Publications – Wagner Lab

2022

Wagner, G. P., Kshitiz, A. Dighe and A. Levchenko (2022). “The Coevolution of Placentation and Cancer.” Annu Rev Anim Biosci. 10: 1 – 15.21

2021

Zierden, H. C., J. I. Ortiz, K. DeLong, J. Yu, G. LI, P. Dimitron, S. Benspouda, V. Laney, A. Bailey, N. Anders, M. Scardina, M. Mahendroo, S. Mesiano, I. Burd, G. P. Wagner, J. Hanes and L. Ensign (2021). “Enhanced drug delivery to the reproductive tract using nanomedicine reveals new therapeutic options for prevention of preterm birth.” Science Transl. Med. 13: eabc6245.

Chavan, A. R., Griffith, O. W., Stadtmauer, D. J., Maziarz, J., Pavličev, M., Fishman, R., Koren, L., Romero, R., and G. P. Wagner. (2021). “Evolution of Embryo Implantation Was Enabled by the Origin of Decidual Stromal Cells in Eutherian Mammals.” Mol Biol Evol 38(3): 1060-1074.

McKenna, K. Z., G. P. Wagner and K. L. Cooper (2021). “A developmental perspective of homology and evolutionary novelty.” Curr Top Dev Biol 141: 1-38

Smith-Paredes, D., Griffith, O., Fabbri, M., Yohe, L., Blackburn, D. G., Siler, C. D., Bhullar, B.-A. S., Wagner, G. P. 2021 Hidden limbs in the “limbless skink” Brachymeles lukbani: developmental observations. Anatomy, 239: 693 – 703.

Lynch, V. J. and Wagner, G. P. 2021 Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11. J. exp. Zool.-B (Molecular and Developmental Evolution), 2021:1-10.

Stadtmauer, D. J. and Wagner, G. P. 2021. Single-cell analysis of prostaglandin E2-induced human decidual cell differentiation: a minimal ancestral deciduogenic signal. Biology of Reproduction, 2021: 1-18.

Hwang, J. Y., J. Maziarz, G. P. Wagner and J. J. Chung (2021). “Molecular Evolution of CatSper in Mammals and Function of Sperm Hyperactivation in Gray Short-Tailed Opossum.” Cells 10(5).

2020

DiFrisco, J., A. C. Love and G. P. Wagner (2020). “Character identity mechanisms: a conceptual model for comparative‑mechanistic biology.” Biology & Philosophy 35: 43 – 44.

Critchley, H. O. D., E. Babayev, S. E. Bulun, S. Clark, I. Garcia-Grau, P. K. Gregersen, A. Kilcoyne, J. J. Kim, M. Lavender, E. E. Marsh, K. A. Matteson, J. A. Maybin, C. N. Metz, I. Moreno, K. Silk, M. Sommer, C. Simon, R. Tariyal, H. S. Taylor, G. P. Wagner and L. G. Griffith (2020). “Menstruation: science and society.” Am J Obstet Gynecol 223(5): 624-664.

Rytkönen, K. T., Heinosalo, T, Mahmoudian, M., Xinghong Ma, X.-H., Perheentupa, A., Elo, A. L., Poutanen, M. and Wagner, G. P. 2020. Transcriptomic responses to hypoxia in endometrial and decidual stromal cells. Reproduction 160: 39-51.

Bergmann, P. J., G. Morinaga, E. S. Freitas, D. J. Irschick, G. P. Wagner and C. D. Siler (2020). “Locomotion and palaeoclimate explain the re-evolution of quadrupedal body form in Brachymeles lizards.” Proc Biol Sci 287(1938): 20201994.

Wagner, G. P., Kshitiz and A. Levchenko (2020). “Comments on Boddy et al. 2020: Available data suggest positive relationship between placental invasion and malignancy.” Evol Med Public Health 2020(1): 211-214.

DeLorenzo, L., A. Vander Linden, P. J. Bergmann, G. P. Wagner, C. D. Siler and D. J. Irschick (2020). “Using 3D-digital photogrammetry to examine scaling of the body axis in burrowing skinks.” J Morphol 281(11): 1382-1390.

Stadtmauer, D., Wagner, G. P. 2020. The Primacy of Maternal Innovations to the Evolution of Embryo Implantation. Integrative and Comparative Biology, 60(3): 742-752.

