{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T11:47:56Z","timestamp":1765885676911},"reference-count":151,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2009,2,1]],"date-time":"2009-02-01T00:00:00Z","timestamp":1233446400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Rev Genet"],"published-print":{"date-parts":[[2009,2]]},"DOI":"10.1038\/nrg2506","type":"journal-article","created":{"date-parts":[[2009,1,2]],"date-time":"2009-01-02T05:41:23Z","timestamp":1230874883000},"page":"83-93","source":"Crossref","is-referenced-by-count":107,"title":["Genetics and the understanding of selection"],"prefix":"10.1038","volume":"10","author":[{"given":"Laurence D.","family":"Hurst","sequence":"first","affiliation":[]}],"member":"297","reference":[{"key":"BFnrg2506_CR1","volume-title":"Darwin's Dangerous Idea","author":"DC Dennett","year":"1995","unstructured":"Dennett, D. C. Darwin's Dangerous Idea (Simon and Schuster, New York, 1995)."},{"key":"BFnrg2506_CR2","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/nrg1319","volume":"5","author":"LD Hurst","year":"2004","unstructured":"Hurst, L. D., Pal, C. & Lercher, M. J. The evolutionary dynamics of eukaryotic gene order. Nature Rev. Genet. 5, 299\u2013310 (2004).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg2506_CR3","doi-asserted-by":"publisher","first-page":"1286","DOI":"10.1101\/gr.6276007","volume":"17","author":"HJ Gierman","year":"2007","unstructured":"Gierman, H. J. et al. Domain-wide regulation of gene expression in the human genome. Genome Res. 17, 1286\u20131295 (2007).","journal-title":"Genome Res."},{"key":"BFnrg2506_CR4","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1038\/nrg1770","volume":"7","author":"JV Chamary","year":"2006","unstructured":"Chamary, J. V., Parmley, J. L. & Hurst, L. D. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nature Rev. Genet. 7, 98\u2013108 (2006). A review that highlights the multiple different mechanisms by which selection can act on synonymous mutations. It also argues that tests based on mechanism rather than genome-scale statistical analyses provide the most convincing data.","journal-title":"Nature Rev. Genet."},{"key":"BFnrg2506_CR5","doi-asserted-by":"publisher","first-page":"1784","DOI":"10.1126\/science.1155761","volume":"320","author":"JR Coleman","year":"2008","unstructured":"Coleman, J. R. et al. Virus attenuation by genome-scale changes in codon pair bias. Science 320, 1784\u20131787 (2008).","journal-title":"Science"},{"key":"BFnrg2506_CR6","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1017\/S0007087404005850","volume":"37","author":"M Bulmer","year":"2004","unstructured":"Bulmer, M. Did Jenkin's swamping argument invalidate Darwin's theory of natural selection? Brit. J. Hist. Sci. 37, 281\u2013297 (2004).","journal-title":"Brit. J. Hist. Sci."},{"key":"BFnrg2506_CR7","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1017\/S0080456800012163","volume":"52","author":"RA Fisher","year":"1918","unstructured":"Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinb. 52, 399\u2013433 (1918).","journal-title":"Trans. R. Soc. Edinb."},{"key":"BFnrg2506_CR8","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1007\/BF02409748","volume":"34","author":"P Hammerstein","year":"1996","unstructured":"Hammerstein, P. Darwinian adaptation, population-genetics and the streetcar theory of evolution. J. Math. Biol. 34, 511\u2013532 (1996). An important paper that provides a population-genetics defence for the application of non-genetics models, such as evolutionary stable strategy theory.","journal-title":"J. Math. Biol."},{"key":"BFnrg2506_CR9","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1111\/j.1420-9101.2006.01262.x","volume":"20","author":"JD Hadfield","year":"2007","unstructured":"Hadfield, J. D., Nutall, A., Osorio, D. & Owens, I. P. Testing the phenotypic gambit: phenotypic, genetic and environmental correlations of colour. J. Evol. Biol. 20, 549\u2013557 (2007).","journal-title":"J. Evol. Biol."},{"key":"BFnrg2506_CR10","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1017\/S0016672300014634","volume":"23","author":"J Maynard Smith","year":"1974","unstructured":"Maynard Smith, J. & Haigh, J. The hitch-hiking effect of a favorable gene. Genet. Res. 23, 23\u201335 (1974). The seminal paper on hitchhiking.","journal-title":"Genet. Res."},{"key":"BFnrg2506_CR11","doi-asserted-by":"publisher","first-page":"12949","DOI":"10.1073\/pnas.202336899","volume":"99","author":"B Harr","year":"2002","unstructured":"Harr, B., Kauer, M. & Schlotterer, C. Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 99, 12949\u201312954 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR12","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1038\/nrg2187","volume":"8","author":"R Nielsen","year":"2007","unstructured":"Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C. & Clark, A. G. Recent and ongoing selection in the human genome. Nature Rev. Genet. 8, 857\u2013868 (2007).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg2506_CR13","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1371\/journal.pbio.0040052","volume":"4","author":"X Wang","year":"2006","unstructured":"Wang, X., Grus, W. E. & Zhang, J. Gene losses during human origins. PLoS Biol. 4, e52 (2006).","journal-title":"PLoS Biol."},{"key":"BFnrg2506_CR14","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1002\/1521-1878(200012)22:12<1057::AID-BIES3>3.0.CO;2-W","volume":"22","author":"PD Sniegowski","year":"2000","unstructured":"Sniegowski, P. D., Gerrish, P. J., Johnson, T. & Shaver, A. The evolution of mutation rates: separating causes from consequences. Bioessays 22, 1057\u20131066 (2000).","journal-title":"Bioessays"},{"key":"BFnrg2506_CR15","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1017\/S0016672300032365","volume":"63","author":"B Charlesworth","year":"1994","unstructured":"Charlesworth, B. The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63, 213\u2013227 (1994).","journal-title":"Genet. Res."},{"key":"BFnrg2506_CR16","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1016\/S0168-9525(01)02409-X","volume":"17","author":"MW Nachman","year":"2001","unstructured":"Nachman, M. W. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17, 481\u2013485 (2001).","journal-title":"Trends Genet."