Resources

Xenopus gastrulation

Both genetic and generic explanations have been invoked for more than a hundred years to explain biological phenomena, sometimes in a spirit of integration, sometimes in a spirit of competition. D’Arcy Thompson famously observed that, “The living medusa has a geometrical symmetry so marked and regular as to suggest a physical or mechanical element in the little creature’s growth and construction …certain simple organic forms might be naturally assumed by one fluid mass within another, when gravity, surface tension and fluid friction play their part” (Thompson 1992 [1942]).  Here we collect a variety of scholarly resources that bear on genetic and generic explanations of development, evolutionary novelty, and evolvability. If you would like to suggest a resource for us to add, please email us the citation information.

Development articles

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Development articles - Author A-E

Making stripes inelegantly
Akam, M. 1989. Making stripes inelegantly. Nature 341:282–283.
The biophysical properties of basal lamina gels depend on the biochemical composition of the gel 
Arends, F., C. Nowald, K. Pflieger, K. Boettcher, S. Zahler, and O. Lieleg. 2015. The biophysical properties of basal lamina gels depend on the biochemical composition of the gel. PLoS ONE 10:e0118090.
Direct laser manipulation reveals the mechanics of cell contacts in vivo
Bambardekar, K., R. Clément, O. Blanc, C. Chardès, and P.-F. Lenne. 2015. Direct laser manipulation reveals the mechanics of cell contacts in vivo. Proceedings of the National Academy of Sciences USA 112:1416–1421.
Bioelectric signaling regulates head and organ size during planarian regeneration 
Beane, W. S., J. Morokuma, J.M. Lemire, and M. Levin. 2013. Bioelectric signaling regulates head and organ size during planarian regeneration. Development (Cambridge, England), 140(2), 313–322. doi:10.1242/dev.086900.
GATA2 provides an early anterior bias and uncovers a global positioning system for polarity in the amniote embryo
Bertocchini, F., and C.D. Stern. 2012. GATA2 provides an early anterior bias and uncovers a global positioning system for polarity in the amniote embryo. Development (Cambridge, England), 139(22), 4232–4238.
Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation
Blanchard, G.B., A.J. Kabla, N.L. Schultz, L.C. Butler, B. Sanson, N. Gorfinkiel, L. Mahadevan, and R.J. Adams. 2009. Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation. Nature Methods 6:458–464.
Interplay of mechanical deformation and patterned gene expression in developing embryos
Brouzés, E., and E. Farge. 2004. Interplay of mechanical deformation and patterned gene expression in developing embryos. Current Opinion in Genetics & Development 14:367-374.
Endogenous voltage potentials and the microenvironment: bioelectric signals that reveal, induce and normalize cancer
Chernet, B. and Levin, M. 2013. Endogenous voltage potentials and the microenvironment: bioelectric signals that reveal, induce and normalize cancer. Journal of Clinical & Experimental Oncology S1:002.
Mechanical basis of morphogenesis and convergent evolution of spiny seashells 
Chirat, R., D.E. Moulton, and A. Goriely. 2013. Mechanical basis of morphogenesis and convergent evolution of spiny seashells. Proceedings of the National Academy of Sciences USA 110:6015-6020
A clock and wavefront model for control of the number of repeated structures during animal morphogenesis 
Cooke, J., and E.C. Zeeman. 1976. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. Journal of Theoretical Biology 58:455–476.
Genomic Regulatory Systems: Development and Evolution
Davidson, E.H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.
The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
Davidson, E.H. 2006. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. San Diego: Academic Press.
Epithelial machines that shape the embryo
Davidson, L.A. 2012. Epithelial machines that shape the embryo. Trends in Cell Biology 22:82-87.
No strings attached: new insights into epithelial morphogenesis
Davidson, L.A. 2012. No strings attached: new insights into epithelial morphogenesis. BMC Biology, 10, 105.
Tissue deformation modulates Twist expression to determine anterior midgut differentiation in Drosophila embryos
Desprat, N., W. Supatto, P.A. Pouille, E. Beaurepaire, and E. Farge. 2008. Tissue deformation modulates Twist expression to determine anterior midgut differentiation in Drosophila embryos. Developmental Cell 15:470-477.
Somites without a clock 
Dias A.S., I. de Almeida, J.M. Belmonte, J.A. Glazier, and C.D. Stern. 2014. Somites without a clock. Science  343(6172):791–5.
Positional information, in bits
Dubuis, J.O., G. Tkačik, E.F. Wieschaus, T. Gregor, and W. Bialek. 2013. Positional information, in bits. Proceedings of the National Academy of Sciences USA 110:16301–16308.
Seeing is believing: the Bicoid morphogen gradient matures
Ephrussi, A., and D. St Johnston. 2004. Seeing is believing: the Bicoid morphogen gradient matures. Cell 116:143–152.