Stadtmauer, D., Wagner, G. P. 2020. Cooperative inflammation: the recruitment of inflammatory signals in marsupial and eutherian pregnancy. Journal of Reproductive Immunology: 137: 102626 NIHMS1544733

2019

Kshitiz Kz, Junaid Afzal, Jamie D. Maziarz, Archer Hamidzadeh, Cong Liang Eric M. Erkenbrack, Hong Nam, Jan-Dirk Haeger, Christiane Pfarrer, Thomas Hoang, Troy Ott, Thomas Spencer, Mihaela Pavličev, Douglas F. Antczak, Andre Levchenko, Günter P. Wagner 2019. Evolution or placental invasion and cancer metastasis are causally linked. Nature Ecology & Evolution, https://doi.org/10.1038/s41559-019-1046-4

Pavličev, M., Zupan, A. M., Barry, A., Walters, S., Milano, K. M., Kliman, H. J., Wagner, G. P. 2019. An experimental test of the ovulatory homolog model of female orgasm. PNAS, 116: 20267-20273.

Stewart, T. A., Liang, C., Cotney, J. L., Noonan, J. P., Sanger, T. J., Wagner, G. P. 2019 Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. Nature Communications: 10:3244.

Martin, J. F., Wagner, G. P. 2019. The origin of platelets enabled the evolution of eutherian placentation. Biology Letters, 15:20190374.

Griffith, O. W., Chavan, A. R., Pavlicev, M., Callahan, R., Maziarz, J., Wagner, G. P. 2019. Endometrial recognition of pregnancy occurs in the grey short tailed opossum (Monodelphis domestica). Roy. Soc. B: Biological Sciences, 286: 20190691. doi: 10.1098/rspb.2019.0691.

Wagner, G. P. 2019. Devo-Evo of cell types. In: The Evolutionary Developmental Biology – A Reference Guide, in press. Springer-Nature.

Wagner, G.P., Erkenbrack, E., Love, A. 2019. Stress-induced evolutionary innovation: mechanism for the origin of cell types. BioEssays, 41, e1800188.

2018

Rytkönen, K. T., E. M. Erkenbrack, M. Poutanen, L. L. Elo, M. Pavličev and G. P. Wagner 2018. “Decidualization of Human Endometrial Stromal Fibroblasts is a Multiphasic Process Involving Distinct Transcriptional Programs.” Reprod Sci: 1933719118802056

Pavličev, M., Wagner, G. P. 2018. Orgasm. In Encyclopedia of Reproduction, 2^nd Edition.

Pavličev, M., Wagner, G. P. 2018. Orgasm. In J. Vonk, T. K. Shackleford (eds.) Encyclopedia of Animal Cognition and Behavior. Springer-Nature.

Erkenbrack, E. M., J. D. Maziarz, O. W. Griffith, C. Liang, A. R. Chavan, M. C. Nnamani and G. P. Wagner 2018. “The mammalian decidual cell evolved from a cellular stress response.” PLoS Biol 16(8): e2005594.

Wagner, G. P., O. W. Griffith, P. J. Bergmann, G. Bello-Hellegouarch, T. Kohlsdorf, A. Bhullar and C. D. Siler 2018. “Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae).” J Morphol 279(8): 1104-1119.

Flatt, T., Wagner G. 2018. Canalization and Robustness. Oxford Bibliographies. DOI: 10.1093/OBO/9780199941728-0109

Wagner, G. P. 2018. Comparative Placentation-Mammals. In In M. K. Skinner (Ed.), Encyclopedia of Reproduction. vol. 2, pp. 455–461. Academic Press: Elsevier.

Griffith, O. W., Chavan, A. R., Romero, R., Wagner, G. P. 2018. Re Liu: inflammation came before implantation. PNAS, 115:E3-E4.

2017

Zhang, G, et al., 2017. Genetic associations with gestational duration and spontaneous preterm birth. New Engl. J. Med. 377:1156-1167

Chavan, A., Griffith, O., Wagner, G. P. 2017. The inflammation paradox in the evolution of mammalian pregnancy: turning a foe into a friend. Curr. Opinions in Genetics and Development, 47:24-32.

Wagner, G. P., Pavlicev, M. 2017. Origin, function and effect of female orgasm: all three are different. Exp. Zool. (Mol. Dev. Evol.) 328B:299-303.

Griffith, O. W., Chavan, A. R., Protopapas, S., Maziarz, J., Romero, R., Wagner, G. P. 2017. Embryo implantation evolved from an ancestral inflammatory attachment reaction. PNAS, 1701129114, , www.pnas.org/cgi/doi/10.1073/pnas.1701129114.

Wagner, G. P., Nnamani, M. C., Chavan, A. R., Maziarz, J., Protopapas, S., Condon, J., Romero, R. 2017. Evolution of gene expression in the uterine cervix related to steroid signaling: conserved features in the regulation of cervical ripening. Scientific Reports, 7:4439.

