TY - BOOK AU - Ohno, S. PY - 1970 DA - 1970// TI - Evolution by Gene Duplication PB - Springer-Verlag 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 - Wolfe, K. H. AU - Li, W. H. PY - 2003 DA - 2003// TI - Molecular evolution meets the genomics revolution. JO - Nat Genet VL - 33 UR - https://doi.org/10.1038/ng1088 DO - 10.1038/ng1088 ID - Wolfe2003 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes. JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Gu, Z. AU - Cavalcanti, A. AU - Chen, F. C. AU - Bouman, P. AU - Li, W. H. PY - 2000 DA - 2000// TI - Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004079 DO - 10.1093/oxfordjournals.molbev.a004079 ID - Gu2000 ER - TY - JOUR AU - Long, M. AU - Thornton, K. PY - 2001 DA - 2001// TI - Gene duplication and evolution. JO - Science VL - 293 UR - https://doi.org/10.1126/science.293.5535.1551a DO - 10.1126/science.293.5535.1551a ID - Long2001 ER - TY - JOUR AU - Sharp, P. M. AU - Li, W. H. PY - 1989 DA - 1989// TI - On the rate of DNA sequence evolution in Drosophila. JO - J Mol Evol VL - 28 UR - https://doi.org/10.1007/BF02603075 DO - 10.1007/BF02603075 ID - Sharp1989 ER - TY - JOUR AU - Chamary, J. V. AU - Parmley, J. L. AU - Hurst, L. D. PY - 2006 DA - 2006// TI - Hearing silence: non-neutral evolution at synonymous sites in mammals. JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1770 DO - 10.1038/nrg1770 ID - Chamary2006 ER - TY - JOUR AU - Teshima, K. M. AU - Innan, H. PY - 2004 DA - 2004// TI - The effect of gene conversion on the divergence between duplicated genes. JO - Genetics VL - 166 UR - https://doi.org/10.1534/genetics.166.3.1553 DO - 10.1534/genetics.166.3.1553 ID - Teshima2004 ER - TY - JOUR AU - Ezawa, K. AU - OOta, S. AU - Saitou, N. PY - 2006 DA - 2006// TI - Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat. JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj093 DO - 10.1093/molbev/msj093 ID - Ezawa2006 ER - TY - JOUR AU - Gao, L. Z. AU - Innan, H. PY - 2004 DA - 2004// TI - Very low gene duplication rate in the yeast genome. JO - Science VL - 306 UR - https://doi.org/10.1126/science.1102033 DO - 10.1126/science.1102033 ID - Gao2004 ER - TY - JOUR AU - Zhang, J. PY - 2003 DA - 2003// TI - Evolution by gene duplication: an update. JO - Trends Ecology Evol VL - 18 UR - https://doi.org/10.1016/S0169-5347(03)00033-8 DO - 10.1016/S0169-5347(03)00033-8 ID - Zhang2003 ER - TY - JOUR AU - Lundin, L. G. PY - 1993 DA - 1993// TI - Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. JO - Genomics VL - 16 UR - https://doi.org/10.1006/geno.1993.1133 DO - 10.1006/geno.1993.1133 ID - Lundin1993 ER - TY - JOUR AU - Sidow, A. PY - 1996 DA - 1996// TI - Genome duplications in the evolution of early vertebrates. JO - Curr Opin Genet Dev VL - 6 UR - https://doi.org/10.1016/S0959-437X(96)80026-8 DO - 10.1016/S0959-437X(96)80026-8 ID - Sidow1996 ER - TY - JOUR AU - Meyer, A. AU - Schartl, M. PY - 1999 DA - 1999// TI - Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. JO - Curr Opin Cell Biol VL - 11 UR - https://doi.org/10.1016/S0955-0674(99)00039-3 DO - 10.1016/S0955-0674(99)00039-3 ID - Meyer1999 ER - TY - JOUR AU - Friedman, R. AU - Hughes, A. L. PY - 2001 DA - 2001// TI - Pattern and timing of gene duplication in animal genomes. JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.155801 DO - 10.1101/gr.155801 ID - Friedman2001 ER - TY - JOUR AU - Hughes, A. L. AU - da Silva, J. AU - Friedman, R. PY - 2001 DA - 2001// TI - Ancient genome duplications did not structure the human Hox-bearing chromosomes. JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.GR-1600R DO - 10.1101/gr.GR-1600R ID - Hughes2001 ER - TY - JOUR AU - Friedman, R. AU - Hughes, A. L. PY - 2003 DA - 2003// TI - The temporal distribution of gene duplication events in a set of highly conserved human gene families. JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg017 DO - 10.1093/molbev/msg017 ID - Friedman2003 ER - TY - JOUR AU - Friedman, R. AU - Hughes, A. L. PY - 2004 DA - 2004// TI - Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse. JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh076 DO - 10.1093/molbev/msh076 ID - Friedman2004 ER - TY - JOUR AU - Shoja, V. AU - Zhang, L. PY - 2006 DA - 2006// TI - A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl085 DO - 10.1093/molbev/msl085 ID - Shoja2006 ER - TY - JOUR AU - Graham, G. PY - 1995 DA - 1995// TI - Tandem genes and clustered genes. JO - J Theor Biol VL - 175 UR - https://doi.org/10.1006/jtbi.1995.0122 DO - 10.1006/jtbi.1995.0122 ID - Graham1995 ER - TY - JOUR AU - Brosius, J. PY - 1991 DA - 1991// TI - Retroposons: seeds of evolution. JO - Science VL - 251 UR - https://doi.org/10.1126/science.1990437 DO - 10.1126/science.1990437 ID - Brosius1991 ER - TY - JOUR AU - Kazazian, H. H. PY - 2004 DA - 2004// TI - Mobile elements: drivers of genome evolution. JO - Science VL - 303 UR - https://doi.org/10.1126/science.1089670 DO - 10.1126/science.1089670 ID - Kazazian2004 ER - TY - JOUR AU - Betran, E. AU - Thornton, K. AU - Long, M. PY - 2002 DA - 2002// TI - Retroposed new genes out of the X in Drosophila. JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.6049 DO - 10.1101/gr.6049 ID - Betran2002 ER - TY - JOUR AU - Long, M. AU - Betran, E. AU - Thornton, K. AU - Wang, W. PY - 2003 DA - 2003// TI - The origin of new genes: glimpses from the young and old. JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1204 DO - 10.1038/nrg1204 ID - Long2003 ER - TY - JOUR AU - Emerson, J. J. AU - Kaessmann, H. AU - Betran, E. AU - Long, M. PY - 2004 DA - 2004// TI - Extensive gene traffic on the mammalian X chromosome. JO - Science VL - 303 UR - https://doi.org/10.1126/science.1090042 DO - 10.1126/science.1090042 ID - Emerson2004 ER - TY - JOUR AU - Marques, A. C. AU - Dupanloup, I. AU - Vinckenbosch, N. AU - Reymond, A. AU - Kaessmann, H. PY - 2005 DA - 2005// TI - Emergence of young human genes after a burst of retroposition in primates. JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030357 DO - 10.1371/journal.pbio.0030357 ID - Marques2005 ER - TY - JOUR AU - Wang, W. AU - Zheng, H. AU - Fan, C. AU - Li, J. AU - Shi, J. AU - Cai, Z. AU - Zhang, G. AU - Liu, D. AU - Zhang, J. AU - Vang, S. PY - 2006 DA - 2006// TI - High rate of chimeric gene origination by retroposition in plant genomes. JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.106.041905 DO - 10.1105/tpc.106.041905 ID - Wang2006 ER - TY - JOUR AU - Vinckenbosch, N. AU - Dupanloup, I. AU - Kaessmann, H. PY - 2006 DA - 2006// TI - Evolutionary fate of retroposed gene copies in the human genome. JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0511307103 DO - 10.1073/pnas.0511307103 ID - Vinckenbosch2006 ER - TY - JOUR AU - Bai, Y. AU - Casola, C. AU - Feschotte, C. AU - Betran, E. PY - 2007 DA - 2007// TI - Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-1-r11 DO - 10.1186/gb-2007-8-1-r11 ID - Bai2007 ER - TY - JOUR AU - Makalowski, W. PY - 2001 DA - 2001// TI - Are we polyploids? A brief history of one hypothesis. JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.188801 DO - 10.1101/gr.188801 ID - Makalowski2001 ER - TY - JOUR AU - Bailey, J. A. AU - Church, D. M. AU - Ventura, M. AU - Rocchi, M. AU - Eichler, E. E. PY - 2004 DA - 2004// TI - Analysis of segmental duplications and genome assembly in the mouse. