2010-11 Eng. Gr.4 &Amp: Fill & Download for Free

Thanks to Justin Ma for the A2A!EDIT: If you want me to add a paper to this list, just comment / message me and I will add it and tag youOh man. This is going to be fun. There are many, many subfields to evolutionary biology. I will cover some in more detail than others, because I know some areas better than others.My main areas are:Population genetics - I am not a mathematician, but I am somewhat familiar with the theoryExperimental evolutionGenomics / molecular evolutionThings I will be undersampling:PhylogeneticsSpeciationDemographicsAnything to do with plant evolution.Things that I am biased towards:Adaptation / selection based papers, as I am very much a selectionist.THIS IS BY NO MEANS A COMPLETE OR COMPREHENSIVE LIST.------------------------------------------------------------------------------If you want to study evolution, you need to understand population genetics, at least a little bit.Population genetics textbooks:These will cover the fundamental concepts and proofs, in varying amounts of detail. They will also extensively cover the population genetic literature. They are the only kind of evolution textbook worth reading over primary papers for a good intro to the field.Hartl and Clark's Principles of Population Genetics. Get an older edition if you want, they are not too expensive. This is what a lot of courses on population genetics are based on.Principles of Population Genetics, Fourth Edition: Daniel L. Hartl, Andrew G. Clark: 9780878933082: Amazon.com: BooksGillespie's Population Genetics, A Concise Guide is what my PI uses to teach popgen. Very short, but dense and a great intro to the field.Population Genetics: A Concise Guide: 9780801880094: Medicine & Health Science Books @ Amazon.comI have heard great things about this book as well, but have not used it personally:Elements of Evolutionary Genetics: Brian Charlesworth, Deborah Charlesworth: 9780981519425: Amazon.com: Books------------------------------------------------------------------------Review ArticlesReview Articles are a great place to start in any field, as they summarize a decade of primary work, give you references to all of them, and give you a big-picture outlook on the field. Note that I have not read some of these, and only skimmed others. I am picking articles based on the diversity of topics covered, and trust that they will give you a good set of references within.Romero, P. a, & Arnold, F. H. (2009). Exploring protein fitness landscapes by directed evolution. Nature Reviews. Molecular Cell Biology, 10(12), 866–76. doi:10.1038/nrm2805De Visser, J. A. G. M., & Krug, J. (2014). Empirical fitness landscapes and the predictability of evolution. Nature Reviews. Genetics, 15(7), 480–90. doi:10.1038/nrg3744Harms, M. J., & Thornton, J. W. (2013). Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nature Reviews. Genetics, 14(8), 559–71. doi:10.1038/nrg3540Barrick, J. E., & Lenski, R. E. (2013). Genome dynamics during experimental evolution. Nature Reviews. Genetics, 14(12), 827–839. doi:10.1038/nrg3564Oleksyk, T. K., Smith, M. W., & O’Brien, S. J. (2010). Genome-wide scans for footprints of natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365(1537), 185–205. doi:10.1098/rstb.2009.0219Sousa, V., & Hey, J. (2013). Understanding the origin of species with genome-scale data: modelling gene flow. Nature Reviews. Genetics, 14(6), 404–14. doi:10.1038/nrg3446Pool, J. E., Hellmann, I., Jensen, J. D., & Nielsen, R. (2010). Population genetic inference from genomic sequence variation. Genome Research, 20(3), 291–300. doi:10.1101/gr.079509.108Hoban, S., Bertorelle, G., & Gaggiotti, O. E. (2012). Computer simulations: tools for population and evolutionary genetics. Nature Reviews Genetics, 13(2), 110–122. doi:10.1038/nrg3130-------------------------------------------------------------------------------------Important Primary Research Articles / Major Articles in the SubfieldThe first experimental evolution. Its just fun to read, and the conclusion is pretty powerful.Dallinger, W. H. (1887). The President’s Address. Journal of the Royal Microscopical Society, (April), 185–199.This paper presents the "fundamental theory of natural selection"Fisher, R. (1930). The genetical theory of natural selection. The Eugenics Review (1st ed., p. 272). Oxford: Oxford at the Clarendon Press. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984947/This paper makes the claim that most mutations that accumulate in genomes must be neutral.Kimura, M. (1968). Evolutionary rate at the molecular level. Nature, 0–2. Retrieved from http://www.genomics.arizona.edu/553/Readings/2012/Kimura1968.pdfOne of the first solid examples of natural selection in the wildReznick, D., & Endler, J. (1982). The impact of predation on life history evolution in Trinidadian guppies (Poecilia reticulata). Evolution. Retrieved from http://www.jstor.org/stable/2407978Tests for selection using molecular dataTajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3), 585–95. Retrieved from Page on nlm.govMcDonald, J., & Kreitman, M. (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652–654. Retrieved from http://ib.berkeley.edu/labs/slatkin/popgenjclub/pdf/mcdonald-kreitman1991.pdfAdaptive diversification:Rainey, P., & Travisano, M. (1998). Adaptive radiation in a heterogeneous environment. Nature, 394, 69–72. Retrieved from http://isites.harvard.edu/fs/docs/icb.topic957318.files/Papers/Rainey and Travisano 1998 - Adaptive radiation in a heterogeneous environment.pdfThe Lenski Experiment - 60k generations and counting of a culture of bacteria evolving in the lab. They have mined this resource extensively for some very cool analysis of evolutionary outcomes.Blount, Z. D., Barrick, J. E., Davidson, C. J., & Lenski, R. E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, 488(7417), 513–518. doi:10.1038/nature11514Blount, Z. D., Borland, C. Z., & Lenski, R. E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 105(23), 7899–906. doi:10.1073/pnas.0803151105Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003). Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli. Proceedings of the National Academy of Sciences of the United States of America, 100(3), 1072–7. doi:10.1073/pnas.0334340100Khan, A. I., Dinh, D. M., Schneider, D., Lenski, R. E., & Cooper, T. F. (2011). Negative epistasis between beneficial mutations in an evolving bacterial population. Science, 332(6034), 1193–6. doi:10.1126/science.1203801Wiser, M. J., Ribeck, N., & Lenski, R. E. (2013). Long-Term Dynamics of Adaptation in Asexual Populations. Science (New York, N.Y.), 1364. doi:10.1126/science.1243357Woods, R. J., Barrick, J. E., Cooper, T. F., Shrestha, U., Kauth, M. R., & Lenski, R. E. (2011). Second-Order Selection for Evolvability in a Large Escherichia coli Population. Science, 331(6023), 1433–1436. doi:10.1126/science.1198914Demographic inference from the Bustamante labNovembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., … Bustamante, C. D. (2008). Genes mirror geography within Europe. Nature, 456(7218), 98–101. doi:10.1038/nature07331A cool example of a Genetic BottleneckKenny, E. E., Timpson, N. J., Sikora, M., Yee, M.-C., Moreno-Estrada, A., Eng, C., … Myles, S. (2012). Melanesian blond hair is caused by an amino acid change in TYRP1. Science, 336(6081), 554. doi:10.1126/science.1217849Reconstructing intermediate genotypes to understand the predictability of evolutionWeinreich, D. M., Delaney, N. F., Depristo, M. a, & Hartl, D. L. (2006). Darwinian evolution can follow only very few mutational paths to fitter proteins. Science (New York, N.Y.), 312(5770), 111–4. doi:10.1126/science.1123539Evolutionary Dynamics of Large PopulationsDesai, M. M., & Fisher, D. S. (2007). Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics, 176(3), 1759–98. doi:10.1534/genetics.106.067678Experiments to show the Dynamics of Large PopulationsKvitek, D. J., & Sherlock, G. (2013). Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment. PLoS Genetics, 9(11), e1003972. doi:10.1371/journal.pgen.1003972Lang, G. I., Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., & Desai, M. M. (2013). Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature. doi:10.1038/nature12344Herron, M. D., & Doebeli, M. (2013). Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. PLoS Biology, 11(2), e1001490. doi:10.1371/journal.pbio.1001490Reconstructing Ancient Proteins:Ortlund, E. a, Bridgham, J. T., Redinbo, M. R., & Thornton, J. W. (2007). Crystal structure of an ancient protein: evolution by conformational epistasis. Science (New York, N.Y.), 317(5844), 1544–8. doi:10.1126/science.1142819Demographic Inference Modeling:Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data. PLoS Genet 5(10): e1000695. doi: 10.1371/journal.pgen.1000695Speciation GenesSun, S., Ting, C.-T., & Wu, C.-I. (2004). The normal function of a speciation gene, Odysseus, and its hybrid sterility effect. Science (New York, N.Y.), 305(5680), 81–3. doi:10.1126/science.1093904Genome Duplication and ResolutionWolfe, K. H., & Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387(6634), 708–713.