Woolhouse, M. E. J., Haydon, D. T., & Antia, R. (2005). Emerging pathogens: the epidemiology and evolution of species jumps. Trends in Ecology & Evolution, 20(5), 238-244. doi:10.1016/j.tree.2005.02.009
Parrish, C. R., Holmes, E. C., Morens, D. M., Park, E.-C., Burke, D. S., Calisher, C. H., … Daszak, P. (2008). Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases. Microbiology and Molecular Biology Reviews, 72(3), 457-470. doi:10.1128/mmbr.00004-08
Holmes, E. C. (2009). The Evolutionary Genetics of Emerging Viruses. Annual Review of Ecology, Evolution, and Systematics, 40(1), 353-372. doi:10.1146/annurev.ecolsys.110308.120248
[+]
Woolhouse, M. E. J., Haydon, D. T., & Antia, R. (2005). Emerging pathogens: the epidemiology and evolution of species jumps. Trends in Ecology & Evolution, 20(5), 238-244. doi:10.1016/j.tree.2005.02.009
Parrish, C. R., Holmes, E. C., Morens, D. M., Park, E.-C., Burke, D. S., Calisher, C. H., … Daszak, P. (2008). Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases. Microbiology and Molecular Biology Reviews, 72(3), 457-470. doi:10.1128/mmbr.00004-08
Holmes, E. C. (2009). The Evolutionary Genetics of Emerging Viruses. Annual Review of Ecology, Evolution, and Systematics, 40(1), 353-372. doi:10.1146/annurev.ecolsys.110308.120248
Elena, S. F., & Froissart, R. (2010). New experimental and theoretical approaches towards the understanding of the emergence of viral infections. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1548), 1867-1869. doi:10.1098/rstb.2010.0088
Anderson, P. K., Cunningham, A. A., Patel, N. G., Morales, F. J., Epstein, P. R., & Daszak, P. (2004). Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends in Ecology & Evolution, 19(10), 535-544. doi:10.1016/j.tree.2004.07.021
Jones, R. A. C. (2009). Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Research, 141(2), 113-130. doi:10.1016/j.virusres.2008.07.028
Elena, S. F., Bedhomme, S., Carrasco, P., Cuevas, J. M., de la Iglesia, F., Lafforgue, G., … Zwart, M. P. (2011). The Evolutionary Genetics of Emerging Plant RNA Viruses. Molecular Plant-Microbe Interactions, 24(3), 287-293. doi:10.1094/mpmi-09-10-0214
Sanjuan, R., Nebot, M. R., Chirico, N., Mansky, L. M., & Belshaw, R. (2010). Viral Mutation Rates. Journal of Virology, 84(19), 9733-9748. doi:10.1128/jvi.00694-10
Duffy, S., Turner, P. E., & Burch, C. L. (2005). Pleiotropic Costs of Niche Expansion in the RNA Bacteriophage Φ6. Genetics, 172(2), 751-757. doi:10.1534/genetics.105.051136
Ferris, M. T., Joyce, P., & Burch, C. L. (2007). High Frequency of Mutations That Expand the Host Range of an RNA Virus. Genetics, 176(2), 1013-1022. doi:10.1534/genetics.106.064634
Agudelo-Romero, P., de la Iglesia, F., & Elena, S. F. (2008). The pleiotropic cost of host-specialization in Tobacco etch potyvirus. Infection, Genetics and Evolution, 8(6), 806-814. doi:10.1016/j.meegid.2008.07.010
Gandon, S. (2004). EVOLUTION OF MULTIHOST PARASITES. Evolution, 58(3), 455-469. doi:10.1111/j.0014-3820.2004.tb01669.x
Remold, S. K., Rambaut, A., & Turner, P. E. (2008). Evolutionary Genomics of Host Adaptation in Vesicular Stomatitis Virus. Molecular Biology and Evolution, 25(6), 1138-1147. doi:10.1093/molbev/msn059
Domingo-Calap, P., Cuevas, J. M., & Sanjuán, R. (2009). The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages. PLoS Genetics, 5(11), e1000742. doi:10.1371/journal.pgen.1000742
Peris, J. B., Davis, P., Cuevas, J. M., Nebot, M. R., & Sanjuán, R. (2010). Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1. Genetics, 185(2), 603-609. doi:10.1534/genetics.110.115162
Elena, & Moya. (1999). Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus. Journal of Evolutionary Biology, 12(6), 1078-1088. doi:10.1046/j.1420-9101.1999.00110.x
Sanjuan, R., Moya, A., & Elena, S. F. (2004). The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proceedings of the National Academy of Sciences, 101(22), 8396-8401. doi:10.1073/pnas.0400146101
Carrasco, P., de la Iglesia, F., & Elena, S. F. (2007). Distribution of Fitness and Virulence Effects Caused by Single-Nucleotide Substitutions in Tobacco Etch Virus. Journal of Virology, 81(23), 12979-12984. doi:10.1128/jvi.00524-07
Sanjuán, R. (2010). Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1548), 1975-1982. doi:10.1098/rstb.2010.0063
Van Opijnen, T., Boerlijst, M. C., & Berkhout, B. (2006). Effects of Random Mutations in the Human Immunodeficiency Virus Type 1 Transcriptional Promoter on Viral Fitness in Different Host Cell Environments. Journal of Virology, 80(13), 6678-6685. doi:10.1128/jvi.02547-05
