Bullaughey K 2013 Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation. Evolution, in press. doi:10.1111/j.1558-5646.2012.01735.x the possibility for compensatory evolution results from epistasis y…

hitachi at NIG

Gillespie JH 1994 Substitution processes in molecular evolution. III. Deleterious alleles. Genetics 138:943-952. there are no biologically reasonable models of molecular evolution where the vast majority of all substitutions are deleteriou…

Razeto-Barry P, Díaz J & Vásquez RA 2012 The nearly neutral and selection theories of molecular evolution under the Fisher geometrical framework: substitution rate, population size, and complexity. Genetics 191:523-534. compensatory mutati…

Razeto-Barry P, Díaz J, Cotras D & Vásquez RA 2011 Molecular evolution, mutation size and gene pleiotropy: a geometric reexamination. Genetics 187:877-885. Gu (2007a,b) used a bottom–up approach for the generation of mutational random vect…

Gu X 2007 Stabilizing selection of protein function and distribution of selection coefficient among sites. Genetica 130:93-97. the evolutionary conservation of protein function can be viewed as a set of several (K) molecular phenotypes tha…

Gu X 2007 Evolutionary framework for protein sequence evolution and gene pleiotropy. Genetics 175:1813–1822. the evolutionary fate of a mutant is largely determined by the prespecified fitness value (the coefficient of selection) and the e…

Hartl DL & Taubes CH 1998 Towards a theory of evolutionary adaptation. Genetica 102/103:525-533. nothing is known about the distribution of selective effects of newly arising mutations the statement that 'most mutations are harmful' is of …

Hartl DL & Taubes CH 1996 Compensatory nearly neutral mutations: selection without adaptation. J Theor Biol 182:303-309. a significant fraction of nucleotide substitutions should be slightly detrimental most genes undergo selectively drive…

Martin G & Lenormand T 2006 A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species. Evolution 60:893-907. there may be a cost to phenotypic complexity although much we…

Waxman D & Welch JJ 2005 Fisher's microscope and Haldane's ellipse. Am Nat 166:447-457.

Welch JJ & Waxman D 2003 Modularity and the cost of complexity. Evolution 57:1723-1734. we examine the claim that the rate of evolution of complex phenotypes could be accelerated through some sort of phenotypic modularity we consider the p…

Orr HA 2000 Adaptation and the cost of complexity. Evolution 54:13-20. fitness is determined by n independent (orthogonal) characters at each of our n characters, fitness falls off as a Gaussian function of distance, zi, from the optimum F…

Poon A & Otto SP 2000 Compensating for our load of mutations: freezing the meltdown of small populations. Evolution 54:1467-1479. new mutations may restore fitness losses incurred by previous mutations without requiring true reversals thes…

Peck JR, Barreau G & Heath SC 1997 Imperfect genes, Fisherian mutation and the evolution of sex. Genetics 145:1171-1199. mutant effects are biased there is a correlation between the state of an allele before mutation, and its postmutation …

Hastings A 1987 Substitution under stabilizing selection. Genetics 116:479-486. one of the most interesting and important questions facing population genetics today is the relationship between selection at the level of the organism and sel…

Cooley AM, Shefner L, McLaughlin WN, Stewart EE & Wittkopp PJ 2012 The ontogeny of color: developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evol Dev 14:317-325. even small and hard-to-detect diffe…

Nakamura T, Yagi Y & Kobayashi K 2012 Mechanistic insight into pentatricopeptide repeat proteins as sequence-specific RNA-binding proteins for organellar RNAs in plants. Plant Cell Physiol 53:1171-1179. the phenotypes of PPR mutants are hi…

Novembre J & Han E 2012 Human population structure and the adaptive response to pathogen-induced selection pressures. Phil Trans R Soc Lond B 367:878-886. selection from standing variation would appear to be the rule in the response to AID…

Draghi JA & Plotkin JB 2011 Molecular evolution: hidden diversity sparks adaptation. Nature 474:45-46. Sewall Wright, a vigorous proponent of the importance of epistasis in evolution, presaged the modern view in his comment11 on Kimura's n…

Leinonen PH, Remington DL, Leppälä J & Savolainen O 2012 Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata. Mol Ecol, in press. doi:10.1111/j.1365-294X.2012.05678.x an allele yielding higher fitness in on…

Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J & Wilczek AM 2011 A map of local adaptation in Arabidopsis thaliana. Science 334:86-89. among the 797 top SNPs, only 12 SNPs were associated with fitness in more than one environm…

Pavlidis P, Metzler D & Stephan W 2012 Selective sweeps in multilocus models of quantitative traits. Genetics, in press. doi:10.1534/genetics.112.142547 we study the trajectory of an allele that affects a polygenic trait selected towards a…

Coop G & Ralph PL 2012 Patterns of neutral diversity under general models of selective sweeps. Genetics, in press. doi:10.1534/genetics.112.141861 we develop a general model of recurrent selective sweeps in a coalescent framework, one that…

Weissman DB & Barton NH 2012 Limits to teh rate of adaptive substitution in sexual populations. PLoS Genet 8:e1002740. when multiple beneficial mutations arise simultaneously, they will typically occur in different individuals and will com…

Knief U, Schielzeth H, Kempenaers B, Ellegren H & Forstmeier W 2012 QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch. Mol Ecol, in press. doi:10.1111/j.1365-294X.…