{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T04:12:11Z","timestamp":1779336731642,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK Health Security Agency","award":["104683ED"],"award-info":[{"award-number":["104683ED"]}]},{"name":"CARAA","award":["5126118"],"award-info":[{"award-number":["5126118"]}]},{"name":"Wellcome Trust Investigator","award":["220885\/Z\/20\/Z"],"award-info":[{"award-number":["220885\/Z\/20\/Z"]}]},{"name":"Population genomic analysis of HIV transmission fitness"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>How population structure can shape genetic diversity is a longstanding problem in population genetics. While the use of geographic locations, when available, can help answer some of these questions, it is still difficult to determine population structure when such metadata are not available or when the potential population structure is not easily observed. Here, we present an updated version of treestructure, an R package that implements a statistical test based on coalescent theory to detect unobserved population structure in a time-scaled phylogenetic tree.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>treestructure is available at CRAN at https:\/\/cloud.r-project.org\/web\/packages\/treestructure\/ and at https:\/\/emvolz-phylodynamics.github.io\/treestructure\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag195","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T11:21:22Z","timestamp":1776684082000},"source":"Crossref","is-referenced-by-count":0,"title":["treestructure: an R package to detect population structure in phylogenetic trees"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9426-6835","authenticated-orcid":false,"given":"Fabr\u00edcia F","family":"Nascimento","sequence":"first","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","place":["United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0006-9337","authenticated-orcid":false,"given":"Vinicius B","family":"Franceschi","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","place":["United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6268-8937","authenticated-orcid":false,"given":"Erik M","family":"Volz","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","place":["United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,4,22]]},"reference":[{"key":"2026052023580191900_btag195-B1","doi-asserted-by":"crossref","first-page":"1600146","DOI":"10.3389\/fmicb.2025.1600146","article-title":"Genomic analysis of the 2017 Aotearoa New Zealand outbreak of Mycoplasma bovis and its position within the global population structure","volume":"16","author":"Binney","year":"2025","journal-title":"Front Microbiol"},{"key":"2026052023580191900_btag195-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/03610927408827101","article-title":"A dendrite method for cluster analysis","volume":"3","author":"Cali\u0144ski","year":"1974","journal-title":"Commun Stat"},{"key":"2026052023580191900_btag195-B3","doi-asserted-by":"crossref","first-page":"7828","DOI":"10.1038\/s41467-024-52159-y","article-title":"Evolutionary dynamics of the successful expansion of pandemic Vibrio parahaemolyticus ST3 in Latin America","volume":"15","author":"Campbell","year":"2024","journal-title":"Nat Commun"},{"key":"2026052023580191900_btag195-B4","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature22040","article-title":"Virus genomes reveal factors that spread and sustained the Ebola epidemic","volume":"544","author":"Dudas","year":"2017","journal-title":"Nature"},{"key":"2026052023580191900_btag195-B5","doi-asserted-by":"crossref","first-page":"veaa082","DOI":"10.1093\/ve\/veaa082","article-title":"Emerging phylogenetic structure of the SARS-CoV-2 pandemic","volume":"6","author":"Fountain-Jones","year":"2020","journal-title":"Virus Evol"},{"key":"2026052023580191900_btag195-B6","doi-asserted-by":"crossref","first-page":"veaf048","DOI":"10.1093\/ve\/veaf048","article-title":"Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom","volume":"11","author":"Franceschi","year":"2025","journal-title":"Virus Evol"},{"key":"2026052023580191900_btag195-B7","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1093\/sysbio\/syab095","article-title":"Bayesian inference of clonal expansions in a dated phylogeny","volume":"71","author":"Helekal","year":"2022","journal-title":"Syst Biol"},{"key":"2026052023580191900_btag195-B8","doi-asserted-by":"crossref","first-page":"evab287","DOI":"10.1093\/gbe\/evab287","article-title":"Global emergence and dissemination of Neisseria gonorrhoeae ST-9363 isolates with reduced susceptibility to azithromycin","volume":"14","author":"Joseph","year":"2022","journal-title":"Genome Biol. Evol"},{"key":"2026052023580191900_btag195-B9","author":"R Core Team","year":"2025"},{"key":"2026052023580191900_btag195-B10","first-page":"mgen001006","article-title":"Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants","volume":"9","author":"Reimche","year":"2023","journal-title":"Microb Genom"},{"key":"2026052023580191900_btag195-B11","doi-asserted-by":"crossref","first-page":"5539","DOI":"10.1093\/nar\/gkz361","article-title":"Fast hierarchical Bayesian analysis of population structure","volume":"47","author":"Tonkin-Hill","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026052023580191900_btag195-B12","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1093\/sysbio\/syaa009","article-title":"Identification of hidden population structure in time-scaled phylogenies","volume":"69","author":"Volz","year":"2020","journal-title":"Syst Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag195\/68143753\/btag195.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/5\/btag195\/68143753\/btag195.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/5\/btag195\/68143753\/btag195.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T03:58:43Z","timestamp":1779335923000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag195\/8661457"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,22]]},"references-count":12,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,5,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag195","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,5]]},"published":{"date-parts":[[2026,4,22]]},"article-number":"btag195"}}