},{"key":"BFnrg2506_CR17","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/356519a0","volume":"356","author":"DJ Begun","year":"1992","unstructured":"Begun, D. J. & Aquadro, C. F. Levels of naturally-occurring DNA polymorphism correlate with recombination rates in Drosophila melanogaster. Nature 356, 519\u2013520 (1992).","journal-title":"Nature"},{"key":"BFnrg2506_CR18","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1016\/S0959-437X(00)00246-X","volume":"11","author":"P Andolfatto","year":"2001","unstructured":"Andolfatto, P. Adaptive hitchhiking effects on genome variability. Curr. Opin. Genet. Dev. 11, 635\u2013641 (2001).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"BFnrg2506_CR19","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1016\/S0960-9822(99)80430-8","volume":"9","author":"J Perry","year":"1999","unstructured":"Perry, J. & Ashworth, A. Evolutionary rate of a gene affected by chromosomal position. Curr. Biol. 9, 987\u2013989 (1999).","journal-title":"Curr. Biol."},{"key":"BFnrg2506_CR20","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/S0168-9525(02)02669-0","volume":"18","author":"MJ Lercher","year":"2002","unstructured":"Lercher, M. J. & Hurst, L. D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18, 337\u2013340 (2002).","journal-title":"Trends Genet."},{"key":"BFnrg2506_CR21","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1086\/375657","volume":"72","author":"I Hellmann","year":"2003","unstructured":"Hellmann, I., Ebersberger, I., Ptak, S. E., Paabo, S. & Przeworski, M. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72, 1527\u20131535 (2003).","journal-title":"Am. J. Hum. Genet."},{"key":"BFnrg2506_CR22","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/0040-5809(74)90052-5","volume":"5","author":"S Karlin","year":"1974","unstructured":"Karlin, S. & McGregor, J. Towards a theory of the evolution of modifier genes. Theor. Popul. Biol. 5, 59\u2013103 (1974).","journal-title":"Theor. Popul. Biol."},{"key":"BFnrg2506_CR23","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1086\/419442","volume":"71","author":"LD Hurst","year":"1996","unstructured":"Hurst, L. D., Atlan, A. & Bengtsson, B. O. Genetic conflicts. Q. Rev. Biol. 71, 317\u2013364 (1996).","journal-title":"Q. Rev. Biol."},{"key":"BFnrg2506_CR24","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1146\/annurev.ge.25.120191.002455","volume":"25","author":"TW Lyttle","year":"1991","unstructured":"Lyttle, T. W. Segregation distorters. Annu. Rev. Genet. 25, 511\u2013557 (1991).","journal-title":"Annu. Rev. Genet."},{"key":"BFnrg2506_CR25","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1111\/j.1469-185X.1993.tb00733.x","volume":"68","author":"LD Hurst","year":"1993","unstructured":"Hurst, L. D. The incidences, mechanisms and evolution of cytoplasmic sex ratio distorters in animals. Biol. Rev. 68, 121\u2013193 (1993).","journal-title":"Biol. Rev."},{"key":"BFnrg2506_CR26","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/oso\/9780198577867.003.0005","volume-title":"Influential Passengers","author":"GDD Hurst","year":"1997","unstructured":"Hurst, G. D. D., Hurst, L. D. & Majerus, M. E. N. in Influential Passengers (eds Hoffmann, A., O'Neill, S. & Werren, J.) 125\u2013154 (Oxford Univ. Press, Oxford 1997)."},{"key":"BFnrg2506_CR27","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/hdy.1993.110","volume":"71","author":"GDD Hurst","year":"1993","unstructured":"Hurst, G. D. D. & Majerus, M. E. N. Why do maternally inherited microorganisms kill males? Heredity 71, 81\u201395 (1993).","journal-title":"Heredity"},{"key":"BFnrg2506_CR28","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1111\/j.1469-8137.1941.tb07028.x","volume":"40","author":"D Lewis","year":"1941","unstructured":"Lewis, D. Male sterility in natural populations of hermaphrodite plants. New Phytol. 40, 158\u2013160 (1941).","journal-title":"New Phytol."},{"key":"BFnrg2506_CR29","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1146\/annurev.ento.42.1.587","volume":"42","author":"JH Werren","year":"1997","unstructured":"Werren, J. H. Biology of Wolbachia. Annu. Rev. Entomol. 42, 587\u2013609 (1997).","journal-title":"Annu. Rev. Entomol."},{"key":"BFnrg2506_CR30","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/0022-2011(78)90102-7","volume":"30","author":"PEM Fine","year":"1978","unstructured":"Fine, P. E. M. On the dynamics of symbiote-dependent cytoplasmic incompatibility in Culicine mosquitoes. J. Invertebr. Pathol. 30, 10\u201318 (1978).","journal-title":"J. Invertebr. Pathol."},{"key":"BFnrg2506_CR31","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/353440a0","volume":"353","author":"M Turelli","year":"1991","unstructured":"Turelli, M. & Hoffmann, A. A. Rapid spread of an inherited incompatibility factor in California Drosophila. Nature 353, 440\u2013442 (1991).","journal-title":"Nature"},{"key":"BFnrg2506_CR32","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1098\/rspb.1995.0196","volume":"262","author":"JH Werren","year":"1995","unstructured":"Werren, J. H., Windsor, D. & Guo, L. R. Distribution of Wolbachia among neotropical arthropods. Proc. R. Soc. Lond. B 262, 197\u2013204 (1995).","journal-title":"Proc. R. Soc. Lond. B"},{"key":"BFnrg2506_CR33","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1111\/j.1574-6968.2008.01110.x","volume":"281","author":"K Hilgenboecker","year":"2008","unstructured":"Hilgenboecker, K., Hammerstein, P., Schlattmann, P., Telschow, A. & Werren, J. H. How many species are infected with Wolbachia? \u2014 a statistical analysis of current data. FEMS Microbiol. Lett. 281, 215\u2013220 (2008).","journal-title":"FEMS Microbiol. Lett."},{"key":"BFnrg2506_CR34","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1126\/science.1163766","volume":"322","author":"TA Price","year":"2008","unstructured":"Price, T. A., Hodgson, D. J., Lewis, Z., Hurst, G. D. & Wedell, N. Selfish genetic elements promote polyandry in a fly. Science 322, 1241\u20131243 (2008).","journal-title":"Science"},{"key":"BFnrg2506_CR35","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/0092-8674(86)90770-1","volume":"44","author":"MF Lyon","year":"1986","unstructured":"Lyon, M. F. Male sterility of the mouse t-complex is due to homozygosity of the distorter genes. Cell 44, 357\u2013363 (1986).","journal-title":"Cell"},{"key":"BFnrg2506_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0022-5193(64)90038-4","volume":"7","author":"WD Hamilton","year":"1964","unstructured":"Hamilton, W. D. The genetical evolution of social behaviour I. J. Theor. Biol. 7, 1\u201316 (1964). The seminal paper that introduced the concept of inclusive fitness.","journal-title":"J. Theor. Biol."