Wagner, G. P., Pavlicev, M. 2017. Origin, function and effect of female orgasm: all three are different. J. Exp. Zool. (Mol. Dev. Evol.) 328B:299-303

Pavlicev, M., Wagner, G. P., Chavan, A. R., Owens, K., Maziarz, J., Dunn-Fletcher, C., Kallapur, S. G., Muglia, L., Jones, H. 2017. Single-cell transcriptomics of the human placenta; inferring the cell communication network of the maternal-fetal interface. Genome Research, March27(3):349-361

Griffith, O. W., Wagner, G. P. 2017. The evolution and origin of vertebrate organs: the molecular processes that lead to the evolution of placentas. Nature Ecol. & Evol., article 0072.

Armstrong, D. L., […], Wagner, G. P., Romero, R., Wildman, D. E. 2017. The core transcriptome of mammalian placentas and the divergent expression with placental shape. Placenta 57: 71-78

2016

Arendt, D., Musser, J. M., […] Wagner, G. P. 2016. The origin and evolution of cell types. Nature Reviews Genetics, 17:744-757.

Park, Y.-W., Nnamani, M. C., Maziarz, J., Wagner, G. P. 2016. Cis-regulatory evolution of forkhead box O1 (FOXO1) expression, a terminal selector for decidual stromal cell type identity. Molecular Biology and Evolution, 33:3161-3169.

Pavlicev, M., Wagner, G. P. 2016.The evolutionary origin of female orgasm. J. exp. Zool. (Mol. Dev. Evol.) 326:326-337

Kin, K., Maziarz, J., Chavan, A. R., Kamat, M., Vasudevan, S., Birt, A., Emera, Lynch, V. J., Ott, T. L., Pavlicev, M., Wagner, G. P. 2016. The transcriptomic evolution of mammalian pregnancy: gene expression innovations in endometrial fibroblasts. Genome Biology and Evolution 8:2459-2473.

Nnamani. M. C., Ganguy, S., Erkenbrack, E. M., Lynch, V., Minoue, L., Tong, Y., Darling, H. L., Fuxreiter, M., Meiler, J., Wagner, G. P. 2016. A derived allosteric switch underlies the evolution of conditional cooperativity between HOXA11 and FOXO1. Cell Reports, 15:2097 – 2108.

Chavan, A. R., Wagner, G. P. 2016. The fetal-maternal interface of the nine-banded armadillo: endothelial cells of the maternal sinus are partially replaced by trophoblast. Zoological Letters, 2:11 DOI 10.1186/s40851-016-0048-1 (10 pages).

Stopper, G. F., Richards-Hrdlicka, K. L., Wagner, G. P. 2016. Hedgehog inhibition causes complete loss of limb outgrowth and transformation of digit identity in Xenopus tropicalis. J. exp. Zool. (Mol. Dev. Evol.) 326B: 110-124.

Chavan, A. R., Bhullar, B.-A., Wagner, G. P. 2016. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy. Placenta 40:40-51.

Wagner, G. P. 2016. What is “Homology Thinking” and what is it for? J. exp. Zool. (Mol. Dev. Evol.) 326B: 3-8

2015

Wagner, G. P. 2015. Homology and the evolutionary process: reply to Haig, Love and Brown on “Homology, Genes and Evolutionary Innovation.” Biol. & Phil. DOI: 10.1007/s10539-015-9492-0

Wagner, G. P. 2015. Evolutionary innovations and novelties: let us get down to business! Zoologischer Anzeiger, 256: 75-81.

Musser, J. M., Wagner G. P. 2015. Character trees from transcriptome data: origin and individuation of morphological characters and the so-called “species signal”. J. exp. Zool. (Mol. Dev. Evol.) DOI: 10.1002/jez.b.22636

Wagner, G. P. 2015. Homology in the age of developmental genomics. pp 25-43 in Volume 1 of A. Wanninger (ed.) Evolutionary Developmental Biology of Invertebrates. Springer Publishers, Vienna, New York.

Singarete, M. E., Grizante, M. B. Milograna, S. R., Nery, M. F. Kin, K., Wagner, G. P. and Kohlsdorf, T. 2015. Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles. Genetics and Molecular Biology, 38: 255-262.

Musser, J. M., Wagner, G. P., Prum, R. O. 2015. Nuclear b-catenin expression supports homology of feathers, avian scutate scales and alligator scales in early development. Evolution & Development, 17: 185-194.

Kin, K., Nnamani, M. C., Lynch, V. J., Michaelides, E., Wagner, G. P. 2015. Cell-type phylogenetics and the origin of endometrial stromal cells. Cell Reports, 10: 1398-1409.

