TY - JOUR AU - Arendt, J. AU - Reznick, D. PY - 2008 DA - 2008// TI - Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? JO - Trends Ecol Evolut VL - 23 UR - https://doi.org/10.1016/j.tree.2007.09.011 DO - 10.1016/j.tree.2007.09.011 ID - Arendt2008 ER - TY - JOUR AU - Manceau, M. AU - Domingues, V. S. AU - Linnen, C. R. AU - Rosenblum, E. B. AU - Hoekstra, H. E. PY - 2010 DA - 2010// TI - Convergence in pigmentation at multiple levels: mutations, genes and function JO - Philos Trans R Soc B Biol Sci VL - 365 UR - https://doi.org/10.1098/rstb.2010.0104 DO - 10.1098/rstb.2010.0104 ID - Manceau2010 ER - TY - JOUR AU - McCracken, K. G. AU - Barger, C. P. AU - Bulgarella, M. AU - Johnson, K. P. AU - Sonsthagen, S. A. AU - Trucco, J. AU - Valqui, T. H. AU - Wilson, R. E. AU - Winker, K. AU - Sorenson, M. D. PY - 2009 DA - 2009// TI - Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl JO - Mol Ecol VL - 18 UR - https://doi.org/10.1111/j.1365-294X.2009.04352.x DO - 10.1111/j.1365-294X.2009.04352.x ID - McCracken2009 ER - TY - JOUR AU - Reed, R. D. AU - Papa, R. AU - Martin, A. AU - Hines, H. M. AU - Counterman, B. A. AU - Pardo-Diaz, C. AU - Jiggins, C. D. AU - Chamberlain, N. L. AU - Kronforst, M. R. AU - Chen, R. AU - Halder, G. PY - 2011 DA - 2011// TI - Optix drives the repeated convergent evolution of butterfly wing pattern mimicry JO - Science VL - 333 UR - https://doi.org/10.1126/science.1208227 DO - 10.1126/science.1208227 ID - Reed2011 ER - TY - JOUR AU - Shapiro, M. D. AU - Bell, M. A. AU - Kingsley, D. M. PY - 2006 DA - 2006// TI - Parallel genetic origins of pelvic reduction in vertebrates JO - Proc Natl Acad Sci VL - 103 UR - https://doi.org/10.1073/pnas.0604706103 DO - 10.1073/pnas.0604706103 ID - Shapiro2006 ER - TY - JOUR AU - Gompel, N. AU - Prud'homme, B. PY - 2009 DA - 2009// TI - The causes of repeated genetic evolution JO - Dev Biol VL - 332 UR - https://doi.org/10.1016/j.ydbio.2009.04.040 DO - 10.1016/j.ydbio.2009.04.040 ID - Gompel2009 ER - TY - JOUR AU - Stern, D. L. AU - Orgogozo, V. PY - 2008 DA - 2008// TI - The loci of evolution: how predictable is genetic evolution? JO - Evolution VL - 62 UR - https://doi.org/10.1111/j.1558-5646.2008.00450.x DO - 10.1111/j.1558-5646.2008.00450.x ID - Stern2008 ER - TY - JOUR AU - Martin, A. AU - Orgogozo, V. PY - 2013 DA - 2013// TI - The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation JO - Evolution VL - 67 ID - Martin2013 ER - TY - JOUR AU - Sucena, E. AU - Delon, I. AU - Jones, I. AU - Payre, F. AU - Stern, D. L. PY - 2003 DA - 2003// TI - Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01768 DO - 10.1038/nature01768 ID - Sucena2003 ER - TY - JOUR AU - Wray, G. A. PY - 2007 DA - 2007// TI - The evolutionary significance of cis-regulatory mutations JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2063 DO - 10.1038/nrg2063 ID - Wray2007 ER - TY - JOUR AU - Burke, G. R. AU - Moran, N. A. PY - 2011 DA - 2011// TI - Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids JO - Genome Biol Evol VL - 3 UR - https://doi.org/10.1093/gbe/evr002 DO - 10.1093/gbe/evr002 ID - Burke2011 ER - TY - JOUR AU - Palmer, J. D. PY - 1990 DA - 1990// TI - Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant JO - Nature