{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T05:17:44Z","timestamp":1783055864865,"version":"3.54.6"},"reference-count":82,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cladistics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>During the COVID\u201019 pandemic, the need for quick public health action often conflicted with the careful methods required in phylogenetics. To explore this, we reviewed 217 SARS\u2010CoV\u20102 studies published from January 2020 to March 2025 in 121 journals. We found many methodological problems that weaken the reliability and reproducibility of these studies. Key issues include missing outgroup sampling, which affects ingroup topology, tree rooting and how we interpret evolutionary changes and relationships. Another issue is the lack of gene annotations, which can cause characters from one gene to align with those of a different gene. Many studies also misinterpret support or other branch statistics, treating them as proof of clade accuracy instead of as measures of relative evidence. In addition, 91% of the studies do not follow FAIR (Findable, Accessible, Interoperable, and Reusable) data principles, with data and code often unavailable. Finally, we also found a \u201cprestige paradox\u201d: journals with higher impact factors do not necessarily have better methods or transparency. Therefore, we offer simple guidelines for authors, reviewers and editors to improve transparency and FAIR data standards in viral phylogenetics, making writing and reviewing papers easier, ensuring published phylogenetic analyses remain a trustworthy resource for future pandemics.<\/jats:p>","DOI":"10.1111\/cla.70050","type":"journal-article","created":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T04:29:58Z","timestamp":1783052998000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Advancing\n                    <scp>FAIR<\/scp>\n                    phylogenetics for health threats: a systematic review of\n                    <scp>SARS<\/scp>\n                    \u2010\n                    <scp>CoV<\/scp>\n                    \u20102 research and guidelines for future outbreaks"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4548-194X","authenticated-orcid":false,"given":"Omkar","family":"Marne","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Genomics, College of Computing and Informatics (CCI) University of North Carolina at Charlotte (UNC Charlotte)  Charlotte NC USA"},{"name":"Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER) University of North Carolina at Charlotte (UNC Charlotte)  Charlotte NC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9858-4515","authenticated-orcid":false,"given":"Denis","family":"Jacob Machado","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, College of Computing and Informatics (CCI) University of North Carolina at Charlotte (UNC Charlotte)  Charlotte NC USA"},{"name":"Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER) University of North Carolina at Charlotte (UNC Charlotte)  Charlotte NC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41576-022-00483-8","article-title":"Phylogenetic and phylodynamic approaches to understanding and combating the early SARS\u2010CoV\u20102 pandemic","volume":"23","author":"Attwood S.W.","year":"2022","journal-title":"Nat. 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