Modern Synthesis and Neo-Darwinism: A Basic Critique

1) Lewontin, R. C. "Foreword" in Oyama, S. 2000. The ontogeny of information: Developmental systems and evolution.Duke University Press, Durham(.pdf)

2) Lewontin, R. C. 1983. Gene, organism and environment. Pp. 273-285 in D. S. Bendall, ed. Evolution: From Molecules to Men. Cambridge University Press, Cambridge (.pdf)

3) Oyama, S. "1. Introduction" Pp. 1-11 in Oyama, S. 2000. The ontogeny of information: Developmental systems and evolution. Duke University Press Durham (.pdf)

Optional:

Antonovics, J. 1987. The evolutionary dys-synthesis: which bottles for which wine? American Naturalist 129:321-331

Nijhout, H. F. 1990. Metaphors and the role of genes in development. BioEssays 12:441-446

Phenotype-to-Genotype or Genotype–to-Phenotype?

1) Wagner, G. P., and J. G. Mezey. 2004. The role of genetic architecture constraints for the origin of variational modularity. Pp. 338-358 in G. Schlosser and G. P. Wagner, eds. Modularity in Development and Evolution. Chicago University Press, Chicago, IL.(.pdf)

2) Wagner, G. P., and L. Altenberg. 1996. Complex adaptation and the evolution of evolvability. Evolution 50:967-976.(.pdf)

3) Force, A. G., W. A. Cresko, and F. B. Pickett. 2004. Information accretion, gene duplication, and the mechanisms of genetic module parcellation. Pp. 315-338 in G. Schlosser and G. P. Wagner, eds.Modularity in Development and Evolution. The University of Chicago Press, Chicago.(.pdf)

Semi-optional:

von Dassow, G., and E. Munro. 1999. Modularity in animal development and evolution: Elements of a conceptual framework for EvoDevo. Journal of Experimental Zoology 285:307-325.(.pdf)

Optional:

Wagner, G. P., and J. G. Mezey. 2000. Modeling the evolution of genetic architecture: a continuum of alleles model with pairwise AxA epistasis. Journal of Theoretical Biology 203:163-175.

Ancel, L. W., and W. Fontana. 2000. Plasticity, evolvability, and modularity in RNA. Journal of Experimental Zoology (Mol Dev Evol) 288:242-283.

Moore, A. J. 1997. The evolution of social signals: Morphological, functional, and genetic integration of the sex pheromone in Nauphoeta cinerea. Evolution 51:1920-1928.

Welch, J. J., and D. Waxman. 2003. Modularity and the cost of complexity. Evolution 57:1723-1734.

Raff, R. A., and B. J. Sly. 2000. Modularity and dissociation in the evolution of gene expression territories in development. Evolution and Development 2:102-113.

Patthy, L. 2003. Modular assembly of genes and the evolution of new functions. Genetica 118:217-231.

Stock, D. W. 2001. The genetic basis of modularity in the development and evolution of the vertebrate dentition. Phil. Trans. R. Soc. Lond. B. 356:1633-1653.

Developmental perspective in evolution

1) Arthur, W. 2002. The emerging conceptual framework of evolutionary developmental biology. Nature 415:757-764(.pdf)

2) Fusco, G. 2001. How many processes are responsible for phenotypic evolution? Evolution and Development 3:279-286(.pdf)

3) Wagner, G. P., and H. C. E. Larsson. 2003. What is the promise of developmental evolution? III. The crucible of developmental evolution. Journal of Experimental Zoology 300B:1-4(.pdf)

4) Arthur, W. 2004. The effect of development on direction of evolution: toward a twenty-first century consensus. Evolution & Development 6: 282-288 (.pdf)

Optional:

Chipman, A. 2001. Developmental exaptation and evolutionary change. Evolution and Development 3:299-301 (.pdf).

Jernvall, J. 2000. Linking development with generation of novelty in mammalian teeth. Proc. Natl. Acad. Sci. 97:2641-2645 (.pdf).

Wagner, G. P., C. Chiu, -H., and M. Laubichler. 2000. Developmental evolution as a mechanistic science: the inference from developmental mechanisms to evolutionary processes. American Zoologist 40:819-831.