},{"key":"BFnrg2506_CR37","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1038\/nature02744","volume":"430","author":"AS Griffin","year":"2004","unstructured":"Griffin, A. S., West, S. A. & Buckling, A. Cooperation and competition in pathogenic bacteria. Nature 430, 1024\u20131027 (2004).","journal-title":"Nature"},{"key":"BFnrg2506_CR38","doi-asserted-by":"publisher","DOI":"10.5962\/bhl.title.27468","volume-title":"The Genetical Theory of Natural Selection","author":"RA Fisher","year":"1930","unstructured":"Fisher, R. A. The Genetical Theory of Natural Selection (Clarendon, Oxford, 1930)."},{"key":"BFnrg2506_CR39","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1126\/science.156.3774.477","volume":"156","author":"WD Hamilton","year":"1967","unstructured":"Hamilton, W. D. Extraordinary sex ratios. Science 156, 477\u2013488 (1967).","journal-title":"Science"},{"key":"BFnrg2506_CR40","first-page":"96","volume":"5","author":"JJ Bull","year":"1988","unstructured":"Bull, J. J. & Charnov, E. L. How fundamental are Fisherian sex ratios? Oxf. Surv. Evol. Biol. 5, 96\u2013135 (1988).","journal-title":"Oxf. Surv. Evol. Biol."},{"key":"BFnrg2506_CR41","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1126\/science.274.5289.993","volume":"274","author":"L Sundstrom","year":"1996","unstructured":"Sundstrom, L., Chapuisat, M. & Keller, L. Conditional manipulation of sex ratios by ant workers: a test of kin selection theory. Science 274, 993\u2013995 (1996).","journal-title":"Science"},{"key":"BFnrg2506_CR42","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1016\/0169-5347(96)30036-0","volume":"11","author":"P Marrow","year":"1996","unstructured":"Marrow, P., Johnstone, R. A. & Hurst, L. D. Riding the evolutionary streetcar \u2014 where population-genetics and game-theory meet. Trends Ecol. Evol. 11, 445\u2013446 (1996).","journal-title":"Trends Ecol. Evol."},{"key":"BFnrg2506_CR43","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1086\/510602","volume":"169","author":"A Gardner","year":"2007","unstructured":"Gardner, A., West, S. A. & Barton, N. H. The relation between multilocus population genetics and social evolution theory. Am. Nat. 169, 207\u2013226 (2007).","journal-title":"Am. Nat."},{"key":"BFnrg2506_CR44","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1038\/267275a0","volume":"267","author":"M Kimura","year":"1977","unstructured":"Kimura, M. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267, 275\u2013276 (1977).","journal-title":"Nature"},{"key":"BFnrg2506_CR45","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511623486","volume-title":"The Neutral Theory of Evolution","author":"M Kimura","year":"1983","unstructured":"Kimura, M. The Neutral Theory of Evolution (Cambridge Univ. Press, Cambridge, 1983)."},{"key":"BFnrg2506_CR46","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1126\/science.164.3881.788","volume":"164","author":"JL King","year":"1969","unstructured":"King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788\u2013798 (1969).","journal-title":"Science"},{"key":"BFnrg2506_CR47","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1007\/BF02984069","volume":"55","author":"JBS Haldane","year":"1957","unstructured":"Haldane, J. B. S. The cost of natural selection. J. Genet. 55, 511\u2013524 (1957).","journal-title":"J. Genet."},{"key":"BFnrg2506_CR48","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1038\/217624a0","volume":"217","author":"M Kimura","year":"1968","unstructured":"Kimura, M. Evolutionary rate at the molecular level. Nature 217, 624\u2013626 (1968).","journal-title":"Nature"},{"key":"BFnrg2506_CR49","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1146\/annurev.es.23.110192.001403","volume":"23","author":"T Ohta","year":"1992","unstructured":"Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. System. 23, 263\u2013286 (1992).","journal-title":"Annu. Rev. Ecol. System."},{"key":"BFnrg2506_CR50","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1093\/genetics\/155.2.909","volume":"155","author":"JH Gillespie","year":"2000","unstructured":"Gillespie, J. H. Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155, 909\u2013919 (2000).","journal-title":"Genetics"},{"key":"BFnrg2506_CR51","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.1111\/j.0014-3820.2001.tb00732.x","volume":"55","author":"JH Gillespie","year":"2001","unstructured":"Gillespie, J. H. Is the population size of a species relevant to its evolution? Evolution 55, 2161\u20132169 (2001).","journal-title":"Evolution"},{"key":"BFnrg2506_CR52","volume-title":"The Genetic Basis of Evolutionary Change","author":"RC Lewontin","year":"1974","unstructured":"Lewontin, R. C. The Genetic Basis of Evolutionary Change (Columbia Univ. Press, New York, 1974)."},{"key":"BFnrg2506_CR53","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1002\/bies.950180812","volume":"18","author":"M Kreitman","year":"1996","unstructured":"Kreitman, M. The neutral theory is dead \u2014 long live the neutral theory. Bioessays 18, 678\u2013683 (1996).","journal-title":"Bioessays"},{"key":"BFnrg2506_CR54","volume-title":"The Causes of Molecular Evolution","author":"JH Gillespie","year":"1991","unstructured":"Gillespie, J. H. The Causes of Molecular Evolution (eds May, R. M. & Harvey, P. H.) (Oxford Univ. Press, Oxford, 1991). A watershed book that challenged the neutral and nearly neutral models, arguing that selection is a better explanation for polymorphism and patterns of molecular evolution than drift."},{"key":"BFnrg2506_CR55","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195069327.001.0001","volume-title":"Natural Selection: Domains, Levels and Challenges","author":"GC Williams","year":"1992","unstructured":"Williams, G. C. Natural Selection: Domains, Levels and Challenges (eds May, R. M. & Harvey, P. H.) (Oxford Univ. Press, New York, 1992)."},{"key":"BFnrg2506_CR56","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1111\/j.1558-5646.1975.tb00836.x","volume":"29","author":"B Wallace","year":"1975","unstructured":"Wallace, B. Hard and soft selection revisited. Evolution 29, 465\u2013473 (1975).","journal-title":"Evolution"},{"key":"BFnrg2506_CR57","volume-title":"Genetic Load: its Biological and Conceptual Aspects","author":"B Wallace","year":"1970","unstructured":"Wallace, B. Genetic Load: its Biological and Conceptual Aspects (Prentice Hall, New Jersey, 1970)."