Lynch, V. J., M. Nnamani, K. J. Brayer, D. Emera, J. O. Werheim, S. L. K. Pond, F. Grützner, S. Bauersachs, A. Graf, A. Kapusta, C. Feschotte, G. P. Wanger 2015. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Reports, 10: 1-11.

Liang, C., FANTOM consortium, Forrest, A. R. R., and Wagner G. P. 2015. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature Communications, 6:6066, doi: 10.1038/ncomm7066.

Wagner, G. P. 2015. Two rules for the detection and quantification of epistasis. Pp 145-158 in J. H. Moore, and S. M. Williams (eds.) Epistasis. Methods and Protocols. Methods in Molecular Biology 1253; Springer Science and Business Media, New York.

Wagner, G. P. 2015. Reinventing the organism: evolvability and homology in post-Dahlem evolutionary biology. Pp 327-342 in A. C. Love (ed.) Conceptual Change in Biology. Boston Studies in the Philosophy of History of Science 307. Springer Science and Business Media, Dordrecht.

2014

Pavličev, M., Wagner, G. P. 2014. Evolutionary systems biology: shifting focus to the context-dependency of genetic effects. Pp 91-107 in L. B. Martin, C. K. Ghalambor and H. A. Woods (eds.) Integrative Organismal Biology, John Wiley & Sons, New Jersey.

Wagner, G. P. 2015. Reinventing the organism: evolvability and homology in post-Dahlem evolutionary biology. Pp 327-342 in A. C. Love (ed.) Conceptual Change in Biology. Boston Studies in the Philosophy of History of Science 307. Springer Science and Business Media, Dordrecht

Wagner, G. P. 2015. Two rules for the detection and quantification of epistasis. Pp 145-158 in J. H. Moore, and S. M. Williams (eds.) Epistasis. Methods and Protocols. Methods in Molecular Biology 1253; Springer Science and Business Media, New York.

D’Souza, A. W., Wagner, G. P. 2014. Malignant cancer and invasive placentation: a case for positive pleiotropy between endometrial and malignancy phenotypes. Evolution, Medicine and Public Health, [2014] pp 136-145.

Wagner, G. P. 2014. Homology, Genes and Evolutionary Innovation. Princeton University Press.

Kin, K., Marzias, J., Wagner, G. P. 2014. Immunohistological study of the endometrial stromal fibroblasts in the opossum, Monodelphis domestica: evidence for homology with eutherian stromal fibroblasts. Biology of Reproduction, 90:111, 1-12.

Watson, R., Wagner, G. P., Weinreich, D., Pavličev, M., Mills, R. 2014. The evolution of phenotypic correlations and ‘developmental memory.’ Evolution, 68:1124-1138.

2013

Nnamani, M., Plaza, S., Romero, R., Wagner, G. P. 2013. Evidence for the independent evolution of functional progesterone withdrawal in primates and guinea pigs. Evolution, Medicine and Public Health, [2013] pp 273-288.

Wagner, G. P., K. Kin and V. J. Lynch 2013. A model based criterion for gene expression calls using RNA-seq data. Theory in Biosciences, 132: 159-164. (cited in F1000)

Pavlicev, M., Wagner, G. P., Noonan, J., Hallgrimsson, B., Cheverud, J. 2013. Genomic correlates of relationship-QTL involved in fore vs. hindlimb divergence in mice. Genome Biology and Evolution: 5: 1926-1936.

2012

Crow, K. D., Smith, C. D., Cheng, J.-F., Wagner, G. P., Amemiya, C. T. 2012. An independent genome duplication inferred from Hox Paralogs in the American Paddlefish – a representative basal ray-finned fish and important comparative reference. Genome Biology and Evolution 4: 937-953.

Wagner, G. P., K. Kin, and V. J. Lynch 2012. Measurement of RNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences, 131: 2181-285.

Larsson, H., and G. P. Wagner 2012. Testing inferences in developmental evolution. J. Exp. Zool. (Mol. Dev. Evol) 318: 489-500.

Wagner, G. P., Y. Tong, D. Emera, and R. Romero 2012. An evolutionary test of the isoform switching hypothesis of functional progesterone withdrawal for parturition: humans have a weaker repressive effect of PR-A than mice. J. Perinat. Med., 40:345-351.

Emera, D., and G. P. Wagner 2012. Transformation of a transposon into a derived PRL promoter in humans with function during human pregnancy. Proc. Natl. Acad. Sci. USA, 109:11246-11251.

Padua, M. B., V. J. Lynch, N, V. Alvarez, M. A. Garthwalte, T. G. Golos, F. W. Balzer, S. Kalkunte, S. Sharma, G. P. Wagner, and P. J. Hansen 2012. ACPE (Uteroferrin); Phylogeny of an ancient and conserved gene expressed in the endmetrium of mammals. Biol. Reprod., 86(4):123-131.