VL - 348 UR - https://doi.org/10.1038/348337a0 DO - 10.1038/348337a0 ID - Palmer1990 ER - TY - JOUR AU - Drummond, D. A. AU - Bloom, J. D. AU - Adami, C. AU - Wilke, C. O. AU - Arnold, F. H. PY - 2005 DA - 2005// TI - Why highly expressed proteins evolve slowly JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0504070102 DO - 10.1073/pnas.0504070102 ID - Drummond2005 ER - TY - JOUR AU - Duret, L. AU - Mouchiroud, D. PY - 2000 DA - 2000// TI - Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026239 DO - 10.1093/oxfordjournals.molbev.a026239 ID - Duret2000 ER - TY - STD TI - Lunzer M, Golding GB, Dean AM. Pervasive cryptic epistasis in molecular evolution. PLoS Genet. 2010; doi: 10.1371/journal.pgen.1001162. ID - ref15 ER - TY - JOUR AU - Poon, A. AU - Chao, L. PY - 2005 DA - 2005// TI - The rate of compensatory mutation in the DNA bacteriophage φX174 JO - Genetics VL - 170 UR - https://doi.org/10.1534/genetics.104.039438 DO - 10.1534/genetics.104.039438 ID - Poon2005 ER - TY - JOUR AU - Bridgham, J. T. AU - Ortlund, E. A. AU - Thornton, J. W. PY - 2009 DA - 2009// TI - An epistatic ratchet constrains the direction of glucocorticoid receptor evolution JO - Nature VL - 461 UR - https://doi.org/10.1038/nature08249 DO - 10.1038/nature08249 ID - Bridgham2009 ER - TY - STD TI - Bridgham JT, Keay J, Ortlund EA, Thornton JW. Vestigialization of an allosteric switch: Genetic and structural mechanisms for the evolution of constitutive activity in a steroid hormone receptor. PLoS Genet. 2014; doi:10.1371/journal.pgen.1004058. ID - ref18 ER - TY - JOUR AU - Smith, S. D. AU - Wang, S. AU - Rausher, M. D. PY - 2013 DA - 2013// TI - Functional evolution of an anthocyanin pathway enzyme during a flower color transition JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mss255 DO - 10.1093/molbev/mss255 ID - Smith2013 ER - TY - JOUR AU - Weinreich, D. M. AU - Delaney, N. F. AU - DePristo, M. A. AU - Hartl, D. L. PY - 2006 DA - 2006// TI - Darwinian evolution can follow only very few mutational paths to fitter proteins JO - Science VL - 312 UR - https://doi.org/10.1126/science.1123539 DO - 10.1126/science.1123539 ID - Weinreich2006 ER - TY - JOUR AU - Wessinger, C. A. AU - Rausher, M. D. PY - 2012 DA - 2012// TI - Lessons from flower colour evolution on targets of selection JO - J Exp Bot VL - 63 UR - https://doi.org/10.1093/jxb/ers267 DO - 10.1093/jxb/ers267 ID - Wessinger2012 ER - TY - JOUR AU - Wright, S. I. AU - Ness, R. W. AU - Foxe, J. P. AU - Barrett, S. C. PY - 2008 DA - 2008// TI - Genomic consequences of outcrossing and selfing in plants JO - Int J Plant Sci VL - 169 UR - https://doi.org/10.1086/523366 DO - 10.1086/523366 ID - Wright2008 ER - TY - JOUR AU - Hersch‐Green, E. I. AU - Myburg, H. AU - Johnson, M. T. PY - 2012 DA - 2012// TI - Adaptive molecular evolution of a defence gene in sexual but not functionally asexual evening primroses JO - J Evol Biol VL - 25 UR - https://doi.org/10.1111/j.1420-9101.2012.02542.x DO - 10.1111/j.1420-9101.2012.02542.x ID - Hersch‐Green2012 ER - TY - JOUR AU - Ross‐Ibarra, J. PY - 2007 DA - 2007// TI - Genome size and recombination in angiosperms: a second look JO - J Evol Biol VL - 20 UR - https://doi.org/10.1111/j.1420-9101.2006.01275.x