{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T18:33:23Z","timestamp":1760985203507,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T00:00:00Z","timestamp":1409184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-0743374","DMS-1222940"],"award-info":[{"award-number":["DBI-0743374","DMS-1222940"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between  biological processes, existing models for duplicate gene retention and data is presented. Existing models are then extended in deriving two new birth\/death models for phylogenetic application in a gene tree\/species tree reconciliation framework to enable probabilistic inference of the mechanisms from model parameterization. The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better models and better inference.<\/jats:p>","DOI":"10.3390\/computation2030112","type":"journal-article","created":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T10:37:35Z","timestamp":1409222255000},"page":"112-130","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["On Mechanistic Modeling of Gene Content Evolution:  Birth-Death Models and Mechanisms of Gene Birth and  Gene Retention"],"prefix":"10.3390","volume":"2","author":[{"given":"Ashley","family":"Teufel","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA"}]},{"given":"Jing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens,  GA 30602, USA"}]},{"given":"Malgorzata","family":"O'Reilly","sequence":"additional","affiliation":[{"name":"School of Mathematics and Physics, University of Tasmania, Hobart, TAS 7001, Australia"}]},{"given":"Liang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens,  GA 30602, USA"}]},{"given":"David","family":"Liberles","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA"}]}],"member":"1968","published-online":{"date-parts":[[2014,8,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/sysbio\/46.3.523","article-title":"Gene trees in species trees","volume":"46","author":"Maddison","year":"1997","journal-title":"Syst. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1002\/jez.b.21124","article-title":"Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms","volume":"308","author":"Roth","year":"2007","journal-title":"J. Exp. Zool. B"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1093\/gbe\/evt151","article-title":"On the need for mechanistic models in computational genomics","volume":"5","author":"Liberles","year":"2013","journal-title":"Genome Biol. Evol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ohno, S. (1970). Evolution by Gene Duplication, Springer.","DOI":"10.1007\/978-3-642-86659-3"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1093\/genetics\/159.4.1789","article-title":"The probability of preservation of a newly arisen gene duplicate","volume":"159","author":"Lynch","year":"2001","journal-title":"Genetics"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1101\/gr.3681406","article-title":"Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity","volume":"16","author":"Freeling","year":"2006","journal-title":"Genome Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nrg2689","article-title":"The evolution of gene duplications: classifying and distinguishing between models","volume":"11","author":"Innan","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The evolutionary fate and consequences of duplicate genes","volume":"290","author":"Lynch","year":"2000","journal-title":"Science"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/1502793.1502796","article-title":"The gene evolution model and computing its associated probabilities","volume":"56","author":"Arvestad","year":"2009","journal-title":"JACM"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1007\/s00239-007-9041-9","article-title":"The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation","volume":"65","author":"Hughes","year":"2007","journal-title":"J. Mol. Evol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/gb-2007-8-5-213","article-title":"Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia","volume":"8","author":"Hughes","year":"2007","journal-title":"Genome Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1093\/gbe\/evr093","article-title":"Toward a general model for the evolutionary dynamics of gene duplicates","volume":"3","author":"Konrad","year":"2011","journal-title":"Genome Biol. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1126\/science.1194167","article-title":"Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate","volume":"330","author":"Denoeud","year":"2010","journal-title":"Science"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i06","article-title":"\u2018DEoptim\u2019: An R package for global optimization by differential evolution","volume":"40","author":"Mullen","year":"2011","journal-title":"J. Stat. Softw."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1023\/A:1022696612931","article-title":"The evolutionary demography of duplicate genes","volume":"3","author":"Lynch","year":"2003","journal-title":"J. Struct. Funct. Genomics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1534\/genetics.111.135590","article-title":"Multiple routes to subfunctionalization and gene duplicate specialization","volume":"190","author":"Proulx","year":"2012","journal-title":"Genetics"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1101\/gr.7105007","article-title":"Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes","volume":"17","author":"Rasmussen","year":"2007","journal-title":"Genome Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1093\/molbev\/msj114","article-title":"On the formation of novel genes by duplication in the Caenorhabditis elegans genome","volume":"23","author":"Katju","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s10709-009-9355-1","article-title":"Population genetic models of duplicated genes","volume":"137","author":"Innan","year":"2009","journal-title":"Genetica"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e42680","DOI":"10.1371\/journal.pone.0042680","article-title":"Mis-assembled \u201csegmental duplications\u201d in two versions of the Bos taurus genome","volume":"7","author":"Zimin","year":"2012","journal-title":"PLoS One"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Cannarozzi, G.M., and Schneider, A. (2012). Codon Evolution: Mechanisms and Models, Oxford University Press.","DOI":"10.1093\/acprof:osobl\/9780199601165.001.0001"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1287\/ijoc.1090.0357","article-title":"On the numerical analysis of inhomogenous continuous-time Markov Chains","volume":"22","author":"Arns","year":"2010","journal-title":"INFORMS J. Comput."},{"key":"ref_23","unstructured":"Massink, M., and Norman, G. (2011, January 1\u20133). On-the-Fly Uniformization of Time-Inhomogenous Infinite Markov Population Models. In Proceedings of the 9th Workshop on Quantitative Aspects of Programming Languages (QAPL\u201911), Saarbr\u00fccken, Germany."},{"key":"ref_24","unstructured":"Bailey, N. (1964). The Elements of Stochastic Processes, with Applications to the Natural Sciences, Wiley."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1214\/aoms\/1177730285","article-title":"On the generalized \u201cbirth-and-death\u201d process","volume":"19","author":"Kendall","year":"1948","journal-title":"Ann. Mathemat. Stat."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1098\/rstb.1994.0068","article-title":"The reconstructed evolutionary process","volume":"344","author":"Nee","year":"1994","journal-title":"Phil. Trans. R. Soc. B"},{"key":"ref_27","unstructured":"Olver, F.W.J., Lozier, D.M., Boisvert, R.F., and Clark, C.W. (2010). NIST Handbook of Mathematical Functions, Cambridge University Press."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"D495","DOI":"10.1093\/nar\/gki090","article-title":"The Adaptive Evolution Database (TAED): A phylogeny based tool for comparative genomics","volume":"33","author":"Roth","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-3197\/2\/3\/112\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T21:15:21Z","timestamp":1760217321000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-3197\/2\/3\/112"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,28]]},"references-count":28,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2014,9]]}},"alternative-id":["computation2030112"],"URL":"https:\/\/doi.org\/10.3390\/computation2030112","relation":{},"ISSN":["2079-3197"],"issn-type":[{"type":"electronic","value":"2079-3197"}],"subject":[],"published":{"date-parts":[[2014,8,28]]}}}