Development articles - Author F-H

The cellular basis of tissue separation
Fagotto, F. 2014. The cellular basis of tissue separation. Development 141:3303–3318.
Mechanical induction of Twist in the Drosophila foregut/stomodeal primordium
Farge, E. 2003. Mechanical induction of Twist in the Drosophila foregut/stomodeal primordium. Current Biology 13:1365-1377.
Stem and progenitor cells in the formation of the pulmonary vasculature
Fisher, K.A., and R.S. Summer. 2006. Stem and progenitor cells in the formation of the pulmonary vasculature. In: Current Topics in Developmental Biology, ed. P. Schatten Gerald, 117-131. Academic Press.
Biological Physics of the Developing Embryo
Forgacs, G., and S.A. Newman. 2005. Biological Physics of the Developing Embryo. New York: Cambridge University Press.
Fluid flows and forces in development: functions, features and biophysical principles
Freund, J.B., J.G. Goetz, K.L. Hill, and J. Vermot. 2012. Fluid flows and forces in development: functions, features and biophysical principles. Development 139:1229–1245.
Segmental pattern and blastoderm cell identities
Gergen, J.P., D. Coulter, and E.F. Wieschaus. 1986. Segmental pattern and blastoderm cell identities. In: Gametogenesis and the Early Embryo, ed. J.G. Gall, 195–220. New York: Alan R. Liss, Inc.
Modeling the morphodynamic galectin patterning network of the developing avian limb skeleton
Glimm, T. Bhat, R., Newman, S.A. 2014. Modeling the morphodynamic galectin patterning network of the developing avian limb skeleton, Journal of Theoretical Biology 346:86-108, http://dx.doi.org/10.1016/j.jtbi.2013.12.004.
Soft matter models of developing tissues and tumors
Gonzalez-Rodriguez, D., K. Guevorkian, S. Douezan, and F. Brochard-Wyart. 2012. Soft matter models of developing tissues and tumors. Science 338:910–917.
A phase-shift model for the spatial and temporal organization of developing systems
Goodwin, B.C., and M.H. Cohen. 1969. A phase-shift model for the spatial and temporal organization of developing systems. Journal of Theoretical Biology 25:49–107.
Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos
Gregor, T., A.P. McGregor, and E.F. Wieschaus. 2008. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Developmental Biology 316:350–358.
Probing the limits to positional information
Gregor, T., D.W. Tank, E.F. Wieschaus, and W. Bialek. 2007. Probing the limits to positional information. Cell 130:153–164.
Mechanics of epithelial tissue homeostasis and morphogenesis
Guillot, C. and T. Lecuit. 2013. Mechanics of epithelial tissue homeostasis and morphogenesis. Science 340:1185-1189.
Damage to the Drosophila follicle cell epithelium produces “false clones” with apparent polarity phenotypes 
Haack, T., D.T. Bergstralh, and D. St Johnston. 2013. Damage to the Drosophila follicle cell epithelium produces “false clones” with apparent polarity phenotypes. Biology Open 2:1313–1320.
Generation of spatially periodic patterns by a mechanical instability: a mechanical alternative to the Turing model
Harris, A.K., P. Warner, and D. Stopak. 1984. Generation of spatially periodic patterns by a mechanical instability: a mechanical alternative to the Turing model. Journal of Embryology and Experimental Morphology 80:1–20.
Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation
He, B., K. Doubrovinski, O. Polyakov, and E. Wieschaus. 2014. Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation. Nature, 508(7496), 392–396.
Intracardiac fluid forces are an essential epigenetic factor for embryonic cardiogenesis
Hove, J.R., R.W. Köster, A.S. Forouhar, G. Acevedo-Bolton, S.E. Fraser, and M. Gharib. 2003. Intracardiac fluid forces are an essential epigenetic factor for embryonic cardiogenesis. Nature 421:172-177.
Turing's next steps: the mechanochemical basis of morphogenesis
Howard, J., S.W. Grill, and J.S. Bois. 2011. Turing's next steps: the mechanochemical basis of morphogenesis. Nature Reviews Molecular Cell Biology 12:392–398.

Development articles - Author K-M

Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines
Keller, E.F. 2002. Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines. Cambridge, MA: Harvard University Press.
Mechanisms of convergence and extension by cell intercalation
Keller, R., L.A. Davidson, A. Edlund, T. Elul, M. Ezin, D. Shook, and P. Skoglund. 2000. Mechanisms of convergence and extension by cell intercalation. Philosophical Transactions of the Royal Society B: Biological Sciences 355:897–922.
Quantitative 4D analyses of epithelial folding during Drosophila gastrulation
Khan Z, Wang YC, Wieschaus EF, Kaschube M. (2014) Quantitative 4D analyses of epithelial folding during Drosophila gastrulation. Development. 141(14):2895-900.
Developmental pattern formation: insights from physics and biology
Kicheva, A., M. Cohen, and J. Briscoe. 2012. Developmental pattern formation: insights from physics and biology. Science 338:210–212.
Mechanochemical actuators of embryonic epithelial contractility 
Kim Y., M. Hazar, D.S. Vijayraghavan, J. Song, T.R. Jackson, S.D. Joshi, W.C. Messner, L.A. Davidson, and P.R. LeDuc. 2014. Mechanochemical actuators of embryonic epithelial contractility. Proceedings of the National Academy of Sciences USA. 111(40):14366-71
Endogenous bioelectrical networks store non‐genetic patterning information during development and regeneration
Levin, M. 2014. Endogenous bioelectrical networks store non‐genetic patterning information during development and regeneration. The Journal of Physiology 592:2295-2305.
Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning
Levin, M. 2012. Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning. Biosystems 109:243–261.
Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo
Levin, M., 2014. Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo, Molecular Biology of the Cell, 25: 3835-3850
Resting Potential, Oncogene-induced Tumorigenesis, and Metastasis: The Bioelectric Basis of Cancer in vivo
Lobikin, M., B. Chernet, D. Lobo, and M. Levin. 2012. Resting Potential, Oncogene-induced Tumorigenesis, and Metastasis: The Bioelectric Basis of Cancer in vivo. Physical Biology, 9(6), 065002. doi:10.1088/1478-3975/9/6/065002.
Explaining the ontogeny of form: Philosophical issues
Love, A.C. 2008b. Explaining the ontogeny of form: Philosophical issues. In The Blackwell Companion to Philosophy of Biology, eds. A. Plutynski, and S. Sarkar, 223-247. Malden, MA: Blackwell Publishers.
Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages
Love, A.C. 2010. Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages. Philosophical Transactions of the Royal Society B: Biological Sciences 365:679-690.
Combining genetic and physical causation in developmental explanations
Love, A.C. forthcoming. Combining genetic and physical causation in developmental explanations. In Causal Reasoning in Biology, eds. C.K. Waters, and J. Woodward, Minnesota Studies in Philosophy of Science. Minneapolis: University of Minnesota Press.
A cell state splitter and differentiation wave working-model for embryonic stem cell development and somatic cell epigenetic reprogramming
Lu, K., T. Cao, and R. Gordon. 2012. A cell state splitter and differentiation wave working-model for embryonic stem cell development and somatic cell epigenetic reprogramming. Biosystems 109:390–396.
Mechanical control of tissue and organ development
Mammoto, T., and D.E. Ingber. 2010. Mechanical control of tissue and organ development. Development 137:1407–1420.
Crocodile head scales are not developmental units but emerge from physical cracking
Milinkovitch, M.C., L. Manukyan, A. Debry, N. Di-Poï, S. Martin, D. Singh, D. Lambert, and M. Zwicker. 2013. Crocodile head scales are not developmental units but emerge from physical cracking. Science 339:78–81.
The interplay between cell signaling and mechanics in developmental processes
Miller, C.J., and L. Davidson. 2013. The interplay between cell signaling and mechanics in developmental processes. Nature Reviews. Genetics, 14(10), 733–744. doi:10.1038/nrg3513.
Mechanistic, mathematical model to predict the dynamics of tissue genesis in bone defects via mechanical feedback and mediation of biochemical factors
Moore, S.R., G.M. Saidel, U. Knothe, and M.L. Knothe Tate. 2014. Mechanistic, mathematical model to predict the dynamics of tissue genesis in bone defects via mechanical feedback and mediation of biochemical factors. PLoS Computational Biology 10:e1003604.
Computational approaches to developmental patterning
Morelli, L.G., K. Uriu, S. Ares, and A.C. Oates. 2012. Computational approaches to developmental patterning. Science 336:187–191.
On growth and force
Mulder, B. 2008. On growth and force. Science 322:1643-1644.