Hodgins-Davis, A., & Townsend, J. P. (2009). Evolving gene expression: from G to E to G×E. Trends in Ecology & Evolution, 24(12), 649-658. doi:10.1016/j.tree.2009.06.011
Futuyma, D. J., & Moreno, G. (1988). The Evolution of Ecological Specialization. Annual Review of Ecology and Systematics, 19(1), 207-233. doi:10.1146/annurev.es.19.110188.001231
Remold, S. K., & Lenski, R. E. (2001). Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proceedings of the National Academy of Sciences, 98(20), 11388-11393. doi:10.1073/pnas.201140198
Soltis, E. D., & Soltis, P. S. (2000). Plant Molecular Biology, 42(1), 45-75. doi:10.1023/a:1006371803911
Novella, I. S., Zárate, S., Metzgar, D., & Ebendick-Corpus, B. E. (2004). Positive Selection of Synonymous Mutations in Vesicular Stomatitis Virus. Journal of Molecular Biology, 342(5), 1415-1421. doi:10.1016/j.jmb.2004.08.003
Ohta, T. (1992). The Nearly Neutral Theory of Molecular Evolution. Annual Review of Ecology and Systematics, 23(1), 263-286. doi:10.1146/annurev.es.23.110192.001403
Johnson, J. B., & Omland, K. S. (2004). Model selection in ecology and evolution. Trends in Ecology & Evolution, 19(2), 101-108. doi:10.1016/j.tree.2003.10.013
Martin, G., & Lenormand, T. (2006). THE FITNESS EFFECT OF MUTATIONS ACROSS ENVIRONMENTS: A SURVEY IN LIGHT OF FITNESS LANDSCAPE MODELS. Evolution, 60(12), 2413-2427. doi:10.1111/j.0014-3820.2006.tb01878.x
Eyre-Walker, A., & Keightley, P. D. (2007). The distribution of fitness effects of new mutations. Nature Reviews Genetics, 8(8), 610-618. doi:10.1038/nrg2146
Wylie, C. S., & Shakhnovich, E. I. (2011). A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proceedings of the National Academy of Sciences, 108(24), 9916-9921. doi:10.1073/pnas.1017572108
Genotype—environment interactions and the estimation of the genomic mutation rate in
Drosophila melanogaster. (1994). Proceedings of the Royal Society of London. Series B: Biological Sciences, 258(1353), 221-227. doi:10.1098/rspb.1994.0166
Via, S., Gomulkiewicz, R., De Jong, G., Scheiner, S. M., Schlichting, C. D., & Van Tienderen, P. H. (1995). Adaptive phenotypic plasticity: consensus and controversy. Trends in Ecology & Evolution, 10(5), 212-217. doi:10.1016/s0169-5347(00)89061-8
Korona, R. (1999). Genetic Load of the Yeast Saccharomyces cerevisiae under Diverse Environmental Conditions. Evolution, 53(6), 1966. doi:10.2307/2640455
Auld, J. R., Agrawal, A. A., & Relyea, R. A. (2009). Re-evaluating the costs and limits of adaptive phenotypic plasticity. Proceedings of the Royal Society B: Biological Sciences, 277(1681), 503-511. doi:10.1098/rspb.2009.1355
Fry, J. D., Heinsohn, S. L., & Mackay, T. F. C. (1996). The Contribution of New Mutations to Genotype-Environment Interaction for Fitness in Drosophila melanogaster. Evolution, 50(6), 2316. doi:10.2307/2410700
Elena, S. F., Agudelo-Romero, P., Carrasco, P., Codoñer, F. M., Martín, S., Torres-Barceló, C., & Sanjuán, R. (2008). Experimental evolution of plant RNA viruses. Heredity, 100(5), 478-483. doi:10.1038/sj.hdy.6801088
Ayme, V., Souche, S., Caranta, C., Jacquemond, M., Chadœuf, J., Palloix, A., & Moury, B. (2006). Different Mutations in the Genome-Linked Protein VPg of Potato virus Y Confer Virulence on the pvr23 Resistance in Pepper. Molecular Plant-Microbe Interactions, 19(5), 557-563. doi:10.1094/mpmi-19-0557
Charron, C., Nicolaï, M., Gallois, J.-L., Robaglia, C., Moury, B., Palloix, A., & Caranta, C. (2008). Natural variation and functional analyses provide evidence for co-evolution between plant eIF4E and potyviral VPg. The Plant Journal, 54(1), 56-68. doi:10.1111/j.1365-313x.2008.03407.x
Bedoya, L. C., & Daròs, J.-A. (2010). Stability of Tobacco etch virus infectious clones in plasmid vectors. Virus Research, 149(2), 234-240. doi:10.1016/j.virusres.2010.02.004
Carrasco, P., Daròs, J. A., Agudelo-Romero, P., & Elena, S. F. (2007). A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments. Journal of Virological Methods, 139(2), 181-188. doi:10.1016/j.jviromet.2006.09.020
Lalić, J., Agudelo-Romero, P., Carrasco, P., & Elena, S. F. (2010). Adaptation of tobacco etch potyvirus to a susceptible ecotype of
Arabidopsis thaliana
capacitates it for systemic infection of resistant ecotypes. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1548), 1997-2007. doi:10.1098/rstb.2010.0044
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