{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T18:33:16Z","timestamp":1786732396884,"version":"build-2736575974"},"reference-count":15,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The study of genetic diversity has a rich history, as it serves as the foundation upon which evolutionary processes act. Numerous methods have been developed to quantify genetic variation within and among populations. While some methods focus solely on allele frequencies, others assess branching patterns within phylogenetic clades without considering genetic distances. Here we introduce the\n                    <jats:bold>P<\/jats:bold>\n                    roportional Diversity\n                    <jats:bold>L<\/jats:bold>\n                    ikelihood\n                    <jats:bold>R<\/jats:bold>\n                    atio Statistic (PLR), a novel method that integrates genetic distances with phylogenetic tree structure to provide a comprehensive measure of genetic diversity. This method evaluates the likelihood of observed genetic data under models with constrained and unconstrained diversity, offering a robust statistical framework for testing hypotheses about genetic differentiation. The PLR approach is broadly applicable, from assessing immune repertoire diversity, such as B-cell diversity before and after vaccination, to evaluating tumor genetic diversity before and after treatment. By combining genetic distance and tree topology, PLR enables deeper insights into evolutionary dynamics and population structure. We demonstrate the use of this approach on SARS-CoV-2 sequences from two different time frames and found that diversity maybe waning. Moreover, we applied PRL to chronic lymphocytic leukemia (CLL) data, revealing that with temporally order sequences from with treatment we do not see a significant drop in diversity.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0356079","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T17:55:03Z","timestamp":1786730103000},"page":"e0356079","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating genetic diversity differences within a likelihood framework"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8672-6261","authenticated-orcid":true,"given":"David C.","family":"Nickle","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"issue":"4","key":"pone.0356079.ref001","first-page":"323","article-title":"The genetical structure of populations","volume":"15","author":"S Wright","year":"1951","journal-title":"Ann Eugen"},{"issue":"4","key":"pone.0356079.ref002","doi-asserted-by":"crossref","first-page":"2011","DOI":"10.1093\/genetics\/155.4.2011","article-title":"A new statistic for detecting genetic differentiation","volume":"155","author":"RR Hudson","year":"2000","journal-title":"Genetics"},{"issue":"6","key":"pone.0356079.ref003","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"J Felsenstein","year":"1981","journal-title":"J Mol Evol"},{"issue":"2","key":"pone.0356079.ref004","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1007\/BF00166252","article-title":"Statistical tests of models of DNA substitution","volume":"36","author":"N Goldman","year":"1993","journal-title":"J Mol Evol"},{"issue":"3","key":"pone.0356079.ref005","first-page":"235","article-title":"Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees","volume":"13","author":"A Rambaut","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"pone.0356079.ref006","volume-title":"PAUP* \u2014 Phylogenetic Analysis Using Parsimony (*and Other Methods)","author":"DL Swofford","year":"2003","edition":"4"},{"issue":"2","key":"pone.0356079.ref007","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/genetics\/131.2.479","article-title":"Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data","volume":"131","author":"L Excoffier","year":"1992","journal-title":"Genetics"},{"issue":"2","key":"pone.0356079.ref008","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/genetics\/6.2.111","article-title":"Systems of mating. I. the biometric relations between parent and offspring","volume":"6","author":"S Wright","year":"1921","journal-title":"Genetics"},{"issue":"2","key":"pone.0356079.ref009","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1093\/genetics\/28.2.114","article-title":"Isolation by distance","volume":"28","author":"S Wright","year":"1943","journal-title":"Genetics"},{"issue":"4","key":"pone.0356079.ref010","first-page":"306","article-title":"The mathematical theory of communication","volume":"14","author":"CE Shannon","year":"1997","journal-title":"MD Comput"},{"issue":"10","key":"pone.0356079.ref011","doi-asserted-by":"crossref","first-page":"5269","DOI":"10.1073\/pnas.76.10.5269","article-title":"Mathematical model for studying genetic variation in terms of restriction endonucleases","volume":"76","author":"M Nei","year":"1979","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pone.0356079.ref012","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/0040-5809(75)90020-9","article-title":"On the number of segregating sites in genetical models without recombination","volume":"7","author":"GA Watterson","year":"1975","journal-title":"Theor Popul Biol"},{"key":"pone.0356079.ref013","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku1207","article-title":"NCBI viral genomes resource","volume":"43","author":"JR Brister","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pone.0356079.ref014","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.cell.2013.01.019","article-title":"Evolution and impact of subclonal mutations in chronic lymphocytic leukemia","volume":"152","author":"DA Landau","year":"2013","journal-title":"Cell"},{"key":"pone.0356079.ref015","author":"DC Nickle","year":"1991","journal-title":"Molecular phylogeographic structure within the Perognathus fasciatus species-group"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0356079","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T17:55:08Z","timestamp":1786730108000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0356079"}},"subtitle":[],"editor":[{"given":"Patrick R","family":"Stephens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,14]]},"references-count":15,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0356079","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,14]]}}}