Development articles - Author N-R

Physico-genetics of morphogenesis: the hybrid nature of developmental mechanisms
Newman, S.A. 2014. Physico-genetics of morphogenesis: the hybrid nature of developmental mechanisms. In: Towards a Theory of Development, eds. A. Minelli, and T. Pradeu. Oxford: Oxford University Press.
Dynamical patterning modules: a "pattern language" for development and evolution of multicellular form
Newman, S.A., and R. Bhat. 2009. Dynamical patterning modules: a pattern language" for development and evolution of multicellular form. International Journal of Developmental Biology 53:693-705.
Plant Physics
Niklas, K.J., and H.-C. Spatz. 2012. Plant Physics. Chicago: University of Chicago Press.
Three-dimensional epithelial morphogenesis in the developing Drosophila egg
Osterfield, M., X. Du, T. Schüpbach, E. Wieschaus, and S.Y. Shvartsman. 2013. Three-dimensional epithelial morphogenesis in the developing Drosophila egg. Developmental Cell, 24(4), 400–410. 
Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis
Palmeirim, I., D. Henrique, D. Ish-Horowicz, and O. Pourquié. 1997. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91:639–648.
Bioelectric signaling regulates size in zebrafish fins
Perathoner, S., J.M. Daane, U. Henrion, G. Seebohm, C.W. Higdon, S.L. Johnson, C. Nüsslein-Volhard, and M.P. Harris. 2014. Bioelectric signaling regulates size in zebrafish fins. PLoS Genetics 10:e1004080.
Precision of hunchback expression in the Drosophila embryo
Perry, M.W., J.P. Bothma, R.D. Luu, and M. Levine. 2012. Precision of hunchback expression in the Drosophila embryo. Current Biology 22:2247-2252.
Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs
Pezzulo, G., and M. Levin. 2015. Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs. Integrative Biology.
Passive Mechanical Forces Control Cell-Shape Change during Drosophila Ventral Furrow Formation
Polyakov, O., B. He, M. Swan, J.W. Shaevitz, M. Kaschube, and E. Wieschaus. 2014. Passive Mechanical Forces Control Cell-Shape Change during Drosophila Ventral Furrow Formation. Biophysics Journal 107(4):998–1010.
Periodic segmental anomalies induced by heat shock in the chick embryo are associated with the cell cycle
Primmett, D. R., W.E. Norris, G.J. Carlson, R.J. Keynes, and C.D. Stern. 1989. Periodic segmental anomalies induced by heat shock in the chick embryo are associated with the cell cycle. Development 105:119–130.
Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients
Raspopovic, J., L. Marcon, L. Russo, and J. Sharpe. 2014. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients. Science 345:566–570.
acal is a long non-coding RNA in JNK signaling in epithelial shape changes during Drosophila dorsal closure
Ríos-Barrera, L.D., I. Gutiérrez-Pérez, M. Domínguez, and J.R. Riesgo-Escovar. 2015. acal is a long non-coding RNA in JNK signaling in epithelial shape changes during Drosophila dorsal closure. PLoS Genetics 11:e1004927.

Development articles - Author S-Z

Physical forces regulate plant development and morphogenesis
Sampathkumar, A., A. Yan, P. Krupinski, and E.M. Meyerowitz. 2014. Physical forces regulate plant development and morphogenesis. Current Biology 24:R475–R483.
On the growth and form of the gut
Savin, T., N. A. Kurpios, A. E. Shyer, P. Florescu, H. Liang, L. Mahadevan, and C. Tabin. 2011. On the growth and form of the gut. Nature 476:57-62.
Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development
Shestopalov, I.A., C.L.W. Pitt, and J.K. Chen. 2012. Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development. Nature Chemical Biology 8:270–276.
Villification: how the gut gets its villi
Shyer, A.E., T. Tallinen, N.L. Nerurkar, Z. Wei, E. Seok Gil, D.L. Kaplan, C.J. Tabin, and L. Mahadevan. 2013. Villification: how the gut gets its villi. Science 342:212–218.
Experimental approaches for gene regulatory network construction: the chick as a model system
Streit, A., M. Tambalo, J.  Chen, T. Grocott, M. Anwar, A. Sosinsky, and C.D. Stern. 2013. Experimental approaches for gene regulatory network construction: the chick as a model system. Genesis (New York, N.Y. : 2000), 51(5), 296–310. 
On Growth and Form
Thompson, D’A. W. 1992 [1942]. On Growth and Form. Complete Revised Edition. New York: Dover Publications, Inc.
Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation
Tseng, A., and M. Levin. 2013. Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation. Communicative & Integrative Biology 6:e22595.
A Unified Model for Left-Right Asymmetry? Comparison and Synthesis of Molecular Models of Embryonic Laterality
Vandenberg, L. N. and M. Levin 2013. A Unified Model for Left-Right Asymmetry? Comparison and Synthesis of Molecular Models of Embryonic Laterality. Developmental Biology, 379(1), 1–15. doi:10.1016/j.ydbio.2013.03.021
Cellular and physical mechanisms of branching morphogenesis
Varner, V.D., and C.M. Nelson. 2014. Cellular and physical mechanisms of branching morphogenesis. Development 141:2750–2759.
Local cell interactions and self-amplifying individual cell ingression drive amniote gastrulation
Voiculescu, O., L. Bodenstein, I.-J. Lau, and C.D. Stern. 2014. Local cell interactions and self-amplifying individual cell ingression drive amniote gastrulation. eLife, 3, e01817. 
Physics and the canalization of morphogenesis: a grand challenge in organismal biology
von Dassow, M. and L.A. Davidson. 2011. Physics and the canalization of morphogenesis: a grand challenge in organismal biology. Physical Biology 8:045002.
Biomechanics and the Thermotolerance of Development
Von Dassow, M., C. J. Miller, and L.A. Davidson. 2014. Biomechanics and the Thermotolerance of Development. PLoS ONE, 9(4), e95670. 
Surprisingly simple mechanical behavior of a complex embryonic tissue
Von Dassow, M., J. Strother, and L.A. Davidson. 2010. Surprisingly simple mechanical behavior of a complex embryonic tissue. PLoS ONE 5:e15359.
Distinct Rap1 activity states control the extent of epithelial invagination via α-Catenin
Wang, Y.-C., Z. Khan, and E.F. Wieschaus. 2013. Distinct Rap1 activity states control the extent of epithelial invagination via α-Catenin. Developmental Cell, 25(3), 299–309. 
Force production and mechanical accommodation during convergent extension
Zhou, J., S. Pal, S. Maiti, and L.A. Davidson. 2015. Force production and mechanical accommodation during convergent extension. Development 142:692–701.

