TY - JOUR AU - Liberles, D. A. AU - Schreiber, D. R. AU - Govindarajan, S. AU - Chamberlain, S. G. AU - Benner, S. A. PY - 2001 DA - 2001// TI - The adaptive evolution database (TAED) JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-8-research0028 DO - 10.1186/gb-2001-2-8-research0028 ID - Liberles2001 ER - TY - JOUR AU - Roth, C. AU - Betts, M. J. AU - Steffansson, P. AU - Saelensminde, G. AU - Liberles, D. A. PY - 2005 DA - 2005// TI - The Adaptive Evolution Database (TAED): a phylogeny-based tool for comparative genomics JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki090 DO - 10.1093/nar/gki090 ID - Roth2005 ER - TY - STD TI - Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong J, Zimin A, Grammes F, et al. (2016) Atlantic salmon genome provides insights into rediploidization. Nature. in press, doi:10.1038/nature17164. ID - ref3 ER - TY - JOUR AU - Rondeau, E. B. AU - Minkley, D. R. AU - Leong, J. S. AU - Messmer, A. M. AU - Jantzen, J. R. AU - Schalburg, K. R. AU - Lemon, C. AU - Bird, N. H. AU - Koop, B. F. PY - 2014 DA - 2014// TI - The genome and linkage map of the Northern Pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0102089 DO - 10.1371/journal.pone.0102089 ID - Rondeau2014 ER - TY - JOUR AU - Berthelot, C. AU - Brunet, F. AU - Chalopin, D. AU - Juanchich, A. AU - Bernard, M. AU - Noel, B. AU - Bento, P. AU - Silva, C. AU - Labadie, K. PY - 2014 DA - 2014// TI - The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates JO - Nat Commun VL - 22 ID - Berthelot2014 ER - TY - JOUR AU - Meyer, A. AU - Peer, Y. PY - 2005 DA - 2005// TI - From 2R to 3R: evidence for a fish-specific genome duplication (FSGD) JO - Bioessays VL - 27 UR - https://doi.org/10.1002/bies.20293 DO - 10.1002/bies.20293 ID - Meyer2005 ER - TY - JOUR AU - Danzmann, R. G. AU - Davidson, E. A. AU - Ferguson, M. M. AU - Gharbi, K. AU - Koop, B. F. AU - Hoyheim, B. AU - Lien, S. AU - Lubieniecki, K. P. AU - Moghadam, H. K. AU - Park, J. AU - Phillips, R. B. AU - Davidson, W. S. PY - 2008 DA - 2008// TI - Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon) JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-557 DO - 10.1186/1471-2164-9-557 ID - Danzmann2008 ER - TY - JOUR AU - Hughes, T. AU - Liberles, D. A. PY - 2008 DA - 2008// TI - Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species JO - J Mol Evol VL - 67 UR - https://doi.org/10.1007/s00239-008-9145-x DO - 10.1007/s00239-008-9145-x ID - Hughes2008 ER - TY - JOUR AU - Donoghue, P. C. J. AU - Purnell, M. A. PY - 2005 DA - 2005// TI - Genome duplication, extinction and vertebrate evolution JO - Trends Ecol Evol VL - 20 UR - https://doi.org/10.1016/j.tree.2005.04.008 DO - 10.1016/j.tree.2005.04.008 ID - Donoghue2005 ER - TY - BOOK AU - Ohno, S. PY - 1970 DA - 1970// TI - Evolution by gene duplication PB - Springer CY - New York UR - https://doi.org/10.1007/978-3-642-86659-3 DO - 10.1007/978-3-642-86659-3 ID - Ohno1970 ER - TY - JOUR AU - Roth, C. AU - Rastogi, S. AU - Arvestad, L. AU - Dittmar, K. AU - Light, S. AU - Ekman, D. AU - Liberles, D. A. PY - 2007 DA - 2007// TI - Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms JO - J Exp Zool (Mol Dev Evol) VL - 306B UR - https://doi.org/10.1002/jez.b.21124 DO - 10.1002/jez.b.21124 ID - Roth2007 ER - TY - JOUR AU - Katju, V. AU - Lynch, M. PY - 2006 DA - 2006// TI - On the formation of novel genes by duplication in the Caenorhabditis elegans genome JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj114 DO - 10.1093/molbev/msj114 ID - Katju2006 ER - TY - JOUR AU - Lynch, M. AU - Katju, V. PY - 2004 DA - 2004// TI - The altered evolutionary trajectories of gene duplicates JO - Trends Gen VL - 20 UR - https://doi.org/10.1016/j.tig.2004.09.001 DO - 10.1016/j.tig.2004.09.001 ID - Lynch2004 ER - TY - JOUR AU - Katju, V. AU - Lynch, M. PY - 2003 DA - 2003// TI - The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome JO - Genetics VL - 165 ID - Katju2003 ER - TY - JOUR AU - Yang, J. AU - Lusk, R. AU - Li, W. H. PY - 2003 DA - 2003// TI - Organismal complexity, protein complexity, and gene duplicability JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.2536672100 DO - 10.1073/pnas.2536672100 ID - Yang2003 ER - TY - JOUR AU - Freeling, M. AU - Thomas, B. C. PY - 2006 DA - 2006// TI - Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.3681406 DO - 10.1101/gr.3681406 ID - Freeling2006 ER - TY - JOUR AU - D’Antonio, M. AU - Ciccarelli, F. D. PY - 2011 DA - 2011// TI - Modification of gene duplicability during the evolution of protein interaction network JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002029 DO - 10.1371/journal.pcbi.1002029 ID - D’Antonio2011 ER - TY - JOUR AU - Zhang, Z. AU - Luo, Z. W. AU - Kishino, H. AU - Kearsey, M. J. PY - 2004 DA - 2004// TI - Divergence pattern of duplicate genes in protein-protein interactions follows the power law JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi034 DO - 10.1093/molbev/msi034 ID - Zhang2004 ER - TY - JOUR AU - McGrath, C. L. AU - Gout, J. F. AU - Johri, P. AU - Doak, T. G. AU - Lynch, M. PY - 2014 DA - 2014// TI - Differential retention and divergent resolution of duplicate genes following whole-genome duplication JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.173740.114 DO - 10.1101/gr.173740.114 ID - McGrath2014 ER - TY - JOUR AU - Smet, R. AU - Adams, K. L. AU - Vandepoele, K. AU - Montagu, M. C. E. AU - Maere, S. AU - Peer, Y. PY - 2013 DA - 2013// TI - Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants JO - Proc Natl Acad Sci USA VL - 110 UR - https://doi.org/10.1073/pnas.1300127110 DO - 10.1073/pnas.1300127110 ID - Smet2013 ER - TY - JOUR AU - Ekman, D. AU - Light, S. AU - Bjorklund, A. K. AU - Elofsson, A. PY - 2006 DA - 2006// TI - What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-6-r45 DO - 10.1186/gb-2006-7-6-r45 ID - Ekman2006 ER - TY - JOUR AU - Konrad, A. AU - Teufel, A. I. AU - Grahnen, J. A. AU - Liberles, D. A. PY - 2011 DA - 2011// TI - Toward a general model for the evolutionary dynamics of gene duplicates JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evr093 DO - 10.1093/gbe/evr093 ID - Konrad2011 ER - TY - JOUR AU - Hughes, T. AU - Liberles, D. A. PY - 2008 DA - 2008// TI - The power-law distribution of gene family size is driven by the pseudogenisation rate’s heterogeneity between gene families JO - Gene VL - 414 UR - https://doi.org/10.1016/j.gene.2008.02.014 DO - 10.1016/j.gene.2008.02.014 ID - Hughes2008 ER - TY - JOUR AU - Hughes, T. AU - Ekman, D. AU - Ardawatia, H. AU - Elofsson, A. AU - Liberles, D. A. PY - 2007 DA - 2007// TI - Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-5-213 DO - 10.1186/gb-2007-8-5-213 ID - Hughes2007 ER - TY - JOUR AU - Teufel, A. I. AU - Liu, L. AU - Liberles, D. A. PY - 2016 DA - 2016// TI - Models for gene duplication when dosage balance works as a transition state to subsequent neo- or sub-functionalization JO - BMC Evol Biol VL - 16 UR - https://doi.org/10.1186/s12862-016-0616-1 DO - 10.1186/s12862-016-0616-1 ID - Teufel2016 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Ye, K. AU - Schulz, M. H. AU - Long, Q. AU - Apweiler, R. AU - Ning, Z. PY - 2009 DA - 2009// TI - Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp394 DO - 10.1093/bioinformatics/btp394 ID - Ye2009 ER - TY - JOUR AU - Lunter, G. AU - Goodson, M. PY - 2011 DA - 2011// TI - Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.111120.110 DO - 10.1101/gr.111120.110 ID - Lunter2011 ER - TY - JOUR AU - Zimin, A. V. AU - Kelley, D. R. AU - Roberts, M. AU - Marcais, G. AU - Salzberg, S. L. AU - Yorke, J. A. PY - 2012 DA - 2012// TI - Mis-assembled “segmental duplications” in two versions of the Bos taurus genome JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0042680 DO - 10.1371/journal.pone.0042680 ID - Zimin2012 ER - TY - JOUR AU - Cunningham, F. AU - Amode, M. R. AU - Barrell, D. AU - Beal, K. AU - Billis, K. PY - 2015 DA - 2015// TI - Ensembl 2015 JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1010 DO - 10.1093/nar/gku1010 ID - Cunningham2015 ER - TY - JOUR AU - Moretti, S. AU - Laurenczy, B. AU - Gharib, W. H. AU - Castella, B. AU - Kuzniar, A. AU - Schabauer, H. AU - Studer, R. A. AU - Valle, M. AU - Salamin, N. AU - Stockinger, H. AU - Robinson-Rechavi, M. PY - 2014 DA - 2014// TI - Selectome update: quality control and computational improvements to a database of positive selection JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1065 DO - 10.1093/nar/gkt1065 ID - Moretti2014 ER - TY - JOUR AU - Matsen, F. A. AU - Kodner, R. B. AU - Armbrust, E. V. PY - 2010 DA - 2010// TI - Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree JO - BMC Bioinforma VL - 11 UR - https://doi.org/10.1186/1471-2105-11-538 DO - 10.1186/1471-2105-11-538 ID - Matsen2010 ER - TY - JOUR AU - Katoh, K. AU - Standley, D. M. PY - 2013 DA - 2013// TI - MAFFT multiple sequence alignment software version 7: improvements in performance and usability JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst010 DO - 10.1093/molbev/mst010 ID - Katoh2013 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Loytynoja, A. AU - Goldman, N. PY - 2010 DA - 2010// TI - webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser JO - BMC Bioinforma VL - 11 UR - https://doi.org/10.1186/1471-2105-11-579 DO - 10.1186/1471-2105-11-579 ID - Loytynoja2010 ER - TY - JOUR AU - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2011 DA - 2011// TI - ProtTest 3: fast selection of best-fit models of protein evolution JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr088 DO - 10.1093/bioinformatics/btr088 ID - Darriba2011 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of Phyml 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogeny JO - Bioinformatics VL - 19 ID - Huelsenbeck2001 ER - TY - JOUR AU - Chauve, C. AU - Doyon, J. P. AU - El-Mabrouk, N. PY - 2008 DA - 2008// TI - Gene family evolution by duplication, speciation, and loss JO - J Comput Biol VL - 15 UR - https://doi.org/10.1089/cmb.2008.0054 DO - 10.1089/cmb.2008.0054 ID - Chauve2008 ER - TY - JOUR AU - Swenson, K. M. AU - El-Mabrouk, N. PY - 2012 DA - 2012// TI - Gene trees and species trees: irreconcilable differences JO - BMC Bioinforma VL - 13 ID - Swenson2012 ER - TY - CHAP AU - Eulenstein, O. AU - Huzurbazar, S. AU - Liberles, D. A. ED - Dittmar, K. ED - Liberles, D. A. PY - 2010 DA - 2010// TI - Reconciling phylogenetic trees BT - Evolution After Duplication PB - Wiley-Blackwell CY - USA ID - Eulenstein2010 ER - TY - JOUR AU - Berglund-Sonnhammer, A. C. AU - Steffansson, P. AU - Betts, M. J. AU - Liberles, D. A. PY - 2006 DA - 2006// TI - Optimal gene trees from sequences and speices trees using a soft interpretation of parsimony JO - J Mol Evol VL - 63 UR - https://doi.org/10.1007/s00239-005-0096-1 DO - 10.1007/s00239-005-0096-1 ID - Berglund-Sonnhammer2006 ER - TY - JOUR AU - Arvestad, L. AU - Berglund, A. C. AU - Lagergren, J. AU - Sennblad, B. PY - 2003 DA - 2003// TI - Bayesian gene/species tree reconciliation and orthology analysis using MCMC JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1000 DO - 10.1093/bioinformatics/btg1000 ID - Arvestad2003 ER - TY - JOUR AU - Arvestad, L. AU - Lagergren, L. AU - Sennblad, B. PY - 2009 DA - 2009// TI - The gene evolution model and computing its associated probabilities JO - J ACM VL - 56 UR - https://doi.org/10.1145/1502793.1502796 DO - 10.1145/1502793.1502796 ID - Arvestad2009 ER - TY - JOUR AU - Gorecki, P. AU - Eulenstein, O. PY - 2014 DA - 2014// TI - Refining discordant gene trees JO - BMC Bioinforma VL - 