{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T11:22:39Z","timestamp":1789557759403,"version":"build-2803163510"},"posted":{"date-parts":[[2025,1,20]]},"group-title":"Bioinformatics","reference-count":24,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T00:00:00Z","timestamp":1737331200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The molecular processes that generate new mutations evolve, but the causal mechanisms are largely unknown. In particular, the relative rates of mutation types (\n                  <jats:italic>e<\/jats:italic>\n                  .\n                  <jats:italic>g<\/jats:italic>\n                  ., C&gt;T), the mutation spectrum, sometimes vary among closely related species and populations. I present an algorithm for subdividing a phylogeny into distinct mutation spectra. By applying this approach to a SARS-CoV-2 phylogeny comprising approximately eight million genome sequences, I identify 10 shifts in the mutation spectrum. I find strong enrichment consistent with candidate causal amino-acid substitutions in the SARS-CoV-2 polymerase, and strikingly three appearances of the same homoplasious substitution are each associated with decreased C&gt;T relative mutation rates. With rapidly growing genomic datasets, this approach and future extensions promises new insights into the mechanisms of evolution of mutational processes.\n                <\/jats:p>","DOI":"10.1101\/2025.01.17.633662","type":"posted-content","created":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T04:00:22Z","timestamp":1737432022000},"source":"Crossref","is-referenced-by-count":1,"title":["A phylogenetic method identifies candidate drivers of the evolution of the SARS-CoV-2 mutation spectrum"],"prefix":"10.64898","author":[{"given":"Russ","family":"Corbett-Detig","sequence":"first","affiliation":[{"name":"Department of Biomolecular Engineering, University of California, Santa Cruz"},{"name":"Genomics Institute, University of California, Santa Cruz"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041022120199000_2025.01.17.633662v1.1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msl091"},{"key":"2026041022120199000_2025.01.17.633662v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad085"},{"key":"2026041022120199000_2025.01.17.633662v1.3","unstructured":"De Maio N , Walker C , Borges R , Weilguny L , Slodkowicz G , Goldman N. 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Rampant C\u2192U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories. mSphere [Internet] 5. 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