Emera. D, and G. P. Wagner 2012. Transposable element recruitment in the mammalian placenta: impacts and mechanisms. Briefings in Functional Genomics, 11:267-276.

Brandley, M. C., R. L. Young, D. L. Warren, M. B. Thompson and G. P. Wagner 2012. Uterine gene expression in the live-bearing lizard Chalcides ocellatus, reveals convergence of spamate reptile and mammalian pregnancy mechanisms. Genome Biol. & Evol., 4(3):394-411.

Pavlicev, M., and G. P. Wagner 2012. A model of developmental evolution: selection, pleiotropy, compensation. Trends in Ecology and Evolution, 27(6):316-322.

Emera, D, C. Casola, V. J. Lynch, D. E. Wildman, D. Agnew, and G. P. Wagner 2012. Convergent evolution of endometrial prolactin expression in primates, mice and elephants through the independent recruitment of transposable elements. Mol. Biol. Evol. 29:239-247.

Rüffler, C., J. Hermisson, and G. P. Wagner 2012. Evolution of functional specialization and division of labor. Proc. Natl. Acad. Sci. USA, 109:E326-325.

Emera, D., R. Romero, and G. P. Wagner 2012. Evolution of menstruation: a case of genetic assimilation. BioEssays, 34:26-35. (F1000)

2011

Lynch, V.J., G. May, and G. P. Wagner 2011. Evolution of gene regulation via adaptive divergence of a phospho-switch in the mammalian transcription factor CEBPB. Nature, 480:383-386.

Lynch, V. J., R. Leclerc, G. May, and G. P. Wagner 2011. Transposon-mediated gene regulatory network innovation during the evolution of pregnancy in mammals. Nature Genetics, 43:1154-1159.

Wang, Z., R. L. Young, H. Xue and G. P. Wagner 2011. Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds. Nature, 477:583-586.

Bever, G. S., J. A. Gauthier, and G. P. Wagner 2011. Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand. Evolution & Development 13:269-279.

Young, R. L., and G. P. Wagner 2011. Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations. J. Exp. Zool. (Mol. Dev. Evol), 316B:165-170.

Rorick, M. M. and G. P. Wagner 2011. Protein structural modularity and robustness are associated with evolvability. Genome Biology and Evoultion, in press.

Houle, D., C. Pelabon, G.P. Wagner, and T.F. Hansen 2011. Measurement and meaning in biology. Quart. Rev. Biol., 86:3-34.

Pavlicev, M., J.M. Cheverud, and G.P. Wagner 2011. Evolution of adaptive phenotypic variation by direct selection for evolvability. Proc. Roy. Soc. B, published online.

Young, R.L., G.S. Bever, Z. Wang, G.P. Wagner 2011. Identity of the avian wing digits: problems resolved and unresolved. Dev. Dyn., 240: 1042-1053.

Wagner, G.P., J. Zhang 2011. The pleiotropic structure of the genotype phenotype map: the evolvability of complex orangisms. Nature Reviews Genetics, 12: 204-213.

Bever, G.S., J.A. Gauthier, and G. P. Wagner 2011. Finding the frame shift: digit loss, developmental variability, and the origin of the avian hand. Evolution & Development, 13:269-279.

Young, R. L. and G.P. Wagner. 2011. Why ontogenetic homology criteria can be misleading: Lessons from digit identity transformations. Journal of Experimental Biology (Molecular and Developmental Evolution) 316B: 165-170.

V.J. Lynch and G.P. Wagner 2011. Revisiting a classic example of transcription factor functional equivalence: are Eyeless and Pax6 functionally equivalent or divergent?. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 316B: 93-98. doi: 10. 1002/jez.b.21373

Lynch, V. J. and G. P. Wagner 2011. Revisiting a classical example of transcription factor functional equivalence: are eyeless and Pax6 functionally equivalent or divergent? J. Exp. Zool. PartB (Mol. Dev. Evol), 316B:93-98.

Brayer, K. J., V. J. Lynch, G. P. Wagner 2011. Evolution of HoxA11/Foxo1a interaction in mammals: a role for intramolecular regulation. Proc. Natl. Acad. Sci. USA, 108: E414-20.

Young, R. L., G. S. Bever, Z. Wang, G. P. Wagner 2011. Identity of the avian wing digits: problems resolved and unresolved. Dev. Dyn., 240:1042-1053.

2010

Pavlicev, M., A. Le Rouzic, J. M. Cheverund, G. P. Wagner, and T. F. Hansen 2010. Directionality of epistasis in a murine intercross population. Genetics, 185:1489-1505.