Evolutionary Novelty articles

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Evolutionary Novelty articles - Author A-K

Emergence, singularities, and symmetry breaking 
Batterman, R.W. 2011. Emergence, singularities, and symmetry breaking. Foundations of Physics 41:1031-1050.
Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand
Bever, G., J. Gauthier, and G. Wagner. 2011. Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand. Evolution & Development 13:269-279.
Conceptualizing evolutionary novelty: Moving beyond definitional debates
Brigandt, I., and A.C. Love. 2012. Conceptualizing evolutionary novelty: Moving beyond definitional debates. Journal of Experimental Zoology (Mol Dev Evol) 318B:417-427.
Genomic Regulatory Systems: Development and Evolution
Davidson, E.H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.
The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
Davidson, E.H. 2006. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. San Diego: Academic Press.
Gene regulatory networks and the evolution of animal body plans
Davidson, E.H., and D.H. Erwin. 2006. Gene regulatory networks and the evolution of animal body plans. Science 311:796-800.
Evolutionary innovation and stability in animal gene networks
Davidson, E.H., and D.H. Erwin. 2010. Evolutionary innovation and stability in animal gene networks. Journal of Experimental Zoology (Mol Dev Evol) 314B:182-186.
An integrated view of precambrian eumetazoan evolution
Davidson, E.H., and D.H. Erwin. 2009. An integrated view of precambrian eumetazoan evolution. Cold Spring Harbor Symposia on Quantitative Biology 74:65-80.
Macroevolution is more than repeated rounds of microevolution
Erwin, D.H. 2000. Macroevolution is more than repeated rounds of microevolution. Evolution & Development 2:78-84.
Novelties that change carrying capacity
Erwin, D.H. 2012. Novelties that change carrying capacity. Journal of Experimental Zoology (Mol Dev Evol) 318:460-465.
The Cambrian Explosion: The Construction of Animal Biodiversity
Erwin, D.H., and J.W. Valentine. 2013. The Cambrian Explosion: The Construction of Animal Biodiversity. Greenwood, CO: Roberts and Company Publishers.
Past Climate Change on Sky Islands Drives Novelty in a Core Developmental Gene Network and Its Phenotype
Favé, Marie-Julie, Robert A. Johnson, Stefan Cover, Stephan Handschuh, B.D. Metscher, G.B. Müller, Shyamalika Gopalan, and Ehab Abouheif. 2015. Past Climate Change on Sky Islands Drives Novelty in a Core Developmental Gene Network and Its Phenotype. BMC Evolutionary Biology, 1–21. doi:10.1186/s12862-015-0448-4.
Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila
Gompel, N., B. Prud'homme, P.J. Wittkopp, V.A. Kassner, and S.B. Carroll. 2005. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433:481-487.
Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology
Griesemer, James 2013. Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):525-536.
Evolution of a novel appendage ground plan in water striders is driven by changes in the Hox Gene Ultrabithorax
​​​​​​​Khila, A., E. Abouheif, and L. Rowe. 2009. Evolution of a novel appendage ground plan in water striders is driven by changes in the Hox Gene Ultrabithorax. PLoS Genet 5:e1000583.
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
​​​​​​​King, N., M.J. Westbrook, S.L. Young, A. Kuo, M. Abedin, J. Chapman, S. Fairclough et al. 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788.

Evolutionary Novelty articles - Author L-M

Biased Polyphenism in Polydactylous Cats Carrying a Single Point Mutation: the Hemingway Model for Digit Novelty
Lange, A., H.L. Nemeschkal, and G.B. Müller. 2014. Biased Polyphenism in Polydactylous Cats Carrying a Single Point Mutation: the Hemingway Model for Digit Novelty. Evolutionary Biology 41: 262–275. doi:10.1007/s11692-013-9267-y.
Limb, tooth, beak: three modes of development and evolutionary innovation of form
Linde-Medina, M., Newman, S,A. 2014. Limb, tooth, beak: three modes of development and evolutionary innovation of form. Journal of Biosciences 239(2):211-23.
Explaining evolutionary innovation and novelty: criteria of explanatory adequacy and epistemological prerequisites
​​​​​​​Love, A.C. 2008a. Explaining evolutionary innovation and novelty: criteria of explanatory adequacy and epistemological prerequisites. Philosophy of Science 75:874-886.
Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages
​​​​​​​Love, A.C. 2010. Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages. Philosophical Transactions of the Royal Society B: Biological Sciences 365:679-690.
Dimensions of integration in interdisciplinary explanations of the origin of evolutionary novelty
​​​​​​​Love, A.C., and G.L. Lugar. 2013. Dimensions of integration in interdisciplinary explanations of the origin of evolutionary novelty. Studies in the History and Philosophy of Biological and Biomedical Sciences. 44(4):537-550.
The frailty of adaptive hypotheses for the origins of organismal complexity
​​​​​​​Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proceedings of the National Academy of Sciences USA 104:8597-8604.
Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy
​​​​​​​Lynch, V.J., Nnamani, M.C., Kapusta, A., Brayer, K., Plaza, S.L., Mazur, E.C., Emera, D., Sheikh, S.Z., Grützner, F., Bauersachs, S., Graf, A., Young, S.L., Lieb, J.D.., DeMayo, F.J., Feschotte, C., Wagner, G.P. 2015. Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy. Cell Reports  pii: S2211-1247(14)01105-X. doi: 10.1016/j.celrep.2014.12.052.
Evolution–The Extended Synthesis
​​​​​​​Müller, G.B. 2010. Epigenetic innovation. In Evolution–The Extended Synthesis, eds. M. Pigliucci, and G.B. Müller, 307-332. Cambridge, MA: MIT Press.
Embryonic Motility: Environmental Influences and Evolutionary Innovation
​​​​​​​Müller, G.B. 2003. Embryonic Motility: Environmental Influences and Evolutionary Innovation. Evolution & Development 5(1): 56–60.
Developmental Mechanisms at the Origin of Morphological Novelty: a Side-Effect Hypothesis
Müller, G.B. 1990. Developmental Mechanisms at the Origin of Morphological Novelty: a Side-Effect Hypothesis. In Evolutionary Innovations, edited by M.H. Nitecki, 99–130. Chicago: University of Chicago Press.
Epigenetic Innovation
​​​​​​​Müller, G.B. 2010. Epigenetic Innovation. In Evolution - The Extended Synthesis, edited by M. Pigliucci and G. B. Müller, 307–332. Cambridge (MA): MIT Press.
Novelty in Evolution: Restructuring the Concept
​​​​​​​​​​​​​​Müller, G.B. and G.P. Wagner. 1991. Novelty in Evolution: Restructuring the Concept. Annual Review of Ecolological Systems 22: 229–56.
Ontogeny of the Syndesmosis Tibiofibularis and the Evolution of the Bird Hindlimb: a Caenogenetic Feature Triggers Phenotypic Novelty
​​​​​​​Müller, G.B., and J Streicher. 1989. Ontogeny of the Syndesmosis Tibiofibularis and the Evolution of the Bird Hindlimb: a Caenogenetic Feature Triggers Phenotypic Novelty. Anatomy and Embryology 179(4): 327–339.
The Innovation Triad: an EvoDevo Agenda
​​​​​​​Müller, G.B., and S.A. Newman. 2005. The Innovation Triad: an EvoDevo Agenda. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution 304(6): 487–503. doi:10.1002/jez.b.21081.
Origination of Organismal Form: the Forgotten Cause in Evolutionary Theory
​​​​​​​Müller, G.B., and S.A. Newman. 2003. Origination of Organismal Form: the Forgotten Cause in Evolutionary Theory. In Origination of Organismal Form, edited by G. B. Müller and S.A. Newman. MIT Press.

