.1007\/s11538-024-01337-6"},{"key":"2026100501100940000_2026.09.24.754193v1.38","unstructured":"Wolfram Research, Inc. (2023) Mathematica. URL https:\/\/www.wolfram.com\/mathematica"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.24.754193","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T08:10:18Z","timestamp":1791187818000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.24.754193"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,29]]},"references-count":38,"URL":"https:\/\/doi.org\/10.64898\/2026.09.24.754193","relation":{},"subject":[],"published":{"date-parts":[[2026,9,29]]},"subtype":"preprint"}}