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2238404 DO - 10.1101/gr.2238404 ID - Bailey2004 ER - TY - JOUR AU - Bailey, J. A. AU - Gu, Z. AU - Clark, R. A. AU - Reinert, K. AU - Samonte, R. V. AU - Schwartz, S. AU - Adams, M. D. AU - Myers, E. W. AU - Li, P. W. AU - Eichler, E. E. PY - 2002 DA - 2002// TI - Recent segmental duplications in the human genome. JO - Science VL - 297 UR - https://doi.org/10.1126/science.1072047 DO - 10.1126/science.1072047 ID - Bailey2002 ER - TY - JOUR AU - Zhang, L. AU - Lu, H. H. AU - Chung, W. Y. AU - Yang, J. AU - Li, W. H. PY - 2005 DA - 2005// TI - Patterns of segmental duplication in the human genome. JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msh262 DO - 10.1093/molbev/msh262 ID - Zhang2005 ER - TY - JOUR AU - Lu, J. AU - Wu, C. I. PY - 2005 DA - 2005// TI - Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0500436102 DO - 10.1073/pnas.0500436102 ID - Lu2005 ER - TY - JOUR AU - Wyckoff, G. J. AU - Malcom, C. M. AU - Vallender, E. J. AU - Lahn, B. T. PY - 2005 DA - 2005// TI - A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. JO - Trends Genet VL - 21 UR - https://doi.org/10.1016/j.tig.2005.05.005 DO - 10.1016/j.tig.2005.05.005 ID - Wyckoff2005 ER - TY - JOUR AU - Yi, S. AU - Ellsworth, D. AU - Li, W. PY - 2002 DA - 2002// TI - Slow molecular clocks in Old World monkeys, apes, and humans. JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004043 DO - 10.1093/oxfordjournals.molbev.a004043 ID - Yi2002 ER - TY - JOUR AU - Shiu, S. H. AU - Byrnes, J. K. AU - Pan, R. AU - Zhang, P. AU - Li, W. H. PY - 2006 DA - 2006// TI - Role of positive selection in the retention of duplicate genes in mammalian genomes. JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0510388103 DO - 10.1073/pnas.0510388103 ID - Shiu2006 ER - TY - JOUR AU - Bailey, J. A. AU - Liu, G. AU - Eichler, E. E. PY - 2003 DA - 2003// TI - An Alu transposition model for the origin and expansion of human segmental duplications. JO - Am J Hum Genet VL - 73 UR - https://doi.org/10.1086/378594 DO - 10.1086/378594 ID - Bailey2003 ER - TY - JOUR AU - Li, W. H. AU - Ellsworth, D. L. AU - Krushkal, J. AU - Chang, B. H. AU - Hewett-Emmett, D. PY - 1996 DA - 1996// TI - Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. JO - Mol Phylogenet Evol VL - 5 UR - https://doi.org/10.1006/mpev.1996.0012 DO - 10.1006/mpev.1996.0012 ID - Li1996 ER - TY - JOUR AU - Waterston, R. H. AU - Lindblad-Toh, K. AU - Birney, E. AU - Rogers, J. AU - Abril, J. F. AU - Agarwal, P. AU - Agarwala, R. AU - Ainscough, R. AU - Alexandersson, M. AU - An, P. PY - 2002 DA - 2002// TI - Initial sequencing and comparative analysis of the mouse genome. JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01262 DO - 10.1038/nature01262 ID - Waterston2002 ER - TY - JOUR AU - Thomas, J. W. AU - Touchman, J. W. AU - Blakesley, R. W. AU - Bouffard, G. G. AU - Beckstrom-Sternberg, S. M. AU - Margulies, E. H. AU - Blanchette, M. AU - Siepel, A. C. AU - Thomas, P. J. AU - McDowell, J. C. PY - 2003 DA - 2003// TI - Comparative analyses of multi-species sequences from targeted genomic regions. JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01858 DO - 10.1038/nature01858 ID - Thomas2003 ER - TY - JOUR AU - Force, A. AU - Lynch, M. AU - Pickett, F. B. AU - Amores, A. AU - Yan, Y. L. AU - Postlethwait, J. PY - 1999 DA - 1999// TI - Preservation of duplicate genes by complementary, degenerative mutations. JO - Genetics VL - 151 ID - Force1999 ER - TY - JOUR AU - Thompson, J. AU - Higgins, D. AU - Gibson, T. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Yang, Z. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood. JO - Comput Appl Biosci VL - 13 ID - Yang1997 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2000 DA - 2000// TI - Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026236 DO - 10.1093/oxfordjournals.molbev.a026236 ID - Yang2000 ER - TY - BOOK PY - 2006 DA - 2006// TI - R: a Language and Environment for Statistical Computing PB - R Foundation for Statistical Computing CY - Vienna, Austria ID - ref46 ER - TY - JOUR AU - Coulombe-Huntington, J. AU - Majewski, J. PY - 2007 DA - 2007// TI - Characterization of intron loss events in mammals. JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5703406 DO - 10.1101/gr.5703406 ID - Coulombe-Huntington2007 ER - TY - STD TI - The Caml Language. [http://caml.inria.fr] UR - http://caml.inria.fr ID - ref48 ER -