Evolutionary Novelty articles - Author N

Epigenetic Mechanisms of Character Origination
Newman, S.A., and G.B. Müller. 2000. Epigenetic Mechanisms of Character Origination. The Journal of Experimental Zoology 288(4): 304–17. doi:10.1002/1097-010X(20001215)288:4<304::AID-JEZ3>3.0.CO;2-G.
From physics to development: The evolution of morphogenetic mechanisms
Newman, S.A. 2003. From physics to development: The evolution of morphogenetic mechanisms. In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, eds. G.B. Müller, and S.A Newman, 221-239. Cambridge, MA: The MIT Press.
Physico-genetic determinants in the evolution of development
Newman, S.A. 2012. Physico-genetic determinants in the evolution of development. Science 338:217-219.
Dynamical patterning modules: physico-genetic determinants of morphological development and evolution
Newman, S.A., and R. Bhat. 2008. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution. Physical Biology 5:1-14.
Dynamical patterning modules: a "pattern language" for development and evolution of multicellular form
​​​​​​​Newman, S.A., and R. Bhat. 2009. Dynamical patterning modules: a "pattern language" for development and evolution of multicellular form. International Journal of Developmental Biology 53:693-705.
Origination and innovation in the vertebrate limb skeleton: an epigenetic perspective
​​​​​​​Newman, S.A., and G.B. Müller. 2005. Origination and innovation in the vertebrate limb skeleton: an epigenetic perspective. Journal of Experimental Zoology (Mol Dev Evol) 304:593-609.
The origins of multicellular organisms
​​​​​​​Newman, S.A., and K.J. Niklas. 2013. The origins of multicellular organisms. Evolution & Development 15:41-52.
Before programs: The physical origination of multicellular forms
​​​​​​​Newman, S.A., G. Forgacs, and G.B. Müller. 2006. Before programs: The physical origination of multicellular forms. International Journal of Developmental Biology 50:289-299.
Gene loss, thermogenesis, and the origin of birds
​​​​​​​Newman, S.A., Mezentseva, N.V. and Badyaev, A.V. 2013. Gene loss, thermogenesis, and the origin of birds. Annals of the New York Academy of Sciences 1289: 36–47. doi: 10.1111/nyas.12090
The evolutionary-developmental origins of multicellularity
​​​​​​​Niklas, K.J. 2014. The evolutionary-developmental origins of multicellularity. American Journal of Botany 101(1):6-25. doi: 10.3732/ajb.1300314.
The evolutionary development of plant body plans
​​​​​​​Niklas, K.J., and U. Kutschera. 2009. The evolutionary development of plant body plans. Functional Plant Biology 36:682-695.
The evo-devo of multinucleate cells, tissues, and organisms, and an alternative route to multicellularity
​​​​​​​Niklas, K.J., Cobb, E.D., Crawford, D.R. 2013. The evo-devo of multinucleate cells, tissues, and organisms, and an alternative route to multicellularity. Evolutionary Development 15(6):466-74. doi: 10.1111/ede.12055.
Did meiosis evolve before sex and the evolution of eukaryotic life cycles?
​​​​​​​Niklas, K.J., Cobb, E.D., Kutschera, U. 2014. Did meiosis evolve before sex and the evolution of eukaryotic life cycles? Bioessays. 36(11):1091-101. doi: 10.1002/bies.201400045.
Evidence for independent evolution of functional progesterone withdrawal in primates and guinea pigs
​​​​​​​Nnamani, M.C., Plaza, S., Romero, R., and Wagner, G.P. 2013. Evidence for independent evolution of functional progesterone withdrawal in primates and guinea pigs Evolution, Medicine and Public Health. 2013(1):273-88. doi: 10.1093/emph/eot022.
The Lateral Mesodermal Divide: an Epigenetic Model of the Origin of Paired Fins
​​​​​​​Nuño de la Rosa, L., G.B. Müller, and B.D. Metscher. 2014. The Lateral Mesodermal Divide: an Epigenetic Model of the Origin of Paired Fins. Evolution & Development 16(1): 38–48. doi:10.1111/ede.12061.