Lynch, V. and G.P. Wagner 2010. Did egg-laying Boas reak Dollo’s law? Phylogenetic evidence for reversal to oviparity in sand boas. Evolution, 64: 207.

Rorick, M. M. and G. P. Wagner 2010. The origin of conserved protein domains and amino acid repreats via adaptive competition for control over amino acid residues. J. Mol. Evol., 70: 29-43

Wagner, G. P. 2010. The measurement theory of fitness. Evolution, 64:1358-1376.

Draghi, J., T. Parsons, G. P. Wagner and J. Plotkin 2010. Mutational robustness can increase or decrease evolvability. Nature, 463: 353-355.

Kohlsdorf, T., V. J. Lynch, M. Rodrigues, M. Brandley, and G. P. Wagner 2010. Data and data interpretation in the study of limb evolution: a reply to Galis et al., on the re-evolution of digits in the lizard genus Bachia. Evolution, 64:2477-2485.

Young, N. M., G. P. Wagner, and B. Hallgímsson 2010. Long legs and short arms: development and the evolvability of human limbs. Proc. Natl. Acad. Sci. USA, 107: 3400-3405.

Wagner, G. P. and V. J. Lynch 2010. Evolutionary novelties. Curr. Biology 20:R48-52.

Wagner, G. P. 2010. Evolvability: the missing piece in the neo-Darwinian synthesis. Pp 197-213 in M. A. Bell, D. J. Futuyma, Walter F. Eanes and J. S. Levinton (eds.) Evolution Since Darwin; the first 150 years. Sinaurer Associates, Sunderland MA.

Pavlicev, M., A. Le Rouzic, J. M. Cheverud, G. P. Wagner, and T. F. Hansen 2010. Directionality of epistasis in a murine intercross population. Genetics, 185:1489-1505.

Wagner, G. P. and J. Draghi 2010. Evolution of evolvability. Pp. 379-399 in M. Pigliucci and Müller G. B. (eds.) Evolution – The Extended Evolutionary Synthesis. MIT Press.

2009

Young, R. L., V. Caputo, M. Giovanotti, T. Kohlsdaorf, A. O. Vargas, G. May and G. P. Wagner 2009. Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift. Evolution and Development, 11: 647-658.

Pavlicev, M., G. P. Wagner, and J. M. Cheverud 2009. Measuring evolutionary constraints through the dimensionality of the phenotype: adjusted bootstrap method to estimate rank of phenotypic covariance matrices. Evol. Biol. 36: 339-353.

Lynch, V. J., B. Gellersen, and G. P. Wagner 2009 HoxA-11 interacts with FOXO1A to regulate decidual prolactin expression: non-equivalence with HoxA-10. PLoS ONE, 4(9):e6845.

Otto, W., P. F. Stader, F. López-Gialdéz, J. P. Townsend, V. J. Lynch, and G. P. Wagner 2009. Measuring transcription factor binding site turnover: a maximum likelihood approach using phylogenies. Genome Biology and Evolution, 1:85-98.

Pavlicev, M., J. M. Cheverud, and G. P. Wagner 2009. Measuring morphological integration using eigen-value variance. Evol. Biol., 36:157-170.

Lynch, V. J. and G. P. Wagner 2009. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes. PLoS Genetics, 5:e1000349.

Crow, K., C. T. Amemiya, J. J. Roth, and G. P. Wagner 2009. Hypermutability of HoxA-13A and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa. Evolution, 63:1574-1592.

Vargas, A. O. and G. P. Wagner 2009. Cartilage formation and digit identity in bird evolution and Cyclopamine-treated wings. Evolution and Development, 11:163-169.

Draghi, J., and G. P. Wagner 2009. Evolution of evolvability in a gene network model. J. Evol. Biol., 22:599-611.

Lynch, V. J., B. Gellersen, and G. P. Wagner 2009 HoxA-11 interacts with FOXO1A to regulate decidual prolactin expression: non-equivalence with HoxA-10. PLoS ONE, 4(9):e6845.

2008

Kohlsdorf, T, V. Lynch, G. F. Stopper, K. Takahashi, G. P. Wagner 2008: What happens to a “limb gene” when limb are lost? Molecular evolution of Hoxa-13 in squamata. J. Mol. Evol., 67: 581-593.

Schosser, G., and G. P. Wagner 2008: A simple model of co-evolutionary dynamics caused by epistatic interactions. J. theor. Biol., 250:48-65.

Draghi, J., G. P. Wagner 2008: A geometric model of the evolution of evolvability. Evolution, 62: 307-315.

Wagner, G. P., and V. J. Lynch 2008 The Gene regulatory logic of transcription factor evolution. Trends in Ecology and Evolution, 23: 377-385.

