{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T01:27:28Z","timestamp":1793669248257,"version":"4.5.1"},"reference-count":46,"publisher":"SAGE Publications","issue":"11-12","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Journal of Computational Biology"],"published-print":{"date-parts":[[2026,12,1]]},"abstract":"<jats:p>\n                    Phylogenetic diversity (PD) plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of\n                    <jats:italic toggle=\"yes\">k<\/jats:italic>\n                    taxa with maximum PD can be found by a simple and efficient greedy algorithm. However, this algorithmic tractability is lost when considering phylogenetic networks, which incorporate reticulate evolutionary events such as hybridization and horizontal gene transfer. To address this challenge, we introduce\n                    <jats:monospace>PaNDA<\/jats:monospace>\n                    (Phylogenetic Network Diversity Algorithms), the first software package and interactive graphical user-interface for exploring, visualizing, and maximizing diversity in phylogenetic networks.\n                    <jats:monospace>PaNDA<\/jats:monospace>\n                    includes a novel algorithm to find a subset of\n                    <jats:italic toggle=\"yes\">k<\/jats:italic>\n                    taxa with maximum diversity, running in polynomial time for networks of bounded\n                    <jats:italic toggle=\"yes\">scanwidth<\/jats:italic>\n                    , a measure of tree-likeness of a network that grows slower than the well-known\n                    <jats:italic toggle=\"yes\">level<\/jats:italic>\n                    measure. This algorithm considers the variant of PD on networks in which the branch lengths of all paths from the root to the selected taxa contribute towards their diversity. We demonstrate the scalability of this algorithm on simulated networks, successfully analyzing level-15 networks with up to 200 taxa in seconds. We also provide a proof-of-concept analysis using a phylogenetic network on\n                    <jats:italic toggle=\"yes\">Xiphophorus<\/jats:italic>\n                    species, illustrating how the tool can support diversity studies based on real genomic data. The software is easily installable and freely available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/nholtgrefe\/panda\">https:\/\/github.com\/nholtgrefe\/panda<\/jats:ext-link>\n                    . Additionally, we extend the definition of PD to semi-directed phylogenetic networks, which are mixed graphs increasingly used in phylogenetic analysis to model uncertainty of the root location. We prove that finding a subset of\n                    <jats:italic toggle=\"yes\">k<\/jats:italic>\n                    taxa with maximum diversity remains NP-hard on semi-directed networks, but do present a polynomial-time algorithm for networks with bounded level.\n                  <\/jats:p>","DOI":"10.1177\/15578666261481955","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T17:46:58Z","timestamp":1788889618000},"page":"1192-1211","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":2,"title":["<tt>PaNDA<\/tt>\n                    : Efficient Optimization of Phylogenetic Diversity in Networks"],"prefix":"10.1177","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6162-9668","authenticated-orcid":false,"given":"Niels","family":"Holtgrefe","sequence":"first","affiliation":[{"name":"Delft University of Technology, Delft, The Netherlands."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leo","family":"van Iersel","sequence":"additional","affiliation":[{"name":"Delft University of Technology, Delft, The Netherlands."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruben","family":"Meuwese","sequence":"additional","affiliation":[{"name":"Delft University of Technology, Delft, The Netherlands."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yukihiro","family":"Murakami","sequence":"additional","affiliation":[{"name":"Delft University of Technology, Delft, The Netherlands."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jannik","family":"Schestag","sequence":"additional","affiliation":[{"name":"Delft University of Technology, Delft, The Netherlands."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"e_1_3_3_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13015-025-00274-w"},{"key":"e_1_3_3_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11538-018-0485-4"},{"key":"e_1_3_3_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2013.05.007"},{"key":"e_1_3_3_5_1","doi-asserted-by":"publisher","DOI":"10.3390\/nu7031798"},{"key":"e_1_3_3_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syy033"},{"key":"e_1_3_3_7_1","doi-asserted-by":"publisher","unstructured":"Berry V Scornavacca C Weller M. Scanning Phylogenetic Networks Is NP-hard. In: Proceedings of the 46th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2020). 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Limits of Kernelization and parametrization for phylogenetic diversity with dependencies. In: Proceedings of the 17th Latin American Theoretical Informatics Symposium (LATIN 2026). Springer; 2026."},{"key":"e_1_3_3_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12064-025-00453-8"},{"key":"e_1_3_3_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaf067"},{"key":"e_1_3_3_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcss.2026.103802"},{"key":"e_1_3_3_23_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000296"},{"key":"e_1_3_3_24_1","doi-asserted-by":"publisher","unstructured":"Jones M Schestag J. How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks. In: Proceedings of the 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). 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