Evolutionary Novelty articles - Author O-Z

Evolution and morphogenetic rules: The shape of the vertebrate limb in ontogeny and phylogeny
Oster, G.F., N. Shubin, J.D. Murray, and P. Alberch. 1988. Evolution 42:862-884.
What Is Evolutionary Novelty? Process Versus Character Based Definitions
Peterson, T. and G.B. Müller. 2013. What Is Evolutionary Novelty? Process Versus Character Based Definitions. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution 320 (6): 345–350. doi:10.1002/jez.b.22508.
Deep homology and the origins of evolutionary novelty
Shubin, N., C. Tabin, and S. Carroll. 2009. Deep homology and the origins of evolutionary novelty. Nature 457:818-823.
First description of a musculoskeletal linkage in an adipose fin: Innovations for active control in a primitively passive appendage
Stewart, T.A. and  Hale, M.E. 2013. First description of a musculoskeletal linkage in an adipose fin: Innovations for active control in a primitively passive appendage. Proceedings of the Royal Society B. vol. 280, no. 1750, 20122159.
Evolution of a unique predatory feeding apparatus: functional anatomy, development and a genetic locus for jaw laterality in Lake Tanganyika scale-eating cichlids
Stewart, T.A. and Albertson, R.C. 2010. Evolution of a unique predatory feeding apparatus: functional anatomy, development and a genetic locus for jaw laterality in Lake Tanganyika scale-eating cichlids. BMC Biology 8:8.
The origins of adipose fins: an analysis of homoplasy and the serial homology of vertebrate appendages
Stewart, T.A., Smith, W.L. and Coates, M.I. 2014. The origins of adipose fins: an analysis of homoplasy and the serial homology of vertebrate appendages. Proceedings of the Royal Society B. vol 281, no 1781, 20133120.
Breaking evolutionary and pleiotropic constraints in mammals. On sloths, manatees and homeotic mutations
​​​​​​​Varela-Lasheras, I., Bakker A.J., van der Mije S.D., J.A.J. Metz, Van Alphen J., and F. Galis. 2011. Breaking evolutionary and pleiotropic constraints in mammals. On sloths, manatees and homeotic mutations. EvoDevo 2:11.
The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems
​​​​​​​Wagner, A. 2011. The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems. New York: Oxford University Press.
What is the promise of developmental evolution? Part I: Why is developmental biology necessary to explain evolutionary innovations?
​​​​​​​Wagner, G.P. 2000. What is the promise of developmental evolution? Part I: Why is developmental biology necessary to explain evolutionary innovations? Journal of Experimental Zoology (Mol Dev Evol) 288:95-98.
Homology, Genes and Evolutionary Innovation
​​​​​​​Wagner, Günter P. 2014. Homology, Genes and Evolutionary Innovation. Princeton NJ: Princeton University Press.
Evolutionary Innovations Overcome Ancestral Constraints: a Re-Examination of Character Evolution in Male Sepsid Flies (Diptera: Sepsidae)
​​​​​​​Wagner, G.P., and G.B. Müller. 2002. Evolutionary Innovations Overcome Ancestral Constraints: a Re-Examination of Character Evolution in Male Sepsid Flies (Diptera: Sepsidae). Evolution & Development 4(1): 1–6–discussion 7–8.
Evolutionary novelties
Wagner, G.P., and V.J. Lynch. 2010. Evolutionary novelties. Current Biology 20:R48-R52.
Evolution of mammalian pregnancy and the origin of the decidual stromal cell
​​​​​​​Wagner, G.P., Kin, K., Muglia, L. and Pavličev, M. 2014. Evolution of mammalian pregnancy and the origin of the decidual stromal cell. International Journal of Developmental Biology 58: 117-126  doi: 10.1387/ijdb.130335gw 

Evolvability articles

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Evolvability articles - Author A-D

An Introduction to Systems Biology: Design Principles of Biological Circuits
Alon, U. 2007. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall/CRC Mathematical & Computational Biology.
Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape
Álvarez-Buylla, E.R., Á. Chaos, M. Aldana, M. Benítez, Y. Cortes-Poza, C. Espinosa-Soto, D.A. Hartasánchez, R.B. Lotto, D. Malkin, G.J. Escalera Santos, and P. Padilla-Longoria. 2008. Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape. PLoS ONE 3(11):e3626.
Systems biology approaches to development beyond bioinformatics: nonlinear mechanistic models using plant systems
Álvarez-Buylla, E.R., J. Dávila-Velderrain, and J.C. Martínez-García. 2016. Systems biology approaches to development beyond bioinformatics: nonlinear mechanistic models using plant systems. BioScience 66:371–383.
Flower development as an interplay between dynamical physical fields and genetic networks
Barrio, R.Á., A. Hernández-Machado, C. Varea, J.R. Romero-Arias, and E.R. Álvarez-Buylla. 2010. Flower development as an interplay between dynamical physical fields and genetic networks. PLoS ONE 5(10): e13523.
Predicting patterns of long-term adaptation and extinction with population genetics
Bertram, J., K. Gomez, and J. Masel. 2017. Predicting patterns of long-term adaptation and extinction with population genetics. Evolution 71:204–214.
Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand
Bever, G., J. Gauthier, and G. Wagner. 2011. Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand. Evolution & Development 13:269-279.
Evolution and evolvability: celebrating Darwin 200
Brookfield, J.F.Y. 2009. Evolution and evolvability: celebrating Darwin 200. Biology Letters 5:44–46.
What evolvability really is
Brown, R.L. 2014. What evolvability really is. The British Journal for the Philosophy of Science 65:549–572.
Engineering and evolvability
Calcott, B. 2014a. Engineering and evolvability. Biology & Philosophy 29:293–313.
The creation and reuse of information in gene regulatory networks
Calcott, B. 2014b. The creation and reuse of information in gene regulatory networks. Philosophy of Science 81:879–90.
Decoupled ecomorphological evolution and diversification in Neogene-Quaternary horses
Cantalapiedra, J.L., J.L. Prado, M. Hernández Fernández, and M.T. Alberdi. 2017. Decoupled ecomorphological evolution and diversification in Neogene-Quaternary horses. Science 355:627-630.
Mechanical basis of morphogenesis and convergent evolution of spiny seashells
Chirat, R., D.E. Moulton, and A. Goriely. 2013. Mechanical basis of morphogenesis and convergent evolution of spiny seashells. Proceedings of the National Academy of Sciences USA 110:6015-6020.
Genomic Regulatory Systems: Development and Evolution
Davidson, E.H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego: Academic Press.
The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
Davidson, E.H. 2006. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. San Diego: Academic Press.
Gene regulatory networks and the evolution of animal body plans
Davidson, E.H., and D.H. Erwin. 2006. Gene regulatory networks and the evolution of animal body plans. Science 311:796-800.
Evolutionary innovation and stability in animal gene networks
Davidson, E.H., and D.H. Erwin. 2010. Evolutionary innovation and stability in animal gene networks. Journal of Experimental Zoology (Mol Dev Evol) 314B:182-186.
Mechanisms and selection of evolvability: experimental evidence
Díaz Arenas, C., and T.F. Cooper. 2013. Mechanisms and selection of evolvability: experimental evidence. FEMS Microbiology Reviews 37:572–582.
Overdominance interacts with linkage to determine the rate of adaptation to a new optimum
Draghi, J.A., and M.C. Whitlock. 2015. Overdominance interacts with linkage to determine the rate ofadaptation to a new optimum. Journal of Evolutionary Biology 28:95–104.
Mutational robustness can facilitate adaptation
Draghi, J.A., T.L. Parsons, G.P. Wagner, and J.B. Plotkin. 2010. Mutational robustness can facilitate adaptation. Nature 463:353-355.
Positional information in bits
Dubuis, J.O., G. Tkačik, E.F. Wieschaus, T. Gregor, and W. Bialek. 2013. Positional information in bits.Proceedings of the National Academy of Sciences USA 110:16301–8.