Lynch, V. J. and G. P. Wagner 2008 Resurrecting the role of transcription factor change in the evolution of development. Evolution, 62:2131-2154.

Lynch, V. J., A. Tanzer, Y. Wang, F. C. Leung, B. Gellersen, and G. P. Wagner 2008 Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proc. Natl. Acad. Sci. USA, 105:14928-14933.

Wagner, G. P., J. P. Kenny-Hunt, M. Pavlicev, J. R. Peck, D. Waxman and J. Cheverund 2008. Pleiotropic scaling of gene effects an the “cost of complexity.” Nature, 452: 470-472.

Wagner, G. P., J. P. Kenny-Hunt, M. Pavlicev, J. R. Peck, D. Waxman and J. Cheverund 2008, Reply to Hermisson and McGregor. Nature, 452: 470-472.

Vargas, O. A., T. Kohlsdorf, J. F. Fallon, J. VandenBrooks, and G. P. Wagner 2008. The evolution of HoxD-11 expression in the bird wing: insights from Alligator mississippiensis. PLoS ONE, 3:e3325.

2007

Wagner, G. P. 2007. The current state and the future of developmental evolution. Pp 525-545 in Maienschein and Laubichler (eds) The History of Evolutionary Developmental Biology. Dibner workshop, MIT Press, Boston, MA.

Wagner, G. P. and H. Larsson 2007 Fins/limbs in the study of evolutionary novelties. Pp 49-61 in B. K. Hall (ed.) Fins into Limbs. Harvard University Press.

Conant, G. C., G. P. Wagner and P. F. Stadler 2007. Modeling amino acid substitution patterns in orthologous and paralogous genes. Mol Phyl. & Evol., 216:743-754.

Stopper, G. F. and G.P. Wagner 2007. Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: parallels to natural digit reduction in urodeles. Developmental Dynamics, 236:321-331.

Wagner, G. P., and A. M. Pyle 2007. Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution. Novartis Foundation workshop, pp116-125.

Wagner, GP, W. Otto, V. Lynch, and PF Stadler 2007. A stochastic model for transcription factor binding site abundance. J. theor, Biol., 247:544-553.

Wagner, G. P. 2007 The developmental genetics of homology. Nature Reviews Genetics 8: 473-479.

Wagner, G. P., M. Pavlicev and J. Cheverud 2007. The road to modularity. Nature Reviews Genetics, 8:921-931.

2006

Crow K. D., Stadler PF, Lynch V, Amemiya C, Wagner GP (2006) The “fish specific” Hox cluster duplication is coincidental with the origin of teleosts. Mol Biol. & Evol, 23:121-136.

Crow K. D. and Wagner G.P. 2006 What is the role of genome duplication in the evolution of complexity and diversity? Mol. Biol. & Evol, 23:887-897.

Herrmann, H. and GP Wagner 2006 Conceptual continuity as a mode of understanding complex systems. Complexity, 11:20-24.

Wagner, GP 2006. How wide and how deep is the divide between population genetics and developmental evolution? A review of Ron Amundsons book “The Changing role of the Embryo in Evolutionary Thought.” Biol. & Phil., published on line DOI: 10.1007/s10539-005-9011-9.

Kohlsdorf, T and G. P. Wagner 2006 Evidence for the reversibility of digit loss: a phylogenetic study of limb evolution in the genus Bachia (Gymnophthalmidae: Squamata). Evolution 60: 1896-1912.

Hansen, T. F., J. M. Álvarez-Castro, A. J. R. Carter, J. Hermisson and G. P. Wagner 2006. Evolution of genetic architecture under directional selection. Evolution, 60:1523-36.

Prohaska, S. J., P. F. Stadler and G. P. Wagner 2006 Evolutionary genomics of Hox gene clusters. In S. Papageorgiou (ed.) Hox Gene Expression. LANDES BIOSCIENCE Editions (ISBN: 1-58706-071-X), published on line.

Dunn, C., and G. P. Wagner 2006. The evolution of colony-level development in Siphonophora (Cnidaria: Hydrozoa). Dev. Genes & Evol., 16:743-754.

Lynch, V. J., J. J. Roth and G. P. Wagner 2006 Adaptive evolution of Hox-gene homeodomains after cluster duplications. BMC Evolutionary Biology, 6:86.

2005

Hermisson, J., and G. P. Wagner 2005 Evolution of phenotypic robustness. Pp 47-69 in E. Jen (ed.) Robust design: a repertoire for Biology, Ecology and Engineering, Oxford University Press.