},{"key":"BFnrg2506_CR58","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1038\/nature04107","volume":"437","author":"P Andolfatto","year":"2005","unstructured":"Andolfatto, P. Adaptive evolution of non-coding DNA in Drosophila. Nature 437, 1149\u20131152 (2005).","journal-title":"Nature"},{"key":"BFnrg2506_CR59","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/246096a0","volume":"246","author":"T Ohta","year":"1973","unstructured":"Ohta, T. Slightly deleterious mutant substitutions in evolution. Nature 246, 96\u201398 (1973).","journal-title":"Nature"},{"key":"BFnrg2506_CR60","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1126\/science.290.5490.331","volume":"290","author":"PD Keightley","year":"2000","unstructured":"Keightley, P. D. & Eyre-Walker, A. Deleterious mutations and the evolution of sex. Science 290, 331\u2013333 (2000).","journal-title":"Science"},{"key":"BFnrg2506_CR61","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1002\/(SICI)1521-1878(199901)21:1<71::AID-BIES9>3.0.CO;2-B","volume":"21","author":"FJ Ayala","year":"1999","unstructured":"Ayala, F. J. Molecular clock mirages. Bioessays 21, 71\u201375 (1999).","journal-title":"Bioessays"},{"key":"BFnrg2506_CR62","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1006\/tpbi.1996.0007","volume":"49","author":"T Ohta","year":"1996","unstructured":"Ohta, T. & Gillespie, J. H. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49, 128\u2013142 (1996). To commemorate the death of Kimura, the chief defender and the harshest critic of the nearly neutral theory unite to provide a clearly argued critique of the history and current standing of the neutral and nearly neutral theories.","journal-title":"Theor. Popul. Biol."},{"key":"BFnrg2506_CR63","doi-asserted-by":"publisher","first-page":"11405","DOI":"10.1073\/pnas.201392198","volume":"98","author":"F Rodriguez-Trelles","year":"2001","unstructured":"Rodriguez-Trelles, F., Tarrio, R. & Ayala, F. J. Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH. Proc. Natl Acad. Sci. USA 98, 11405\u201311410 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR64","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1093\/molbev\/msm281","volume":"25","author":"SH Kim","year":"2008","unstructured":"Kim, S. H. & Yi, S. V. Mammalian nonsynonymous sites are not overdispersed: comparative genomic analysis of index of dispersion of mammalian proteins. Mol. Biol. Evol. 25, 634\u2013642 (2008).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR65","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1093\/genetics\/158.3.1227","volume":"158","author":"JC Fay","year":"2001","unstructured":"Fay, J. C., Wyckoff, G. J. & Wu, C. I. Positive and negative selection on the human genome. Genetics 158, 1227\u20131234 (2001).","journal-title":"Genetics"},{"key":"BFnrg2506_CR66","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1038\/4151022a","volume":"415","author":"NGC Smith","year":"2002","unstructured":"Smith, N. G. C. & Eyre-Walker, A. Adaptive protein evolution in Drosophila. Nature 415, 1022\u20131024 (2002).","journal-title":"Nature"},{"key":"BFnrg2506_CR67","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1038\/4151024a","volume":"415","author":"JC Fay","year":"2002","unstructured":"Fay, J. C., Wyckoff, G. J. & Wu, C. I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415, 1024\u20131026 (2002).","journal-title":"Nature"},{"key":"BFnrg2506_CR68","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1038\/nature04240","volume":"437","author":"CD Bustamante","year":"2005","unstructured":"Bustamante, C. D. et al. Natural selection on protein-coding genes in the human genome. Nature 437, 1153\u20131157 (2005).","journal-title":"Nature"},{"key":"BFnrg2506_CR69","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1093\/molbev\/msh134","volume":"21","author":"N Bierne","year":"2004","unstructured":"Bierne, N. & Eyre-Walker, A. The genomic rate of adaptive amino acid substitution in Drosophila. Mol. Biol. Evol. 21, 1350\u20131360 (2004).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR70","doi-asserted-by":"publisher","first-page":"6504","DOI":"10.1073\/pnas.0701572104","volume":"104","author":"SA Sawyer","year":"2007","unstructured":"Sawyer, S. A., Parsch, J., Zhang, Z. & Hartl, D. L. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc. Natl Acad. Sci. USA 104, 6504\u20136510 (2007).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR71","doi-asserted-by":"publisher","first-page":"2271","DOI":"10.1073\/pnas.0610385104","volume":"104","author":"JA Shapiro","year":"2007","unstructured":"Shapiro, J. A. et al. Adaptive genic evolution in the Drosophila genomes. Proc. Natl Acad. Sci. USA 104, 2271\u20132276 (2007).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR72","doi-asserted-by":"publisher","first-page":"7882","DOI":"10.1073\/pnas.0502300102","volume":"102","author":"SH Williamson","year":"2005","unstructured":"Williamson, S. H. et al. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl Acad. Sci. USA 102, 7882\u20137887 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR73","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1093\/molbev\/msn005","volume":"25","author":"J Charlesworth","year":"2008","unstructured":"Charlesworth, J. & Eyre-Walker, A. The McDonald\u2013Kreitman test and slightly deleterious mutations. Mol. Biol. Evol. 25, 1007\u20131015 (2008).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR74","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.1016\/j.cub.2004.07.026","volume":"14","author":"AD Chipman","year":"2004","unstructured":"Chipman, A. D., Arthur, W. & Akam, M. A double segment periodicity underlies segment generation in centipede development. Curr. Biol. 14, 1250\u20131255 (2004).","journal-title":"Curr. Biol."},{"key":"BFnrg2506_CR75","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1002\/bies.10366","volume":"25","author":"F Galis","year":"2003","unstructured":"Galis, F. & Metz, J. A. Anti-cancer selection as a source of developmental and evolutionary constraints. Bioessays 25, 1035\u20131039 (2003).","journal-title":"Bioessays"},{"key":"BFnrg2506_CR76","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/hdy.1982.86","volume":"49","author":"MA Toro","year":"1982","unstructured":"Toro, M. A. & Charlesworth, B. An attempt to detect genetic variation in sex ratio of Drosophila melanogaster. Heredity 49, 199\u2013209 (1982).","journal-title":"Heredity"},{"key":"BFnrg2506_CR77","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/0169-5347(92)90122-R","volume":"7","author":"LD Hurst","year":"1992","unstructured":"Hurst, L. D. & Vollrath, F. Sex ratio adjustment in solitary and social spiders. Trends Ecol. Evol. 7, 326\u2013327 (1992).","journal-title":"Trends Ecol. Evol."