DO - 10.1111/j.1420-9101.2006.01275.x ID - Ross‐Ibarra2007 ER - TY - JOUR AU - Porter, M. L. AU - Crandall, K. A. PY - 2003 DA - 2003// TI - Lost along the way: the significance of evolution in reverse JO - Trends Ecol Evol VL - 18 UR - https://doi.org/10.1016/S0169-5347(03)00244-1 DO - 10.1016/S0169-5347(03)00244-1 ID - Porter2003 ER - TY - JOUR AU - Wiens, J. J. PY - 2001 DA - 2001// TI - Widespread loss of sexually selected traits: how the peacock lost its spots JO - Trends Ecol Evol VL - 16 UR - https://doi.org/10.1016/S0169-5347(01)02217-0 DO - 10.1016/S0169-5347(01)02217-0 ID - Wiens2001 ER - TY - JOUR AU - Cui, J. AU - Pan, Y. H. AU - Zhang, Y. AU - Jones, G. AU - Zhang, S. PY - 2011 DA - 2011// TI - Progressive pseudogenization: vitamin C synthesis and its loss in bats JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msq286 DO - 10.1093/molbev/msq286 ID - Cui2011 ER - TY - JOUR AU - Wickett, N. J. AU - Fan, Y. AU - Lewis, P. O. AU - Goffinet, B. PY - 2008 DA - 2008// TI - Distribution and evolution of pseudogenes, gene losses, and a gene rearrangement in the plastid genome of the nonphotosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida) JO - J Mol Evol VL - 67 UR - https://doi.org/10.1007/s00239-008-9133-1 DO - 10.1007/s00239-008-9133-1 ID - Wickett2008 ER - TY - JOUR AU - Marshall, C. R. AU - Raff, E. C. AU - Raff, R. A. PY - 1994 DA - 1994// TI - Dollo’s law and the death and resurrection of genes JO - Proc Natl Acad Sci VL - 91 UR - https://doi.org/10.1073/pnas.91.25.12283 DO - 10.1073/pnas.91.25.12283 ID - Marshall1994 ER - TY - JOUR AU - Niemiller, M. L. AU - Fitzpatrick, B. M. AU - Shah, P. AU - Schmitz, L. AU - Near, T. J. PY - 2013 DA - 2013// TI - Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae) JO - Evolution VL - 67 UR - https://doi.org/10.1111/j.1558-5646.2012.01822.x DO - 10.1111/j.1558-5646.2012.01822.x ID - Niemiller2013 ER - TY - STD TI - Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS. Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet. 2009; doi:10.1371/journal.pgen.1000634. ID - ref31 ER - TY - JOUR AU - Des Marais, D. L. AU - Rausher, M. D. PY - 2008 DA - 2008// TI - Escape from adaptive conflict after duplication in an anthocyanin pathway gene JO - Nature VL - 454 ID - Des Marais2008 ER - TY - JOUR AU - Hahn, M. W. PY - 2009 DA - 2009// TI - Distinguishing among evolutionary models for the maintenance of gene duplicates JO - J Hered VL - 100 UR - https://doi.org/10.1093/jhered/esp047 DO - 10.1093/jhered/esp047 ID - Hahn2009 ER - TY - BOOK AU - Ohno, S. PY - 1970 DA - 1970// TI - Evolution by gene duplication PB - Business Media 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 - Taylor, J. S. AU - Raes, J. PY - 2004 DA - 2004// TI - Duplication and divergence: the evolution of new genes and old ideas JO - Annu Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.38.072902.092831 DO - 10.1146/annurev.genet.38.072902.092831 ID - Taylor2004 ER - TY - JOUR AU - Smith, S. D. AU - Baum, D. A. PY - 2006 DA - 2006// TI - Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae) JO - Am J Bot VL - 93 UR - https://doi.org/10.3732/ajb.93.8.1140 DO - 10.3732/ajb.93.8.1140 ID - Smith2006 ER - TY - JOUR AU - Winkel-Shirley, B. PY - 