{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T12:26:01Z","timestamp":1773836761341,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012191","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T00:00:00Z","timestamp":1720569600000}}],"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR 14 CE22-0021"],"award-info":[{"award-number":["ANR 14 CE22-0021"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-19-P3IA-0001"],"award-info":[{"award-number":["ANR-19-P3IA-0001"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Research Council","award":["SEQUOIA-724063"],"award-info":[{"award-number":["SEQUOIA-724063"]}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chair program Mathematical Modelling and Biodiversity of Veolia Environment-Ecole Polytechnique-National Museum of Natural History- Foundation X"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species\u2019 ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence\/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012191","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T21:13:16Z","timestamp":1719522796000},"page":"e1012191","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Assessing the extinction risk of the spontaneous flora in urban tree bases"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1820-5648","authenticated-orcid":true,"given":"Apolline","family":"Louvet","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cl\u00e9ment","family":"Mantoux","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Machon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,6,27]]},"reference":[{"issue":"1","key":"pcbi.1012191.ref001","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1146\/annurev.ecolsys.34.011802.132419","article-title":"Effects of habitat fragmentation on biodiversity","volume":"34","author":"L Fahrig","year":"2003","journal-title":"Annual review of ecology, evolution, and systematics"},{"issue":"2","key":"pcbi.1012191.ref002","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s11252-013-0319-y","article-title":"Effects of urban structure on plant species richness in a large European city","volume":"17","author":"KJ Schmidt","year":"2014","journal-title":"Urban Ecosystems"},{"key":"pcbi.1012191.ref003","unstructured":"Maurel N. De l\u2019introduction \u00e0 l\u2019invasion : les plantes exotiques en milieu urbain. Paris, Mus\u00e9um National d\u2019Histoire Naturelle. 2010."},{"key":"pcbi.1012191.ref004","volume-title":"Ecology of tropical and subtropical vegetation","author":"H Walter","year":"1971"},{"issue":"8","key":"pcbi.1012191.ref005","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1111\/j.1600-0706.2010.18959.x","article-title":"Colonization and extinction dynamics of an annual plant metapopulation in an urban environment","volume":"120","author":"A Dornier","year":"2011","journal-title":"Oikos"},{"issue":"3","key":"pcbi.1012191.ref006","first-page":"237","article-title":"Some demographic and genetic consequences of environmental heterogeneity for biological control","volume":"15","author":"R Levins","year":"1969","journal-title":"American Entomologist"},{"issue":"3","key":"pcbi.1012191.ref007","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s10592-014-0676-y","article-title":"Multivariate analysis of polyploid data reveals the role of railways in the spread of the invasive South African Ragwort (Senecio inaequidens)","volume":"16","author":"\u00c9 Blanchet","year":"2015","journal-title":"Conservation Genetics"},{"issue":"15","key":"pcbi.1012191.ref008","doi-asserted-by":"crossref","first-page":"8414","DOI":"10.1002\/ece3.4954","article-title":"Colonization and extinction dynamics among the plant species at tree bases in Paris (France)","volume":"9","author":"M Omar","year":"2019","journal-title":"Ecology and Evolution"},{"issue":"10","key":"pcbi.1012191.ref009","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1073\/pnas.0708446105","article-title":"Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta","volume":"105","author":"PO Cheptou","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1012191.ref010","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.ufug.2018.08.018","article-title":"Drivers of the distribution of spontaneous plant communities and species within urban tree bases","volume":"35","author":"M Omar","year":"2018","journal-title":"Urban Forestry & Urban Greening"},{"issue":"4","key":"pcbi.1012191.ref011","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1111\/2041-210X.13547","article-title":"Detecting seed bank influence on plant metapopulation dynamics","volume":"12","author":"A Louvet","year":"2021","journal-title":"Methods in Ecology and Evolution"},{"key":"pcbi.1012191.ref012","unstructured":"Machon N. Floristic monitoring of the 1,324 alignment tree bases of 15 streets in the district of Bercy, Paris, France, from 2009 to 2018 (dataset). Zenodo. 2020."