},{"key":"BFnrg2506_CR78","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/384236a0","volume":"384","author":"PM Brakefield","year":"1996","unstructured":"Brakefield, P. M. et al. Development, plasticity and evolution of butterfly eyespot patterns. Nature 384, 236\u2013242 (1996). An important empirical evaluation of the relevance of developmental constraint that suggests it is largely irrelevant.","journal-title":"Nature"},{"key":"BFnrg2506_CR79","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1038\/416844a","volume":"416","author":"P Beldade","year":"2002","unstructured":"Beldade, P., Koops, K. & Brakefield, P. M. Developmental constraints versus flexibility in morphological evolution. Nature 416, 844\u2013847 (2002).","journal-title":"Nature"},{"key":"BFnrg2506_CR80","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1146\/annurev.ecolsys.39.110707.173542","volume":"39","author":"LEB Kruuk","year":"2008","unstructured":"Kruuk, L. E. B., Slate, J. & Wilson, A. J. New answers for old questions: the evolutionary quantitative genetics of wild animal populations. Annu. Rev. Ecol. System. 39, 525\u2013548 (2008).","journal-title":"Annu. Rev. Ecol. System."},{"key":"BFnrg2506_CR81","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1016\/S0959-437X(02)00353-2","volume":"12","author":"L Duret","year":"2002","unstructured":"Duret, L. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12, 640\u2013649 (2002).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"BFnrg2506_CR82","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1093\/molbev\/msj035","volume":"23","author":"JL Parmley","year":"2006","unstructured":"Parmley, J. L., Chamary, J. V. & Hurst, L. D. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 23, 301\u2013309 (2006).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR83","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/molbev\/msm104","volume":"24","author":"JL Parmley","year":"2007","unstructured":"Parmley, J. L. & Hurst, L. D. Exonic splicing regulatory elements skew synonymous codon usage near intron\u2013exon boundaries in mammals. Mol. Biol. Evol. 24, 1600\u20131603 (2007).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR84","doi-asserted-by":"publisher","first-page":"2755","DOI":"10.1093\/molbev\/msm210","volume":"24","author":"T Warnecke","year":"2007","unstructured":"Warnecke, T. & Hurst, L. D. Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Mol. Biol. Evol. 24, 2755\u20132762 (2007).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR85","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1126\/science.1131262","volume":"314","author":"AG Nackley","year":"2006","unstructured":"Nackley, A. G. et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314, 1930\u20131933 (2006).","journal-title":"Science"},{"key":"BFnrg2506_CR86","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1007\/s00239-005-0273-2","volume":"63","author":"LD Hurst","year":"2006","unstructured":"Hurst, L. D. Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J. Mol. Evol. 63, 174\u2013182 (2006).","journal-title":"J. Mol. Evol."},{"key":"BFnrg2506_CR87","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1126\/science.1135308","volume":"315","author":"C Kimchi-Sarfaty","year":"2007","unstructured":"Kimchi-Sarfaty, C. et al. A \u201csilent\u201d polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525\u2013528 (2007).","journal-title":"Science"},{"key":"BFnrg2506_CR88","doi-asserted-by":"publisher","first-page":"e1000250","DOI":"10.1371\/journal.pgen.1000250","volume":"4","author":"T Warnecke","year":"2008","unstructured":"Warnecke, T., Batada, N. N. & Hurst, L. D. The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet. 4, e1000250 (2008).","journal-title":"PLoS Genet."},{"key":"BFnrg2506_CR89","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/35080577","volume":"2","author":"A Eyre-Walker","year":"2001","unstructured":"Eyre-Walker, A. & Hurst, L. D. The evolution of isochores. Nature Rev. Genet. 2, 549\u2013555 (2001).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg2506_CR90","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1093\/genetics\/159.2.907","volume":"159","author":"N Galtier","year":"2001","unstructured":"Galtier, N., Piganeau, G., Mouchiroud, D. & Duret, L. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159, 907\u2013911 (2001).","journal-title":"Genetics"},{"key":"BFnrg2506_CR91","unstructured":"Berglund, J., Pollard, K. S. & Webster, M. T. Hotspots of biased nucleotide substitutions in humans genes. PLoS Biol. (in the press). This paper shows that putative signals of positive selection from K A \/K S methodology require more scrutiny, as they can result from processes such as biased gene conversion."},{"key":"BFnrg2506_CR92","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1093\/molbev\/msj050","volume":"23","author":"M Lynch","year":"2006","unstructured":"Lynch, M. The origins of eukaryotic gene structure. Mol. Biol. Evol. 23, 450\u2013468 (2006).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR93","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1126\/science.1089370","volume":"302","author":"M Lynch","year":"2003","unstructured":"Lynch, M. & Conery, J. S. The origins of genome complexity. Science 302, 1401\u20131404 (2003). A wide-ranging analysis arguing that weakened selection that is associated with reduced population size (hence, the nearly neutral theory) can explain the accumulation of genomic elements, such as mobile elements and introns.","journal-title":"Science"},{"key":"BFnrg2506_CR94","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1093\/molbev\/msi100","volume":"22","author":"M Lynch","year":"2005","unstructured":"Lynch, M., Scofield, D. G. & Hong, X. The evolution of transcription-initiation sites. Mol. Biol. Evol. 22, 1137\u20131146 (2005).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR95","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1093\/molbev\/msn044","volume":"25","author":"M Reuter","year":"2008","unstructured":"Reuter, M., Engelstadter, J., Fontanillas, P. & Hurst, L. D. A test of the null model for 5\u2032 UTR evolution based on GC content. Mol. Biol. Evol. 25, 801\u2013804 (2008).