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Here, we study how classical homeotic mutations reshape the epigenetic landscape of the floral gene regulatory network of\n                    <jats:italic>Arabidopsis thaliana<\/jats:italic>\n                    . We represent this landscape as an Epigenetic Forest: a collection of rooted in-arborescences induced by the state transition graph of a Boolean gene regulatory network, where each tree is the basin of attraction of a stable gene expression pattern associated with a floral or meristematic identity. We apply this framework to the wild-type network, three single homeotic mutants (\n                    <jats:italic>ap1<\/jats:italic>\n                    ,\n                    <jats:italic>pi<\/jats:italic>\n                    , and\n                    <jats:italic>ag<\/jats:italic>\n                    ), and three double mutants (\n                    <jats:italic>ap3\u2013pi<\/jats:italic>\n                    ,\n                    <jats:italic>ag\u2013pi<\/jats:italic>\n                    , and\n                    <jats:italic>ap1\u2013ag<\/jats:italic>\n                    ). For each genotype, we quantify landscape organization using complementary descriptors of basin structure, convergence depth, fate diversity, dominance, inequality, and Jensen\u2013Shannon divergence from wild type. The resulting landscapes reveal distinct modes of mutant-induced deformation. The\n                    <jats:italic>ap1<\/jats:italic>\n                    mutant restricts fate accessibility and concentrates trajectories into dominant basins, whereas\n                    <jats:italic>pi<\/jats:italic>\n                    eliminates B-function-dependent identities while largely preserving global basin organization. In contrast,\n                    <jats:italic>ag<\/jats:italic>\n                    increases effective fate diversity despite the loss of reproductive identity, reflecting defective meristem termination and convergence to\n                    <jats:italic>WUS<\/jats:italic>\n                    -associated states. Double mutants exhibit non-additive deformation:\n                    <jats:italic>ap3\u2013pi<\/jats:italic>\n                    is indistinguishable from\n                    <jats:italic>pi<\/jats:italic>\n                    across all reported descriptors, consistent with logical saturation of the AND-like B-function module, whereas\n                    <jats:italic>ag\u2013pi<\/jats:italic>\n                    and\n                    <jats:italic>ap1\u2013ag<\/jats:italic>\n                    produce distinct redistributions of fate accessibility. The framework recovers canonical floral identities and experimentally observed mutant phenotypes while treating the epigenetic landscape as a finite, computable object determined by regulatory logic. The framework thus provides a topology-based description of developmental robustness, epistasis, and mutant-induced landscape deformation.\n                  <\/jats:p>","DOI":"10.1007\/s11538-026-01688-2","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:03:35Z","timestamp":1782306215000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Topological Structure of Epigenetic Forests in Flower Morphogenesis"],"prefix":"10.1007","volume":"88","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1856-9206","authenticated-orcid":false,"given":"Yuriria","family":"Cort\u00e9s-Poza","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7739-4779","authenticated-orcid":false,"given":"J. 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