2001 DA - 2001// TI - Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology JO - Plant Physiol VL - 126 UR - https://doi.org/10.1104/pp.126.2.485 DO - 10.1104/pp.126.2.485 ID - Winkel-Shirley2001 ER - TY - STD TI - Berardi AE, Hildreth SB, Helm RF, Winkel BS, Smith SD. Evolutionary correlations in flavonoid production across flowers and leaves in the Iochrominae (Solanaceae). Phytochemistry (in revision). ID - ref38 ER - TY - JOUR AU - Särkinen, T. AU - Bohs, L. AU - Olmstead, R. G. AU - Knapp, S. PY - 2013 DA - 2013// TI - A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree JO - BMC Evol Biol VL - 13 UR - https://doi.org/10.1186/1471-2148-13-214 DO - 10.1186/1471-2148-13-214 ID - Särkinen2013 ER - TY - JOUR AU - Smith, S. D. AU - Baum, D. A. PY - 2007 DA - 2007// TI - Systematics of Iochrominae (Solanaceae): patterns in floral diversity and interspecific crossability JO - Acta Horticulturae VL - 745 UR - https://doi.org/10.17660/ActaHortic.2007.745.10 DO - 10.17660/ActaHortic.2007.745.10 ID - Smith2007 ER - TY - JOUR AU - Smith, S. D. AU - Goldberg, E. E. PY - 2015 DA - 2015// TI - Tempo and mode of flower color evolution JO - Am J Bot VL - 102 UR - https://doi.org/10.3732/ajb.1500163 DO - 10.3732/ajb.1500163 ID - Smith2015 ER - TY - BOOK AU - Eich, E. PY - 2008 DA - 2008// TI - Solanaceae and Convolvulaceae: Secondary metabolites: Biosynthesis, chemotaxonomy, biological and economic significance (a handbook) PB - Business Media CY - Berlin UR - https://doi.org/10.1007/978-3-540-74541-9 DO - 10.1007/978-3-540-74541-9 ID - Eich2008 ER - TY - JOUR AU - Chalker-Scott, L. PY - 1999 DA - 1999// TI - Environmental significance of anthocyanins in plant stress responses JO - Photochem Photobiol VL - 70 UR - https://doi.org/10.1111/j.1751-1097.1999.tb01944.x DO - 10.1111/j.1751-1097.1999.tb01944.x ID - Chalker-Scott1999 ER - TY - JOUR AU - Ryan, K. G. AU - Swinny, E. E. AU - Markham, K. R. AU - Winefield, C. PY - 2002 DA - 2002// TI - Flavonoid gene expression and UV photoprotection in transgenic and mutant Petunia leaves JO - Phytochemistry VL - 59 UR - https://doi.org/10.1016/S0031-9422(01)00404-6 DO - 10.1016/S0031-9422(01)00404-6 ID - Ryan2002 ER - TY - JOUR AU - Mo, Y. AU - Nagel, C. AU - Taylor, L. P. PY - 1992 DA - 1992// TI - Biochemical complementation of chalcone synthase mutants defines a role for flavonols in functional pollen JO - Proc Natl Acad Sci VL - 89 UR - https://doi.org/10.1073/pnas.89.15.7213 DO - 10.1073/pnas.89.15.7213 ID - Mo1992 ER - TY - JOUR AU - Shirley, B. W. PY - 1996 DA - 1996// TI - Flavonoid biosynthesis:‘new’functions for an ‘old’pathway JO - Trends Plant Sci VL - 1 ID - Shirley1996 ER - TY - JOUR AU - Jong, W. S. AU - Eannetta, N. T. AU - Jong, D. M. AU - Bodis, M. PY - 2004 DA - 2004// TI - Candidate gene analysis of anthocyanin pigmentation loci in the Solanaceae JO - Theor Appl Genet VL - 108 UR - https://doi.org/10.1007/s00122-003-1455-1 DO - 10.1007/s00122-003-1455-1 ID - Jong2004 ER - TY - JOUR AU - Tunen, A. J. AU - Koes, R. E. AU - Spelt, C. E. AU - Krol, A. R. AU - Stuitje, A. R. AU - Mol, J. N. PY - 1988 DA - 1988// TI - Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: coordinate, light-regulated and differential expression of