Evolvability articles - Author E-J

Temporal acuity and the rate and dynamics of mass extinctions
Erwin, D. H. 2014. Temporal acuity and the rate and dynamics of mass extinctions. Proceedings of the National Academy of Sciences of the United States of America, 111(9), 3203–3204. doi:10.1073/pnas.1400431111
Macroevolution of ecosystem engineering, niche construction and diversity
Erwin, D.H. 2008. Macroevolution of ecosystem engineering, niche construction and diversity. Trends in Ecology & Evolution 23:304–310.
Anatomical networks reveal the musculoskeletal modularity of the human head
Esteve-Altava, B., R. Diogo, C. Smith, J.C. Boughner, and D. Rasskin-Gutman. 2015. Anatomical networks reveal the musculoskeletal modularity of the human head. Scientific Reports 5:8298.
Pervasive robustness in biological systems
Felix, M.-A., and M. Barkoulas. 2015. Pervasive robustness in biological systems. Nature Reviews Genetics 16:483-496.
Non-adaptive origins of interactome complexity
Fernández, A. and M. Lynch. 2011. Non-adaptive origins of interactome complexity. Nature 474:502-505.
Mutation rules and the evolution of sparseness and modularity in biological systems
Friedlander, T., A.E. Mayo, T. Tlusty, and U. Alon. 2013. Mutation rules and the evolution of sparseness and modularity in biological systems. PLoS ONE 8:e70444.
The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network
Garfield, D.A., D.E. Runcie, C.C. Babbitt, R. Haygood, W.J. Nielsen, and G.A. Wray. 2013. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biology 11:e1001696.
The theory of facilitated variation
Gerhart, J., and M. Kirschner. 2007. The theory of facilitated variation. Proceedings of the National Academy of Sciences USA 104:8582-8589.
Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology
Griesemer, James 2013. Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):525-536.
Heuristic reductionism and the relative significance of epigenetic inheritance in evolution
Griesemer, J. 2011. Heuristic reductionism and the relative significance of epigenetic inheritance in evolution. In Epigenetics: Linking Genotype and Phenotype in Development and Evolution, eds. B. Hallgrímmson, and B.K. Hall, 14-40. Berkeley and Los Angeles: University of California Press.
Measuring and comparing evolvability and constraint in multivariate character
Hansen, T.F., and D. Houle. 2008. Measuring and comparing evolvability and constraint in multivariate characters. Journal of Evolutionary Biology 21:1201–1219.
Heritability is not evolvability
Hansen, T.F., C. Pelabon, and D. Houle. 2011. Heritability is not evolvability. Evolutionary Biology 38:258–277.
Engineering the Cambrian explosion: the earliest bioturbators as ecosystem engineers
Herringshaw, L.G., R.H.T. Callow, and D. McIlroy. 2017. Engineering the Cambrian explosion: the earliest bioturbators as ecosystem engineers. In: Brasier, A.T., D. McIlroy, and N. McLoughlin (eds) Earth System Evolution and Early Life. Geological Society, London, Special Publications, 448.18.
Comparing mutational variabilities
Houle, D., B. Morikawa, and M. Lynch. 1996. Comparing mutational variabilities. Genetics 143:1467-1483.
Smoothness within ruggedness: the role of neutrality in adaptation
Huynen, M.A., P.F. Stadler, and W. Fontana. 1996. Smoothness within ruggedness: the role of neutrality in adaptation. Proceedings of the National Academy of Sciences USA 93:397–401.
Heritability at the species level: analysis of geographic ranges of Cretaceous mollusks
Jablonski, D. 1987. Heritability at the species level: analysis of geographic ranges of Cretaceous mollusks. Science 238:360–363.
Dynamics of gene circuits shapes evolvability
Jiménez, A. J. Cotterell, A. Munteanu, and J. Sharpe. 2015, Dynamics of gene circuits shapes evolvability. Proceedings of the National Academy of Sciences USA 112:2103–2108.

Evolvability articles - Author K-N

The Origins of Order: Self-Organisation and Selection in Evolution
Kauffman, S.A. 1993. The Origins of Order: Self-Organisation and Selection in Evolution. New York: Oxford University Press.
Evolvability
Kirschner, M., and J. Gerhart. 1998. Evolvability. Proceedings of the National Academy of Sciences USA 95:8420-8427.
Biological robustness
Kitano, H. 2004. Biological robustness. Nature Reviews Genetics 5:826-837.
Genetic properties influencing the evolvability of gene expression
Landry, C.R., B. Lemos, S.A. Rifkin, W.J. Dickinson, and D.L. Hartl. 2007. Genetic properties influencing the evolvability of gene expression. Science 317:118-121.
Form and function in Evo Devo: historical and conceptual reflections
Laubichler, M.D. 2009. Form and function in Evo Devo: historical and conceptual reflections. In Form and Function in Developmental Evolution, eds. M.D. Laubichler, and J. Maienschein, 10-46. New York: Cambridge University Press.
The Genetic Basis of Evolutionary Change
Lewontin, R. 1974. The Genetic Basis of Evolutionary Change. New York: Columbia University Press.
Geometry shapes evolution of early multicellularity
Libby, E., W.C. Ratcliff, M. Travisano, and B. Kerr. 2014. Geometry shapes evolution of early multicellularity. PLoS Computational Biology 10:e1003803.
A mixability theory for the role of sex in evolution
Livnat, A., C. Papadimitriou, J. Dushoff, and M.W. Feldman. 2008. A mixability theory for the role of sex in evolution. Proceedings of the National Academy of Sciences USA 105:19803–19808.
Evolvability, dispositions, and intrinsicality
Love, A.C. 2003. Evolvability, dispositions, and intrinsicality. Philosophy of Science 70:1015-1027.
The frailty of adaptive hypotheses for the origins of organismal complexity
Lynch, M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proceedings of the National Academy of Sciences USA 104:8597-8604.
Genetics and Analysis of Quantitative Traits
Lynch, M., and B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates, Inc.
Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy
Lynch, V.J., Nnamani, M.C., Kapusta, A., Brayer, K., Plaza, S.L., Mazur, E.C., Emera, D., Sheikh, S.Z., Grützner, F., Bauersachs, S., Graf, A., Young, S.L., Lieb, J.D.., DeMayo, F.J., Feschotte, C., Wagner, G.P. 2015. Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy. Cell Reports  pii: S2211-1247(14)01105-X. doi: 10.1016/j.celrep.2014.12.052.
Robustness and evolvability
Masel, J. and M.V. Trotter. 2010. Robustness and evolvability. Trends in Genetics 26:406–414.
Is the genotype-phenotype map modular? A statistical approach using mouse quantitative trait loci data
Mezey, J.G., J.M. Cheverud, and G.P. Wagner. 2000. Is the genotype-phenotype map modular? A statistical approach using mouse quantitative trait loci data. Genetics 156:305-311.
From physics to development: The evolution of morphogenetic mechanisms
Newman, S.A. 2003. From physics to development: The evolution of morphogenetic mechanisms. In Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, eds. G.B. Müller, and S.A Newman, 221-239. Cambridge, MA: The MIT Press.
Physico-genetic determinants in the evolution of development
Newman, S.A. 2012. Physico-genetic determinants in the evolution of development. Science 338:217-219.
Form and function remixed: developmental physiology in the evolution of vertebrate body plans
Newman, S.A. 2014. Form and function remixed: developmental physiology in the evolution of vertebrate body plans. The Journal of Physiology 592: 2403–2412. doi: 10.1113/jphysiol.2014.271437
Biophysical and size-dependent perspectives on plant evolution
Niklas, K.J. 2013. Biophysical and size-dependent perspectives on plant evolution. Journal of Experimental Botany 64(15):4817-27. doi: 10.1093/jxb/ers379.
Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications
Niklas, K.J., S.E. Bondos, A.K. Dunker, and S.A. Newman. 2015. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Frontiers in Cell and Developmental Biology 3:8.