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR96","doi-asserted-by":"publisher","first-page":"R233","DOI":"10.1186\/gb-2007-8-11-r233","volume":"8","author":"JF Poyatos","year":"2007","unstructured":"Poyatos, J. F. & Hurst, L. D. The determinants of gene order conservation in yeasts. Genome Biol. 8, R233 (2007).","journal-title":"Genome Biol."},{"key":"BFnrg2506_CR97","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1016\/S0168-9525(02)02813-5","volume":"18","author":"LD Hurst","year":"2002","unstructured":"Hurst, L. D., Williams, E. J. & Pal, C. Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet. 18, 604\u2013606 (2002).","journal-title":"Trends Genet."},{"key":"BFnrg2506_CR98","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/ng887","volume":"31","author":"MJ Lercher","year":"2002","unstructured":"Lercher, M. J., Urrutia, A. O. & Hurst, L. D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet. 31, 180\u2013183 (2002).","journal-title":"Nature Genet."},{"key":"BFnrg2506_CR99","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/ng1111","volume":"33","author":"C Pal","year":"2003","unstructured":"Pal, C. & Hurst, L. D. Evidence for co-evolution of gene order and recombination rate. Nature Genet. 33, 392\u2013395 (2003).","journal-title":"Nature Genet."},{"key":"BFnrg2506_CR100","doi-asserted-by":"publisher","first-page":"e72","DOI":"10.1371\/journal.pbio.0040072","volume":"4","author":"BF Voight","year":"2006","unstructured":"Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).","journal-title":"PLoS Biol."},{"key":"BFnrg2506_CR101","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.1371\/journal.pgen.0030090","volume":"3","author":"SH Williamson","year":"2007","unstructured":"Williamson, S. H. et al. Localizing recent adaptive evolution in the human genome. PLoS Genet. 3, e90 (2007).","journal-title":"PLoS Genet."},{"key":"BFnrg2506_CR102","doi-asserted-by":"publisher","first-page":"2832","DOI":"10.1073\/pnas.0409853102","volume":"102","author":"SL Sawyer","year":"2005","unstructured":"Sawyer, S. L., Wu, L. I., Emerman, M. & Malik, H. S. Positive selection of primate TRIM5\u03b1 identifies a critical species-specific retroviral restriction domain. Proc. Natl Acad. Sci. USA 102, 2832\u20132837 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR103","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/nrg1870","volume":"7","author":"SP Sinkins","year":"2006","unstructured":"Sinkins, S. P. & Gould, F. Gene drive systems for insect disease vectors. Nature Rev. Genet. 7, 427\u2013435 (2006).","journal-title":"Nature Rev. Genet."},{"key":"BFnrg2506_CR104","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1038\/nature01025","volume":"418","author":"W Enard","year":"2002","unstructured":"Enard, W. et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869\u2013872 (2002).","journal-title":"Nature"},{"key":"BFnrg2506_CR105","volume-title":"Evolution and the Genetics of Populations: The Theory of Gene Frequencies","author":"S Wright","year":"1969","unstructured":"Wright, S. Evolution and the Genetics of Populations: The Theory of Gene Frequencies (Chicago Univ. Press, Chicago, 1969)."},{"key":"BFnrg2506_CR106","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1016\/j.tig.2003.09.003","volume":"19","author":"ME Majerus","year":"2003","unstructured":"Majerus, M. E. & Mundy, N. I. Mammalian melanism: natural selection in black and white. Trends Genet. 19, 585\u2013588 (2003).","journal-title":"Trends Genet."},{"key":"BFnrg2506_CR107","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/nature02177","volume":"426","author":"DW Coltman","year":"2003","unstructured":"Coltman, D. W. et al. Undesirable evolutionary consequences of trophy hunting. Nature 426, 655\u2013658 (2003).","journal-title":"Nature"},{"key":"BFnrg2506_CR108","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1890\/03-5066","volume":"14","author":"S Barot","year":"2004","unstructured":"Barot, S., Heino, M., O'Brien, L. & Dieckmann, U. Long-term trend in the maturation reaction norm of two cod stocks. Ecol. Appl. 14, 1257\u20131271 (2004).","journal-title":"Ecol. Appl."},{"key":"BFnrg2506_CR109","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/S0169-5347(00)01994-7","volume":"15","author":"ZH Yang","year":"2000","unstructured":"Yang, Z. H. & Bielawski, J. P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15, 496\u2013503 (2000).","journal-title":"Trends Ecol. Evol."},{"key":"BFnrg2506_CR110","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/ng852","volume":"30","author":"J Zhang","year":"2002","unstructured":"Zhang, J., Zhang, Y. P. & Rosenberg, H. F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nature Genet. 30, 411\u2013415 (2002). An example of positive selection that uses both statistical and experimental approaches, and shows how RNASE1B has evolved rapidly under positive selection for enhanced ribonucleolytic activity in an altered microenvironment.","journal-title":"Nature Genet."},{"key":"BFnrg2506_CR111","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.tree.2006.03.015","volume":"21","author":"M Andersson","year":"2006","unstructured":"Andersson, M. & Simmons, L. W. Sexual selection and mate choice. Trends Ecol. Evol. 21, 296\u2013302 (2006).","journal-title":"Trends Ecol. Evol."},{"key":"BFnrg2506_CR112","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1101\/gr.6902","volume":"12","author":"M Blanchette","year":"2002","unstructured":"Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739\u2013748 (2002).","journal-title":"Genome Res."},{"key":"BFnrg2506_CR113","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/0022-2836(88)90011-3","volume":"203","author":"DA Tagle","year":"1988","unstructured":"Tagle, D. A. et al. Embryonic \u025b and \u03b3 globin genes of a prosimian primate (Galago crassicaudatus): nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439\u2013455 (1988).","journal-title":"J. Mol. Biol."},{"key":"BFnrg2506_CR114","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1016\/j.tig.2008.09.003","volume":"24","author":"S Washietl","year":"2008","unstructured":"Washietl, S., Machne, R. & Goldman, N. Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24, 583\u2013587 (2008).","journal-title":"Trends Genet."