flavonoid genes JO - EMBO J VL - 7 ID - Tunen1988 ER - TY - JOUR AU - Tunen, A. J. AU - Hartman, S. A. AU - Mur, L. A. AU - Mol, J. N. PY - 1989 DA - 1989// TI - Regulation of chalcone flavanone isomerase (CHI) gene expression in Petunia hybrida: the use of alternative promoters in corolla, anthers and pollen JO - Plant Mol Biol VL - 12 UR - https://doi.org/10.1007/BF00036968 DO - 10.1007/BF00036968 ID - Tunen1989 ER - TY - JOUR AU - Lu, Y. AU - Rausher, M. D. PY - 2003 DA - 2003// TI - Evolutionary rate variation in anthocyanin pathway genes JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg197 DO - 10.1093/molbev/msg197 ID - Lu2003 ER - TY - JOUR AU - Streisfeld, M. A. AU - Liu, D. AU - Rausher, M. D. PY - 2011 DA - 2011// TI - Predictable patterns of constraint among anthocyanin‐regulating transcription factors in Ipomoea JO - New Phytol VL - 191 UR - https://doi.org/10.1111/j.1469-8137.2011.03671.x DO - 10.1111/j.1469-8137.2011.03671.x ID - Streisfeld2011 ER - TY - JOUR AU - Yang, Z. AU - Wong, W. S. AU - Nielsen, R. PY - 2005 DA - 2005// TI - Bayes empirical Bayes inference of amino acid sites under positive selection JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi097 DO - 10.1093/molbev/msi097 ID - Yang2005 ER - TY - JOUR AU - Woolley, S. AU - Johnson, J. AU - Smith, M. J. AU - Crandall, K. A. AU - McClellan, D. A. PY - 2003 DA - 2003// TI - TreeSAAP: selection on amino acid properties using phylogenetic trees JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg043 DO - 10.1093/bioinformatics/btg043 ID - Woolley2003 ER - TY - JOUR AU - McClellan, D. A. AU - McCracken, K. G. PY - 2001 DA - 2001// TI - Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003892 DO - 10.1093/oxfordjournals.molbev.a003892 ID - McClellan2001 ER - TY - JOUR AU - Campanella, J. J. AU - Smalley, J. V. AU - Dempsey, M. E. PY - 2014 DA - 2014// TI - A phylogenetic examination of the primary anthocyanin production pathway of the Plantae JO - Bot Stud VL - 55 UR - https://doi.org/10.1186/1999-3110-55-10 DO - 10.1186/1999-3110-55-10 ID - Campanella2014 ER - TY - CHAP AU - Rausher, M. D. ED - Grotewold, E. R. PY - 2006 DA - 2006// TI - The evolution of flavonoids and their genes BT - The science of flavonoids PB - Springer CY - New York UR - https://doi.org/10.1007/978-0-387-28822-2_7 DO - 10.1007/978-0-387-28822-2_7 ID - Rausher2006 ER - TY - JOUR AU - Shimada, S. AU - Takahashi, K. AU - Sato, Y. AU - Sakuta, M. PY - 2004 DA - 2004// TI - Dihydroflavonol 4-reductase cDNA from non-anthocyanin-producing species in the Caryophyllales JO - Plant Cell Physiol VL - 45 UR - https://doi.org/10.1093/pcp/pch156 DO - 10.1093/pcp/pch156 ID - Shimada2004 ER - TY - JOUR AU - Bovy, A. AU - Schijlen, E. AU - Hall, R. D. PY - 2007 DA - 2007// TI - Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics JO - Metabolomics VL - 3 UR - https://doi.org/10.1007/s11306-007-0074-2 DO - 10.1007/s11306-007-0074-2 ID - Bovy2007 ER - TY - JOUR AU - Coburn, R. C. AU - Griffin, R. H. AU - Smith, S. D. PY - 2015 DA - 2015// TI - Genetic basis of a rare floral mutant in an Andean species of Solanaceae JO - Am J Bot VL - 102 UR - https://doi.org/10.3732/ajb.1400395 DO - 10.3732/ajb.1400395 ID - Coburn2015 ER - TY - JOUR