15 UR - https://doi.org/10.1186/1471-2105-15-S13-S3 DO - 10.1186/1471-2105-15-S13-S3 ID - Gorecki2014 ER - TY - JOUR AU - Szklarczyk, D. AU - Franceschini, A. AU - Wyder, S. AU - Forslund, K. AU - Heller, D. AU - Huerta-Cepas, J. AU - Simonovic, M. AU - Roth, A. AU - Santos, A. AU - Tsafou, K. P. AU - Kuhn, M. AU - Bork, P. AU - Jensen, L. J. AU - Mering, C. PY - 2015 DA - 2015// TI - STRING v10: protein-protein interaction networks, integrated over the tree of life JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1003 DO - 10.1093/nar/gku1003 ID - Szklarczyk2015 ER - TY - JOUR AU - Li, J. T. AU - Hou, G. Y. AU - Kong, X. F. AU - Li, C. Y. AU - Zeng, J. M. AU - Li, H. D. AU - Xiao, G. B. AU - Li, X. M. AU - Sun, X. W. PY - 2015 DA - 2015// TI - The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio) JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep08199 DO - 10.1038/srep08199 ID - Li2015 ER - TY - JOUR AU - Pfeifer, M. AU - Kugler, K. G. AU - Sandve, S. R. AU - Zhan, B. AU - Rudi, H. AU - Hvidsten, T. R. AU - Mayer, K. F. AU - Olsen, O. A. PY - 2014 DA - 2014// TI - Genome interplay in the grain transcriptome of hexaploid bread wheat JO - Science VL - 345 UR - https://doi.org/10.1126/science.1250091 DO - 10.1126/science.1250091 ID - Pfeifer2014 ER - TY - JOUR AU - Hughes, T. E. AU - Langdale, J. A. AU - Kelly, S. PY - 2014 DA - 2014// TI - The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole genome duplication in maize JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.172684.114 DO - 10.1101/gr.172684.114 ID - Hughes2014 ER - TY - JOUR AU - Gerstein, M. B. AU - Rozowsky, J. AU - Yan, K. K. AU - Wang, D. AU - Cheng, C. AU - Brown, J. B. AU - Davis, C. A. AU - Hillier, L. AU - Sisu, C. AU - Li, J. J. PY - 2014 DA - 2014// TI - Comparative analysis of the transcriptome across distant species JO - Nature VL - 512 UR - https://doi.org/10.1038/nature13424 DO - 10.1038/nature13424 ID - Gerstein2014 ER - TY - JOUR AU - Huang, L. AU - Schiefelbein, J. PY - 2015 DA - 2015// TI - Conserved gene expression programs in developing roots from diverse plants JO - Plant Cell VL - 27 UR - https://doi.org/10.1105/tpc.15.00328 DO - 10.1105/tpc.15.00328 ID - Huang2015 ER - TY - JOUR AU - Rastogi, S. AU - Liberles, D. A. PY - 2005 DA - 2005// TI - Subfunctionalization of duplicated genes as a transition state to neofunctionalization JO - BMC Evol Biol VL - 5 UR - https://doi.org/10.1186/1471-2148-5-28 DO - 10.1186/1471-2148-5-28 ID - Rastogi2005 ER - TY - JOUR AU - He, X. AU - Zhang, J. PY - 2005 DA - 2005// TI - Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution JO - Genetics VL - 169 UR - https://doi.org/10.1534/genetics.104.037051 DO - 10.1534/genetics.104.037051 ID - He2005 ER - TY - JOUR AU - Rohlfs, R. V. AU - Nielsen, R. PY - 2015 DA - 2015// TI - Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution JO - Syst Biol VL - 64 UR - https://doi.org/10.1093/sysbio/syv042 DO - 10.1093/sysbio/syv042 ID - Rohlfs2015 ER - TY - JOUR AU - Rohlfs, R. V. AU - Harrigan, P. AU - Nielsen, R. PY - 2014 DA - 2014// TI - Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/mst190 DO - 10.1093/molbev/mst190 ID - Rohlfs2014 ER - TY - JOUR AU - Teufel, A. I. AU - Zhao, J. AU - O’Reilly, M. AU - Liu, L. AU - Liberles, D. A. PY - 2014 DA - 2014// TI - On mechanistic modeling of gene content evolution: birth-death models and mechanisms of gene birth and gene retention JO - Computation VL - 2 UR - https://doi.org/10.3390/computation2030112 DO - 10.3390/computation2030112 ID - Teufel2014 ER - TY - JOUR AU - Zhao, J. AU - Teufel, A. I. AU - Liberles, D. A. AU - Liu, L. PY - 2015 DA - 2015// TI - A generalized birth and death process for modeling the fates of gene duplication JO - BMC Evol Biol VL - 15 UR - https://doi.org/10.1186/s12862-015-0539-2 DO - 10.1186/s12862-015-0539-2 ID - Zhao2015 ER -