Evolvability articles - Author O-T

Evolution and morphogenetic rules: The shape of the vertebrate limb in ontogeny and phylogeny
Oster, G.F., N. Shubin, J.D. Murray, and P. Alberch. 1988. Evolution and morphogenetic rules: The shape of the vertebrate limb in ontogeny and phylogeny. Evolution 42:862-884.
The robustness and evolvability of transcription factor binding sites
Payne, J.L., and A. Wagner. 2014. The robustness and evolvability of transcription factor binding sites. Science 343:875–877.
Is evolvability evolvable?
Pigliucci, M. 2008. Is evolvability evolvable? Nature Reviews Genetics 9:75-82.
Emerging principles of regulatory evolution
Prud’homme, B., N. Gompel, and S.B. Carroll. 2007. Emerging principles of regulatory evolution. Proceedings of the National Academy of Sciences USA 104:8605–12.
Evolution of molecular error rates and the consequences for evolvability
Rajon, E. and J. Masel. 2011. Evolution of molecular error rates and the consequences for evolvability. Proceedings of the National Academy of Sciences USA 8:286–292.
Origins of multicellular evolvability in snowflake yeast
Ratcliff, W.C., J.D. Fankhauser, D.W. Rogers, D. Greig, and M. Travisano. 2015. Origins of multicellular evolvability in snowflake yeast. Nature Communications 6:6102.
Evolutionary Quantiative Genetics
Roff, D.A. 1997. Evolutionary Quantiative Genetics. New York: Chapman & Hall.
Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data
Serra, R., M. Villani, A. Graudenzi, and S.A. Kauffman. 2007. Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. Journal of Theoretical Biology 246:449-460.
Evolution, Development, and the Predictable Genome
Stern, D.L. 2011. Evolution, Development, and the Predictable Genome. Greenwood Village, CO: Roberts and Company Publishers.
Evolvability as a function of purifying selection in TEM-1 β-lactamase
Stiffler, M.A., D.R. Hekstra, and R. Ranganathan. 2015. Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell 160:882–892.
Population Genetics and Microevolutionary Theory
Templeton, A.R. 2006. Population Genetics and Microevolutionary Theory. Hoboken, NJ: John Wiley & Sons, Inc.
Criticality is an emergent property of genetic networks that exhibit evolvability
Torres-Sosa, C., S. Huang, and M. Aldana. 2012. Criticality is an emergent property of genetic networks that exhibit evolvability. PLoS Computational Biology 8:e1002669.

Evolvability articles - Author U-Z

General theory of genotype to phenotype mapping: derivation of epigenetic landscapes from N-node complex gene regulatory networks
Villarreal, C., P. Padilla-Longoria, and E.R. Álvarez-Buylla. 2012. General theory of genotype to phenotype mapping: derivation of epigenetic landscapes from N-node complex gene regulatory networks. Physical Review Letters 109:118102.
The role of robustness in phenotypic adaptation and innovation
Wagner, A. 2012. The role of robustness in phenotypic adaptation and innovation. Proceedings of the Royal Society B: Biological Sciences 279:1249–1258.
Robustness and Evolvability in Living Systems
Wagner, A. 2005. Robustness and Evolvability in Living Systems. Princeton: Princeton University Press.
The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems
Wagner, A. 2011. The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems. New York: Oxford University Press.
The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms
Wagner, G., and J. Zhang. 2011. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nature Reviews Genetics 12:204-213.
Perspective: complex adaptations and the evolution of evolvability
Wagner, G.P., and L. Altenberg. 1996. Perspective: complex adaptations and the evolution of evolvability. Evolution 50:967-976.
The red queen beats the jack-of-all trades: limitations on the evolution of phenotypic plasticity and niche breadth
Whitlock, M.C. 1996. The red queen beats the jack-of-all trades: limitations on the evolution of phenotypic plasticity and niche breadth. The American Naturalist 148:S65–S77.
Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth
Wilson, B.A., S.G. Foy, R. Neme, and J. Masel. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nature Ecology & Evolution. 1. doi:10.1038/s41559-017-0146. Published online: 24 April 2017.
Developmental constraints, generative entrenchment and the innate-acquired distinction 
Wimsatt, W.C. 1986. Developmental constraints, generative entrenchment and the innate-acquired distinction. In Integrating Scientific Disciplines, ed. W. Bechtel, 185-208. Dordrecht: Martinus Nijhoff.
Using false models to elaborate constraints on processes: blending inheritance in organic and cultural evolution 
Wimsatt, W.C. 2002. Using false models to elaborate constraints on processes: blending inheritance in organic and cultural evolution. Philosophy of Science 69:S12-S24.
Evolution and the Stability of Functional Architectures 
Wimsatt, William C. 2013. Evolution and the Stability of Functional Architectures. In Philippe Huneman (ed.), Functions: Selection and Mechanisms. New York: Springer. 19–41.
Generative entrenchment, modularity, and evolvability: when genic selection meets the whole organism
Wimsatt, W.C., and J. C Schank. 2004. Generative entrenchment, modularity, and evolvability: when genic selection meets the whole organism. In Modularity in Evolution and Development, eds. G Schlosser, and G. Wagner, 359-394. Chicago: University of Chicago Press.
Bias in the introduction of variation as an orienting factor in evolution
Yampolsky, L.Y. and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evolution & Development 3:73–83.
The evolutionary potential of phenotypic mutations
Yanagida, H., A. Gispan, N. Kadouri, S. Rozen, M. Sharon, N. Barkai, and D.S. Tawfik. 2015. The evolutionary potential of phenotypic mutations. PLoS Genetics 11: e1005445.
Development and the evolvability of human limbs
Young, N.M., G.P. Wagner, and B. Hallgrímsson. 2010. Development and the evolvability of human limbs. Proceedings of the National Academy of Sciences USA 107:3400–3405.
Coevolution drives the emergence of complex traits and promotes evolvability
Zaman, L., J.R. Meyer, S. Devangam, D.M. Bryson, R.E. Lenski, and C. Ofria. 2014. Coevolution drives the emergence of complex traits and promotes evolvability. PLoS Biology 12:e1002023.