Palopoli, M. F., and N. H. Patel. 1996. Neo-Darwinian developmental evolution: can we bridge the gap between pattern and process? Current Opinion in Genetics and Development 6:502-508 (.pdf).

Sockman, K. W., T. Q. Gentner, and G. F. Ball. 2002. Recent experience modulates forebrain gene-expression in response to mate choice cues in European starlings. Proceedings of Royal Society London: Biological Sciences 269:2479-2485 (.pdf).

Roth, G., and D. B. Wake. 1985. Trends in the functional morphology and sensorimotor control of feeding behavior in salamanders: an example of the role of internal dynamics in evolution. Acta Biotheoretica 34:175-192.

Nonaka, S., H. Shiratori, Y. Saijoh, and H. Hamada. 2002. Determination of left-right patterning of the mouse embryo by artificial nodal flow. Nature 418:96-100(.pdf) .

Petersson, P., A. Waldenstrom, C. Fahraeus, and J. Schouenborg. 2003. Spontaneous muscle twitches during sleep guide spinal self-organization. Nature 424:72-75 (.pdf).

Grieco, F., A. J. Noordwijk, and M. Visser. 2002. Evidence for the effects of learning on timing of reproduction in blue tits. Science 296:136-138 (.pdf).

Hove, et al. 2003. Intracardiac fluid forces are an essential factor for embryonic cardiogenesis. Nature 421:172-177 (.pdf)

Jablonka, E., and M.J. Lamb. 1995. Neo-darwinian explanations of the inheritance of acquired characters. Pp. 30-51 in Epigenetic Inheritance and Evolution.Oxford Univ Press (.pdf)

Optional:

Jablonka, E., B. Oborny, I. Molnar, E. Kisdi, J. Hofbauer, and T. Czaran. 1995. The adaptive advantage of phenotypic memory in changing environments. Philosophical Transactions of the Royal Society of London B Biological Sciences 350:133-141. (.pdf)

Jablonka, E., M. Lachmann, and M. J. Lamb. 1992. Evidence, mechanisms and models for the inheritance of acquired characters. J. theor. Biol. 158:245-268.

Lambert, J. D. 2002. Asymmetric inheritance of centrosomally localized mRNAs during embryonic cleavages. Nature 420:682-686. (.pdf)

Muller, G. B. 2003. Embryonic motility: Environmental influences and evolutionary innovation. Evolution and Development 5:56-60. (.pdf)

1) Laland, K.N. Odling-Smee, F.J. Feldman, M.W. 2001. Niche construction, ecological inheritance, and cycles of contingency in evolution. Pp. 117-126. in (S. Oyama, P, Griffiths, and R.D. Gray, eds) Cycles of Contigency: Developmental Systems and Evolution. MIT Press.(.pdf)

2) Jablonka, E. 2001. The systems of inheritance. Pp 98-116 in in ( S. Oyama, P. E. Griffiths and R. D. Gray, eds.) Cycles of Contingency: Developmental Systems and Evolution. MIT Press, Cambridge.(.pdf)

Semi-Optional:

3) Odling-Smee, F. J., K. N. Laland, and M. W. Feldman. 2003. Evolutionary consequences of niche construction. Chapter 3 (part) in Niche Construction: The Neglected Process in Evolution. Princeton University Press.(.pdf)

Optional:

Sorenson, M. D., K. M. Sefc, and R. B. Payne. 2003. Speciation by host switch in brood parasitic indigobirds. Nature 424:928-931.(.pdf)

Freedberg, S., and M. Wade. 2001. Cultural inheritance as a mechanism for population sex-ratio bias in reptiles. Evolution 55:1049-1055. (.pdf)

Getty, T., and E. A. Capaldi. 1994. Inheritance of rank requires inheritance of social environment. Animal Behaviour 48:982-983.

Kamo, M., S. Ghirlanda, and M. Enquist. 2002. The evolution of signal form: effects of learned versus inherited recognition. Proceedings of Royal Society, Lond. Series B. 269:1765-1771.(.pdf)

Müller, W., C. M. Eising, C. Dijkstra, and T. G. G. Groothuis. 2002. Sex differences in yolk hormones depend on maternal social status in Leghorn chickens (Gallus gallus domesticus). Proceedings of Royal Society, Lond. Series B. 269:2249-2255.(.pdf)

28 Oct

@4PM

Random or directed genetic and phenotypic variation?