},{"issue":"4","key":"pcbi.1012191.ref013","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.ecolmodel.2004.04.019","article-title":"SPOMSIM: software for stochastic patch occupancy models of metapopulation dynamics","volume":"179","author":"A Moilanen","year":"2004","journal-title":"Ecological Modelling"},{"key":"pcbi.1012191.ref014","doi-asserted-by":"crossref","first-page":"e13822","DOI":"10.1111\/ddi.13822","article-title":"Broadening applications of stochastic patch occupancy models over three decades","author":"C Guti\u00e9rrez-Arellano","year":"2024","journal-title":"Diversity and Distributions"},{"issue":"3","key":"pcbi.1012191.ref015","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1046\/j.1365-2745.2002.00692.x","article-title":"Large-scale spatial dynamics of plants: metapopulations, regional ensembles and patchy populations","volume":"90","author":"RP Freckleton","year":"2002","journal-title":"Journal of Ecology"},{"issue":"6","key":"pcbi.1012191.ref016","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1111\/1365-2745.12141","article-title":"Inferring seed bank from hidden Markov models: new insights into metapopulation dynamics in plants","volume":"101","author":"H Fr\u00e9ville","year":"2013","journal-title":"Journal of Ecology"},{"issue":"9","key":"pcbi.1012191.ref017","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1111\/ele.13097","article-title":"A general method for estimating seed dormancy and colonisation in annual plants from the observation of existing flora","volume":"21","author":"M Pluntz","year":"2018","journal-title":"Ecology Letters"},{"key":"pcbi.1012191.ref018","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.tpb.2022.02.003","article-title":"Extinction threshold and large population limit of a plant metapopulation model with recurrent extinction events and a seed bank component","volume":"145","author":"A Louvet","year":"2022","journal-title":"Theoretical Population Biology"},{"issue":"19","key":"pcbi.1012191.ref019","doi-asserted-by":"crossref","first-page":"13166","DOI":"10.1002\/ece3.8038","article-title":"Does seed mass drive interspecies variation in the effect of management practices on weed demography?","volume":"11","author":"E Kazakou","year":"2021","journal-title":"Ecology and Evolution"},{"key":"pcbi.1012191.ref020","unstructured":"Gargominy O, Tercerie S, R\u00e9gnier C, Ramage T, Schoelinck C, Dupont P, et al. TAXREF v8.0, r\u00e9f\u00e9rentiel taxonomique pour la France: M\u00e9thodologie, mise en oeuvre et diffusion. Rapport SPN. 2014;42:2014."},{"key":"pcbi.1012191.ref021","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-28982-8","volume-title":"Inference in Hidden Markov Models","author":"O Capp\u00e9","year":"2005"},{"issue":"2","key":"pcbi.1012191.ref022","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1109\/5.18626","article-title":"A tutorial on hidden Markov models and selected applications in speech recognition","volume":"77","author":"LR Rabiner","year":"1989","journal-title":"Proceedings of the IEEE"},{"issue":"6","key":"pcbi.1012191.ref023","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1111\/j.1365-2745.2008.01430.x","article-title":"The LEDA traitbase: a database of life-history traits of the Northwest European flora","volume":"96","author":"M Kleyer","year":"2008","journal-title":"Journal of Ecology"},{"issue":"11","key":"pcbi.1012191.ref024","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1111\/2041-210X.12797","article-title":"rptR: Repeatability estimation and variance decomposition by generalized linear mixed-effects models","volume":"8","author":"MA Stoffel","year":"2017","journal-title":"Methods in Ecology and Evolution"},{"key":"pcbi.1012191.ref025","unstructured":"Julve P. Baseflor. Index Botanique, Ecologique et Chronologique de la Flore de France. Version 2019. Available online at http:\/\/philippe.julve.pagesperso-orange.fr\/catminat.html.; 2019."},{"issue":"2","key":"pcbi.1012191.ref026","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/s00285-021-01639-6","article-title":"A branching process model for dormancy and seed banks in randomly fluctuating environments","volume":"83","author":"J Blath","year":"2021","journal-title":"Journal of Mathematical Biology"},{"key":"pcbi.1012191.ref027","doi-asserted-by":"crossref","first-page":"e1008698","DOI":"10.1371\/journal.pgen.1008698","article-title":"Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data","author":"TPP Sellinger","year":"2020","journal-title":"PLoS Genetics"},{"key":"pcbi.1012191.ref028","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1007\/s00484-014-0892-7","article-title":"Assessing accuracy in citizen science-based plant phenology monitoring","volume":"59","author":"KK Fuccillo","year":"2015","journal-title":"International Journal of Biometeorology"},{"issue":"10","key":"pcbi.1012191.ref029","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1111\/2041-210X.12581","article-title":"Data reliability in citizen science: learning curve and the effects of training method, volunteer background and experience on identification accuracy of insects visiting ivy flowers","volume":"7","author":"FLW Ratnieks","year":"2016","journal-title":"Methods in Ecology and Evolution"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1012191","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T00:00:00Z","timestamp":1720569600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012191","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T17:49:06Z","timestamp":1720633746000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012191"}},"subtitle":[],"editor":[{"given":"Jere","family":"Koskela","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,27]]},"references-count":29,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012191","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1012191","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,27]]}}}