{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T11:14:18Z","timestamp":1775819658171,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009899","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,4]],"date-time":"2022-03-04T00:00:00Z","timestamp":1646352000000}}],"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence \/ absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium\n                    <jats:italic>Pseudomonas syringae<\/jats:italic>\n                    and growth phenotypes of the\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009899","type":"journal-article","created":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T13:42:02Z","timestamp":1645537322000},"page":"e1009899","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["RecPD: A Recombination-aware measure of phylogenetic diversity"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8741-4457","authenticated-orcid":true,"given":"Cedoljub","family":"Bundalovic-Torma","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4270-2791","authenticated-orcid":true,"given":"Darrell","family":"Desveaux","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-3869","authenticated-orcid":true,"given":"David S.","family":"Guttman","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,2,22]]},"reference":[{"issue":"1","key":"pcbi.1009899.ref001","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1111\/j.1461-0248.2009.01405.x","article-title":"Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history","volume":"13","author":"MW Cadotte","year":"2010","journal-title":"Ecol Lett"},{"issue":"18","key":"pcbi.1009899.ref002","doi-asserted-by":"crossref","first-page":"3514","DOI":"10.1002\/ece3.1155","article-title":"Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories","volume":"4","author":"EK Morris","year":"2014","journal-title":"Ecol Evol"},{"issue":"4","key":"pcbi.1009899.ref003","first-page":"679","article-title":"Measuring the diversity of the human microbiota with targeted next-generation sequencing","volume":"19","author":"F Finotello","year":"2018","journal-title":"Brief Bioinform"},{"issue":"1","key":"pcbi.1009899.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","article-title":"Conservation evaluation and phylogenetic diversity","volume":"61","author":"DP Faith","year":"1992","journal-title":"Biol Conserv"},{"issue":"6","key":"pcbi.1009899.ref005","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1111\/jse.12436","article-title":"Phylogenetic diversity is a better measure of biodiversity than taxon counting","volume":"56","author":"JT Miller","year":"2018","journal-title":"Journal of Systematics and Evolution"},{"issue":"2","key":"pcbi.1009899.ref006","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1111\/brv.12252","article-title":"A guide to phylogenetic metrics for conservation, community ecology and macroecology","volume":"92","author":"CM Tucker","year":"2017","journal-title":"Biol Rev Camb Philos Soc"},{"issue":"12","key":"pcbi.1009899.ref007","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"1662","key":"pcbi.1009899.ref008","doi-asserted-by":"crossref","first-page":"20140011","DOI":"10.1098\/rstb.2014.0011","article-title":"Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses","volume":"370","author":"DP Faith","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1","key":"pcbi.1009899.ref009","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/s41467-019-08600-8","article-title":"Global conservation of phylogenetic diversity captures more than just functional diversity","volume":"10","author":"NR Owen","year":"2019","journal-title":"Nat Commun"},{"key":"pcbi.1009899.ref010","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1111\/j.1600-0587.2009.05880.x","article-title":"A diversity of beta diversities: Straightening up a concept gone awry. 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