1) Caropale, L. H. 1999. Chance favors the prepared genome. Annals New York Academy of Sciences 870:1-21.(.pdf)

2) Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335:142-145.(.pdf)

3) Wright, B.E. 2004. Stress-directed adaptive mutations and evolution. Molecular Microbiology 52:643-650.(.pdf)

4) Gans, C. 1979. Momentary excessive construction as the basis for protoadaptation. Evolution 33:227-233.(.pdf)

Optional:

Wright, B. E. 2000. Minireview: A biochemical mechanism for nonrandom mutations and evolution. J. Bacteriol. 182:2993-3002.(.pdf)

Brisson, D. 2004. The directed mutation controversity in an evolutionary context. Critical Reviews in Microbiology 29: 25-35. (.pdf)

Kishony,R., and S. Leibler. 2003. Environmental stresses can alleviate the average deleterious effect of mutations. Jounal of Biology 2:14-19.

McClintock, B. 1984. The significance of responses of the genome to challenge. Science 226:792-801.

Bjedov, I., Tenaillon, O., Gerard, B., Souza, V., Denamur, E., Radman, M., Taddei, F. & Matic, I. 2003 Stress-induced mutagenesis in bacteria. Science 300, 1404-1409.

Goho, S. & Bell, G. 2000 Mild environmental stress elicits mutations affecting fitness in Chlamydomonas. Proceedings of Royal Society London: Biological Sciences 267, 123-129.

Hall, B. G. 1990 Spontaneous point mutations that occur more often when advantageous than when neutral. Genetics 126, 5-16.

Sniegowski, P., Gerrish, P., Johnson, T. & Shever, A. 2000 The evolution of mutation rates: separating causes from consequences. BioEssays 22, 1057-1066.

Steele, D. F. & Jinks-Robertson, S. 1992 An examination of adaptive reversion in Saccaharomyces cerevisiae. Genetics 132, 9-21.

Szafraniec, K., Borts, R. H. & Korona, R. 2001 Environmental stress and mutational load in diploid strains of the yeast Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 98, 1107-1112.

1) Masel, J. 2004. Genetic assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic. Journal of Evolutionary Biology 17: 1106-1110 .(.pdf)

2) Waddington, C.H. 1953. Genetic assimilation of an acquired character. Evolution 7: 118126. (.pdf)

3) Masel, J. ms. Evolutionary capacitance may be favored by natural selection. Genetics. (.pdf)

Optional:

Correspondence arising from Waddington's paper:

Stern, C. 1958 Selection for Subthreshold Differences and the Origin of Pseudoexogenous Adaptations. Am. Nat. 92:313-316.(.pdf)

Waddington C.H. 1958 Comment on Professor Stern's letter Am. Nat. 92:375-376 (.pdf)

Other optional:

Ho, M.W., Tucker, C., Keeley, D. & Saunders, P.T. 1983. Effects of successive generations of ether treatment on penetrance and expression of the bithorax phenocopy in Drosophila melanogaster. J. Exp. Zool. 225: 357368.(.pdf)

Rutherford & Lindquist 1998 Hsp90 as a capacitor for morphological evolution Nature 396:336-342(.pdf)

True, H.L. & Lindquist, S.L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity Nature 407:477-483(.pdf)

Bergman, A., and M. L. Siegal. 2003. Evolutionary capacitance as a general feature of complex gene networks. Nature 424:549-552

Eshel, I., and C. Matessi. 1998. Canalization, genetic assimilation and preadaptation: A quantitave genetic model. Genetics 149:2119-2133.

Ancel, L. W. 2000. Undermining the Baldwin expediting effect: does phenotypic plasticity accelerate evolution. heoretical Population Biology 58:307-319.

Ruden, D. M., M. D. Garfinkel, V. E. Sollars, and X. Lu. 2003. Waddington's widget: Hsp90 and the inheritance of acquired characters. Seminars in Cell & Developmental Biology 14:301-310.

