{"paper":{"title":"Smoothly Time-Varying Continuous Time Markov Chains in Phylogenetics","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["stat.ME"],"primary_cat":"q-bio.PE","authors_text":"Marc A. Suchard, Philippe Lemey, Pratyusa Datta","submitted_at":"2026-06-24T21:42:24Z","abstract_excerpt":"The dependence of evolutionary rate estimates on the timeframe of sampling poses a fundamental challenge for reconstructing evolutionary histories from molecular sequence data, which is central to evolutionary biology and infectious disease research. We present a novel and flexible approach to accommodate time-varying evolutionary rates by modeling the sequence substitution process using inhomogeneous continuous-time Markov chains (ICTMCs) acting along the branches of the phylogeny, and parameterizing the log transformed rate as a smooth function of time using a cubic B-spline basis expansion."},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.26402","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.26402/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}