{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T22:19:06Z","timestamp":1793830746759,"version":"4.6.1"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"S20","license":[{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which can be difficult to estimate. Prior work has explored the relationship between event costs and maximum parsimony reconciliations in the duplication-loss and duplication-transfer-loss models, but no studies have addressed this relationship in the more complicated duplication-loss-coalescence model.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We provide a fixed-parameter tractable algorithm for computing Pareto-optimal reconciliations and recording all events that arise in those reconciliations, along with their frequencies. We apply this method to a case study of 16 fungi to systematically characterize the complexity of MPR space across event costs and identify events supported across this space.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This work provides a new framework for studying the relationship between event costs and reconciliations that incorporates both macro-evolutionary events and population effects and is thus broadly applicable across eukaryotic species.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-019-3206-6","type":"journal-article","created":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T01:02:24Z","timestamp":1576544544000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model"],"prefix":"10.1186","volume":"20","author":[{"given":"Ross","family":"Mawhorter","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ran","family":"Libeskind-Hadas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Chieh","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,17]]},"reference":[{"issue":"2","key":"3206_CR1","doi-asserted-by":"publisher","first-page":"132","DOI":"10.2307\/2412519","volume":"28","author":"M Goodman","year":"1979","unstructured":"Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G. 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