AU - Wu, C. A. AU - Streisfeld, M. A. AU - Nutter, L. I. AU - Cross, K. A. PY - 2013 DA - 2013// TI - The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the repeatability of evolution JO - Public Libr Sci One VL - 8 ID - Wu2013 ER - TY - JOUR AU - Smith, S. D. AU - Rausher, M. D. PY - 2011 DA - 2011// TI - Gene loss and parallel evolution contribute to species difference in flower color JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr109 DO - 10.1093/molbev/msr109 ID - Smith2011 ER - TY - JOUR AU - Wessinger, C. A. AU - Rausher, M. D. PY - 2014 DA - 2014// TI - Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus JO - Evolution VL - 68 UR - https://doi.org/10.1111/evo.12340 DO - 10.1111/evo.12340 ID - Wessinger2014 ER - TY - JOUR AU - Wolfe, A. D. AU - Randle, C. P. AU - Datwyler, S. L. AU - Morawetz, J. J. AU - Arguedas, N. AU - Diaz, J. PY - 2006 DA - 2006// TI - Phylogeny, taxonomic affinities, and biogeography of Penstemon (Plantaginaceae) based on ITS and cpDNA sequence data JO - Am J Bot VL - 93 UR - https://doi.org/10.3732/ajb.93.11.1699 DO - 10.3732/ajb.93.11.1699 ID - Wolfe2006 ER - TY - JOUR AU - Wang, X. AU - Thomas, S. D. AU - Zhang, J. PY - 2004 DA - 2004// TI - Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes JO - Hum Mol Genet VL - 13 UR - https://doi.org/10.1093/hmg/ddh289 DO - 10.1093/hmg/ddh289 ID - Wang2004 ER - TY - JOUR AU - Beisswanger, S. AU - Stephan, W. PY - 2008 DA - 2008// TI - Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0710892105 DO - 10.1073/pnas.0710892105 ID - Beisswanger2008 ER - TY - JOUR AU - Zhang, J. PY - 2003 DA - 2003// TI - Evolution by gene duplication: an update JO - Trends Ecol 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 - Vitkup, D. AU - Kharchenko, P. AU - Wagner, A. PY - 2006 DA - 2006// TI - Influence of metabolic network structure and function on enzyme evolution JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-5-r39 DO - 10.1186/gb-2006-7-5-r39 ID - Vitkup2006 ER - TY - JOUR AU - Hahn, M. W. AU - Conant, G. C. AU - Wagner, A. PY - 2004 DA - 2004// TI - Molecular evolution in large genetic networks: does connectivity equal constraint? JO - J Mol Evol VL - 58 UR - https://doi.org/10.1007/s00239-003-2544-0 DO - 10.1007/s00239-003-2544-0 ID - Hahn2004 ER - TY - JOUR AU - Rausher, M. D. AU - Miller, R. E. AU - Tiffin, P. PY - 1999 DA - 1999// TI - Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026108 DO - 10.1093/oxfordjournals.molbev.a026108 ID - Rausher1999 ER - TY - JOUR AU - Rausher, M. D. AU - Lu, Y. AU - Meyer, K. PY - 2008 DA - 2008// TI - Variation in constraint versus positive selection as an explanation for evolutionary rate variation among anthocyanin genes JO - J Mol Evol VL - 67 UR - https://doi.org/10.1007/s00239-008-9105-5 DO - 10.1007/s00239-008-9105-5 ID - Rausher2008 ER - TY - JOUR AU - Holton, T. A. AU - Cornish, E. C. PY - 1995 DA - 1995// TI - Genetics and biochemistry of anthocyanin biosynthesis JO - Plant Cell VL - 7 UR - https://doi.org/10.1105/tpc.7.7.1071 DO - 10.1105/tpc.7.7.1071 ID - Holton1995 ER - TY - JOUR AU - Jez, J. M. AU - Bowman, M. E. AU - Dixon, R. A. AU - Noel, J. P. PY - 2000 DA - 2000// TI - Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase JO - Nat Struct Mol Biol VL - 7 UR - https://doi.org/10.1038/79025 DO - 10.1038/79025 ID - Jez2000 ER - TY - STD TI - Cui J, Yuan X, Wang L, Jones G, Zhang S. Recent loss of vitamin C biosynthesis ability in bats. PloS One. 2011; doi:10.1371/journal.pone.0027114. ID - ref73 ER - TY - JOUR AU - He, X. AU - Zhang, J. PY - 2006 DA - 2006// TI - Toward a molecular understanding of pleiotropy JO - Genetics VL - 173 UR - https://doi.org/10.1534/genetics.106.060269 DO - 10.1534/genetics.106.060269 ID - He2006 ER - TY - JOUR AU - Akashi, H. PY - 2003 DA - 2003// TI - Translational selection and yeast proteome evolution JO - Genetics VL - 164 ID - Akashi2003 ER - TY - JOUR AU - Drummond, D. A. AU - Raval, A. AU - Wilke, C. O. PY - 2006 DA - 2006// TI - A single determinant dominates the rate of yeast protein evolution JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj038 DO - 10.1093/molbev/msj038 ID - Drummond2006 ER - TY - JOUR AU - Whittall, J. B. AU - Voelckel, C. AU - Kliebenstein, D. J. AU - Hodges, S. A. PY - 2006 DA - 2006// TI - Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia JO - Mol Ecol VL - 15 UR - https://doi.org/10.1111/j.1365-294X.2006.03114.x DO - 10.1111/j.1365-294X.2006.03114.x ID - Whittall2006 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Yang, Z. PY - 1998 DA - 1998// TI - Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025957 DO - 10.1093/oxfordjournals.molbev.a025957 ID - Yang1998 ER - TY - JOUR AU - Yang, Z. AU - Swanson, W. J. PY - 2002 DA - 2002// TI - Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003981 DO - 10.1093/oxfordjournals.molbev.a003981 ID - Yang2002 ER - TY - JOUR AU - Zhang, J. AU - Nielsen, R. AU - Yang, Z. PY - 2005 DA - 2005// TI - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi237 DO - 10.1093/molbev/msi237 ID - Zhang2005 ER - TY - JOUR AU - Wong, W. S. AU - Yang, Z. AU - Goldman, N. AU - Nielsen, R. PY - 2004 DA - 2004// TI - Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites JO - Genetics VL - 168 UR - https://doi.org/10.1534/genetics.104.031153 DO - 10.1534/genetics.104.031153 ID - Wong2004 ER - TY - JOUR AU - McClellan, D. A. AU - Palfreyman, E. J. AU - Smith, M. J. AU - Moss, J. L. AU - Christensen, R. G. AU - Sailsbery, J. K. PY - 2005 DA - 2005// TI - Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi028 DO - 10.1093/molbev/msi028 ID - McClellan2005 ER - TY - JOUR AU - Petit, P. AU - Granier, T. AU - d'Estaintot, B. L. AU - Manigand, C. AU - Bathany, K. AU - Schmitter, J. M. AU - Lauvergeat, V. AU - Hamdi, S. AU - Gallois, B. PY - 2007 DA - 2007// TI - Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis JO - J Mol Biol VL - 368 UR - https://doi.org/10.1016/j.jmb.2007.02.088 DO - 10.1016/j.jmb.2007.02.088 ID - Petit2007 ER - TY - JOUR AU - Guex, N. AU - Peitsch, M. C. PY - 1997 DA - 1997// TI - SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling JO - Electrophoresis VL - 18 UR - https://doi.org/10.1002/elps.1150181505 DO - 10.1002/elps.1150181505 ID - Guex1997 ER - TY - JOUR AU - Muchhala, N. AU - Johnsen, S. AU - Smith, S. D. PY - 2014 DA - 2014// TI - Competition for hummingbird pollination shapes flower color variation in Andean Solanaceae JO - Evolution VL - 68 ID - Muchhala2014 ER -