Heil, M., S. Greiner, H. Meimberg, R. Kruger, J.-L. Noyer, G. Heubl, K. E. Linsenmair, and W. Boland. 2004.Evolutionary change from induced to constituive expression of an indirect plant resistance. Nature 430:205-208.

1) Meiklejohn, C. D., and D. L. Hartl. 2002. A single mode of canalization. Trends in Ecology and Evolution 17:468-473.(.pdf)

2) Badyaev, A. V. 2005. Stress-induced variation in evolution: from behavioral plasticity to genetic assimilation. Proceedings of Royal Society, Biological Sciences. Lond. In press .(.pdf) (I would greatly appreciate any comments as I am working on the revision of this paper. If you can, please mark any comments directly on the manuscript and bring to the class)

Optional:

Gibson G. I. Dworkin. 2004. Uncovering cryptic genetic variation. Nature Reviews 5: 681-690.

Siegal, M. L., and A. Bergman. 2002. Waddington's canalization revisited: Developmental stability and evolution. Proceedings of the National Academy of Sciences of the United States of America 99:10528-10532.

Robinson, B. W., and R. Dukas. 1999. The influence of phenotypic modifications on evolution: the Baldwin effect and modern perspectives. Oikos 85:582-589.

Gibson, G., and G. P. Wagner. 2000. Canalization in evolutionary genetics: a stabilizing theory? BioEssays 22:372-380.

Rutherford, S. L. 2000. From genotype to phenotype: buffering mechanisms and the storage of genetic information. BioEssays 22:1095-1105.

Rutherford, S. L. 2003. Between genotype and phenotype: Protein chaperones and evolvability. Nature Reviews 4: 263-274.

Waxman, D., and J. R. Peck. 1998. Pleiotropy and the preservation of perfection. Science 279:1210-1213.

Nijhout, H. F. 2002. The nature of robustness in development. BioEssays 24:553-563

Raberg, L., M. Grahn, D. Hasselquist, and E. Svensson. 1998. On the adaptive significance of stress-induced immunosuppression. Proceedings of Royal Society, Lond. Series B. 265:1637-1641.

Shors, T., C. Weiss, and R. F. Thompson. 1992. Stress-induced facilitation of classical conditioning. Science 257:537-539.

Sollars, V., X. Lu, et al. 2003. Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution. Nature Genetics 33: 70 - 74.

Kondrashov, A. S. & Houle, D. 1994 Genotype-environment interactions and the estimation of the genomic mutation rate in Drosophila melanogaster. Proc. R. Soc. Lond. B. 258, 221-227.

Lauter, N. & Doebley, J. 2002 Genetic variation for phenotypically invariant traits detected in teosine: Implications for the evolution of novel forms. Genetics 160, 333-342.

Leips, J. & MacKay, T. F. C. 2000 Quantitative trait loci for life span in Drosophila melanogaster: Interactions with genetic background and larval density. Genetics 160, 333-342.

Methods in molecular genetics: Review of assumptions and inference

1) Erickson DL, Fenster CB, Stenoien HK, Price D. (2004) Quantitative trait locus analyses and the study of evolutionary process. Mol Ecol. 13:2505-22.(.pdf)

2) Gibson G. (2002) Microarrays in ecology and evolution: a preview. Mol Ecol. 11:17-24.(.pdf)

3) Mello, C. C. and Conte Jr., D. (2004) Revealing the world of RNA interference Nature 431, 338 ­ 342(.pdf)

Optional:

Doerge RW. (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet. 3:43-52.(.pdf)

Carlborg O., Haley C. S. (2004) Opinion: Epistasis: too often neglected in complex trait studies? Nature Reviews Genetics 5, 618-625(.pdf)

Barton NH, Keightley PD. (2002) Understanding quantitative genetic variation. Nat Rev Genet. 3:11-21(.pdf)

Meister, G. and Tuschl, T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343 - 349(.pdf)

Sarkar, S. 2001. Reductionism in genetics and the human genome project. pp. 235-252 in Thinking about Evolution (eds Singh, C.B. Krimbas, D.B. Paul, J. Beaty). Cambridge Univ Press. (.pdf)