},{"key":"BFnrg2506_CR115","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/35066628","volume":"410","author":"DW Pfennig","year":"2001","unstructured":"Pfennig, D. W., Harcombe, W. R. & Pfennig, K. S. Frequency-dependent Batesian mimicry. Nature 410, 323\u2013323 (2001).","journal-title":"Nature"},{"key":"BFnrg2506_CR116","doi-asserted-by":"publisher","first-page":"e125","DOI":"10.1371\/journal.pone.0000125","volume":"1","author":"NJ Gemmell","year":"2006","unstructured":"Gemmell, N. J. & Slate, J. Heterozygote advantage for fecundity. PLoS ONE 1, e125 (2006).","journal-title":"PLoS ONE"},{"key":"BFnrg2506_CR117","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.tree.2008.04.010","volume":"23","author":"M Salathe","year":"2008","unstructured":"Salathe, M., Kouyos, R. D. & Bonhoeffer, S. The state of affairs in the kingdom of the Red Queen. Trends Ecol. Evol. 23, 439\u2013445 (2008).","journal-title":"Trends Ecol. Evol."},{"key":"BFnrg2506_CR118","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/ng1202-569","volume":"32","author":"ME Woolhouse","year":"2002","unstructured":"Woolhouse, M. E., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nature Genet. 32, 569\u2013577 (2002).","journal-title":"Nature Genet."},{"key":"BFnrg2506_CR119","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1046\/j.1420-9101.2002.00366.x","volume":"15","author":"TJ Little","year":"2002","unstructured":"Little, T. J. The evolutionary significance of parasitism: do parasite-driven genetic dynamics occur ex silico? J. Evol. Biol. 15, 1\u20139 (2002).","journal-title":"J. Evol. Biol."},{"key":"BFnrg2506_CR120","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/1471-2148-7-91","volume":"7","author":"JP Webster","year":"2007","unstructured":"Webster, J. P., Shrivastava, J., Johnson, P. J. & Blair, L. Is host\u2013schistosome coevolution going anywhere? BMC Evol. Biol. 7, 91 (2007).","journal-title":"BMC Evol. Biol."},{"key":"BFnrg2506_CR121","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/nature06291","volume":"450","author":"E Decaestecker","year":"2007","unstructured":"Decaestecker, E. et al. Host\u2013parasite 'Red Queen' dynamics archived in pond sediment. Nature 450, 870\u2013873 (2007).","journal-title":"Nature"},{"key":"BFnrg2506_CR122","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/nature07152","volume":"455","author":"SE Forde","year":"2008","unstructured":"Forde, S. E. et al. Understanding the limits to generalizability of experimental evolutionary models. Nature 455, 220\u2013223 (2008).","journal-title":"Nature"},{"key":"BFnrg2506_CR123","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.1534\/genetics.106.055715","volume":"173","author":"KL Bubb","year":"2006","unstructured":"Bubb, K. L. et al. Scan of human genome reveals no new loci under ancient balancing selection. Genetics 173, 2165\u20132177 (2006).","journal-title":"Genetics"},{"key":"BFnrg2506_CR124","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1741-7007-5-12","volume":"5","author":"BE Baysal","year":"2007","unstructured":"Baysal, B. E., Lawrence, E. C. & Ferrell, R. E. Sequence variation in human succinate dehydrogenase genes: evidence for long-term balancing selection on SDHA. BMC Biol. 5, 12 (2007).","journal-title":"BMC Biol."},{"key":"BFnrg2506_CR125","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1016\/j.cub.2007.09.051","volume":"17","author":"A Kawabe","year":"2007","unstructured":"Kawabe, A., Fujimoto, R. & Charlesworth, D. High diversity due to balancing selection in the promoter region of the medea gene in Arabidopsis lyrata. Curr. Biol. 17, 1885\u20131889 (2007).","journal-title":"Curr. Biol."},{"issue":"2","key":"BFnrg2506_CR126","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1101\/gr.082768.108","volume":"19","author":"M. Fumagalli","year":"2008","unstructured":"Fumagalli, M. et al. Widespread balancing selection and pathogen-driven selection at blood group antigen genes. Genome Res. 7 Nov 2008 (doi:10.1101\/gr.082768.108).","journal-title":"Genome Research"},{"key":"BFnrg2506_CR127","doi-asserted-by":"publisher","first-page":"R143","DOI":"10.1186\/gb-2008-9-9-r143","volume":"9","author":"R Cagliani","year":"2008","unstructured":"Cagliani, R. et al. The signature of long-standing balancing selection at the human defensin \u03b2-1 promoter. Genome Biol. 9, R143 (2008).","journal-title":"Genome Biol."},{"key":"BFnrg2506_CR128","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1007\/s00239-006-0207-7","volume":"64","author":"JL Parmley","year":"2007","unstructured":"Parmley, J. L. & Hurst, L. D. How common are intragene windows with KA&gt;KS owing to purifying selection on synonymous mutations? J. Mol. Evol. 64, 646\u2013655 (2007). A provocative paper showing that within genes, more K A \/K S >1 peaks are present, owing to unusually low synonymous rates rather than positive selection on proteins. Repeatable peaks tend to be in alternative exons.","journal-title":"J. Mol. Evol."},{"key":"BFnrg2506_CR129","first-page":"555","volume":"13","author":"Z Yang","year":"1997","unstructured":"Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13, 555\u2013556 (1997).","journal-title":"CABIOS"},{"key":"BFnrg2506_CR130","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/351652a0","volume":"351","author":"JH McDonald","year":"1991","unstructured":"McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652\u2013654 (1991). The paper that introduced the McDonald\u2013Kreitman test.","journal-title":"Nature"},{"key":"BFnrg2506_CR131","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1093\/genetics\/116.1.153","volume":"116","author":"RR Hudson","year":"1987","unstructured":"Hudson, R. R., Kreitman, M. & Aguade, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153\u2013159 (1987).","journal-title":"Genetics"},{"key":"BFnrg2506_CR132","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/sj.hdy.6801059","volume":"100","author":"JM Comeron","year":"2008","unstructured":"Comeron, J. M., Williford, A. & Kliman, R. M. The Hill\u2013Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100, 19\u201331 (2008). A recent review on Hill\u2013Robertson interference.","journal-title":"Heredity"},{"key":"BFnrg2506_CR133","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1093\/genetics\/161.1.389","volume":"161","author":"JM Comeron","year":"2002","unstructured":"Comeron, J. M. & Kreitman, M. Population, evolutionary and genomic consequences of interference selection. Genetics 161, 389\u2013410 (2002).","journal-title":"Genetics"},{"key":"BFnrg2506_CR134","doi-asserted-by":"publisher","first-page":"2323","DOI":"10.1093\/oxfordjournals.molbev.a003779","volume":"18","author":"C Pal","year":"2001","unstructured":"Pal, C., Papp, B. & Hurst, L. D. Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol. Biol. Evol. 18, 2323\u20132326 (2001).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR135","doi-asserted-by":"publisher","first-page":"13616","DOI":"10.1073\/pnas.212277199","volume":"99","author":"AJ Betancourt","year":"2002","unstructured":"Betancourt, A. J. & Presgraves, D. C. Linkage limits the power of natural selection in Drosophila. Proc. Natl Acad. Sci. USA 99, 13616\u201313620 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg2506_CR136","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/nature05049","volume":"443","author":"PD Keightley","year":"2006","unstructured":"Keightley, P. D. & Otto, S. P. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 443, 89\u201392 (2006).","journal-title":"Nature"},{"key":"BFnrg2506_CR137","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/genetics\/74.1.175","volume":"74","author":"RC Lewontin","year":"1973","unstructured":"Lewontin, R. C. & Krakauer, J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74, 175\u2013195 (1973).","journal-title":"Genetics"},{"key":"BFnrg2506_CR138","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1093\/genetics\/158.4.1811","volume":"158","author":"R Vitalis","year":"2001","unstructured":"Vitalis, R., Dawson, K. & Boursot, P. Interpretation of variation across marker loci as evidence of selection. Genetics 158, 1811\u20131823 (2001).","journal-title":"Genetics"},{"key":"BFnrg2506_CR139","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1093\/molbev\/msg092","volume":"20","author":"M Kayser","year":"2003","unstructured":"Kayser, M., Brauer, S. & Stoneking, M. A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol. Biol. Evol. 20, 893\u2013900 (2003).","journal-title":"Mol. Biol. Evol."},{"key":"BFnrg2506_CR140","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1101\/gr.631202","volume":"12","author":"JM Akey","year":"2002","unstructured":"Akey, J. M., Zhang, G., Zhang, K., Jin, L. & Shriver, M. D. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12, 1805\u20131814 (2002).","journal-title":"Genome Res."},{"key":"BFnrg2506_CR141","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1111\/j.1365-294X.2004.02125.x","volume":"13","author":"MA Beaumont","year":"2004","unstructured":"Beaumont, M. A. & Balding, D. J. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13, 969\u2013980 (2004).","journal-title":"Mol. Ecol."},{"key":"BFnrg2506_CR142","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/nature06250","volume":"449","author":"PC Sabeti","year":"2007","unstructured":"Sabeti, P. C. et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913\u2013918 (2007).","journal-title":"Nature"},{"key":"BFnrg2506_CR143","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/genetics\/88.2.405","volume":"88","author":"GA Watterson","year":"1978","unstructured":"Watterson, G. A. The homozygosity test of neutrality. Genetics 88, 405\u2013417 (1978).","journal-title":"Genetics"},{"key":"BFnrg2506_CR144","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","volume":"123","author":"F Tajima","year":"1989","unstructured":"Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585\u2013595 (1989).","journal-title":"Genetics"},{"key":"BFnrg2506_CR145","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1093\/genetics\/133.3.693","volume":"133","author":"YX Fu","year":"1993","unstructured":"Fu, Y. X. & Li, W. H. Statistical tests of neutrality of mutations. Genetics 133, 693\u2013709 (1993).","journal-title":"Genetics"},{"key":"BFnrg2506_CR146","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/genetics\/143.1.557","volume":"143","author":"YX Fu","year":"1996","unstructured":"Fu, Y. X. New statistical tests of neutrality for DNA samples from a population. Genetics 143, 557\u2013570 (1996).","journal-title":"Genetics"},{"key":"BFnrg2506_CR147","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/genetics\/147.2.915","volume":"147","author":"YX Fu","year":"1997","unstructured":"Fu, Y. X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915\u2013925 (1997).","journal-title":"Genetics"},{"key":"BFnrg2506_CR148","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1038\/nature01140","volume":"419","author":"PC Sabeti","year":"2002","unstructured":"Sabeti, P. C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832\u2013837 (2002).","journal-title":"Nature"},{"key":"BFnrg2506_CR149","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1146\/annurev.genet.39.073003.112420","volume":"39","author":"R Nielsen","year":"2005","unstructured":"Nielsen, R. Molecular signatures of natural selection. Annu. Rev. Genet. 39, 197\u2013218 (2005). An excellent review of tests for selection.","journal-title":"Annu. Rev. Genet."},{"key":"BFnrg2506_CR150","doi-asserted-by":"publisher","first-page":"e171","DOI":"10.1371\/journal.pbio.0050171","volume":"5","author":"K Tang","year":"2007","unstructured":"Tang, K., Thornton, K. R. & Stoneking, M. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5, e171 (2007).","journal-title":"PLoS Biol."},{"key":"BFnrg2506_CR151","volume-title":"Basic Concepts in Population, Quantitative and Evolutionary Genetics","author":"JF Crow","year":"1986","unstructured":"Crow, J. F. Basic Concepts in Population, Quantitative and Evolutionary Genetics (W.H. Freeman and Co., New York, 1986)."}],"container-title":["Nature Reviews Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nrg2506.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg2506","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg2506.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,8]],"date-time":"2024-03-08T10:20:42Z","timestamp":1709893242000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nrg2506"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2]]},"references-count":151,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2009,2]]}},"alternative-id":["BFnrg2506"],"URL":"https:\/\/doi.org\/10.1038\/nrg2506","relation":{},"ISSN":["1471-0056","1471-0064"],"issn-type":[{"value":"1471-0056","type":"print"},{"value":"1471-0064","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,2]]}}}