Wagner, G. P., J. Mesey, and Raffaele Callabretta 2005 Natural selection and the origin of modules. Pp 33-49 in W. Callebaut and D. Raskin-Gutman (eds.) Modularity: understanding the development and evolution of complex systems. MIT Press.

Wagner, G. P., K. Takahashi, V. Lynch, S. J. Prohaska, C. Fried, P. F. Stadler, and C. Amamiya 2005 Molecular evolution of duplicated ray finned fish HoxA cluster: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. J. Mol. Evol., 60:665-676.

Metscher, B. D., K. Talkahashi, K. Crow, C. Amemiya, D. Nonaka, and G. P. Wagner 2005: Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray finned fish, Polyodon spathula: implications for the origin of the tetrapod limbs. Evolution and Development, 7:186-195.

Wagner, G. P. and V. J. Lynch 2005. Molecular evolution of evolutionary novelties: the vagina and uterus of placental mammals. J. Exp. Zool. Part B: Mol. Dev. Evol.: 304B:580-592.

Roth, J. J., M. Breitenbach and G. P. Wagner 2005. Repressor domain and nuclear localization signal of the murine HoxA11 protein are located in the homeodomain: no evidence for role of poly-Alanine stretches in transcriptional repression. J. Exp. Zool. Part B: Mol. & Dev. Evol. 304B:468-475.

Stopper, G. F. and G. P. Wagner 2005. Of chicken wings and frog legs: a smorgasbord of evolutionary variation in mechanisms of tetrapod limb development. Dev. Biol., 288:21-39.

Wagner, G. P. 2005. The developmental evolution of avian digit homology: an update. Theory in BioSci.,124:165-183.

Lynch, VJ and GP Wagner 2005 The birth of the uterus. Nat. Hist. Magazine: December2005/January 2006, 36-41

2004

Wagner, G. P., and J. 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.

Bagheri-Chaichian, H., and G. P. Wagner 2004 Evolution of dominance in metabolic pathways. Genetics 168: 1713-1735.

G. Schlosser and G. P. Wagner (eds.) 2004 Modularity in Development and Evolution. Chicago University Press, Chicago, IL.

Prohaska, S. J., C. Fried, C. Flamm, G. P. Wagner, and P. F. Stadler 2004 Surveying plylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol. Phylog. Evol. 31: 581-604.

Chiu^,C-h., K. Dewar, G. P. Wagner, K. Takahashi, F. Ruddle, C. Ledje, P. Bartsch, J.-L. Scemama, E. Stellwag, C. Fried, S. J. Prohaska, P. F. Stadler, C. T. Amemiya 2004 Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res. 14:11-17.

Prohaska, S. J., C. Fried, C. T. Amemiya, F. H. Ruddle, G. P. Wagner, and P. F. Stadler 2004 Shark HoxN cluster is homologous to the human HoxD cluster. J. Mol. Evol.,58:212-217.

Wagner, G. P. and M. D. Laubichler 2004 Rupert Riedl and the re-synthesis of evolutionary and developmental biology: body plans and evolvability. J Exp Zool B: Mol Dev Evol. 302B:92-102.

Stadler, P. F., C. Fried, S. J. Prohaska, W. J. Bailey, B. Y. Misof, F. H. Ruddle, and G. P. Wagner 2004. Evidence for independent Hox gene duplications in the hagfish lineage: A PCR based gene inventory of Eptatretus stoutii. Mol Phyl Evol. 32:686-694.

Lynch, V., Roth, J. J., Takahashi, K., Dunn, C., Nonaka, D. F., Stopper, G., and Wagner, G. P. 2004 Adaptive evolution of Hoxa-11 and Hoxa-13 at the origin of the uterus in mammals. Proc. Roy. Soc. London B, 271: 2201-2207.

Hermisson, J., and G. P. Wagner 2004 The population genetic theory of hidden variation and genetic robustness. Genetics, 168:2271-2284.

Wagner, G. P., C. Fried, S. J. Prohaska and P. F. Stadler 2004. Divergence of conserved non-coding sequences: rate estimates and relative rate tests. Mol. Biol. Evol. 21:2116-2121.

Campos, P. R. A., V. M. de Olivera, G. P. Wagner, and P. F. Stadler 2004. Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners. J. theor. Biol, 231:197-202.

Shpak, M., P. Stadler, G. P. Wagner, L. Altenberg 2004. Simon-Ando decomposability and fitness landscapes. Theor. Biosci. 123:139-180.

2003

Schwenk, K., and G. P. Wagner 2003 Constraint. Pp 52-61 in B. K. Hall and W. Olson (Eds.) Keywords in Evolutionary Developmental Biology. Harvard University Press, Cambridge MA.

Müller, G. B., and G. P. Wagner 2003 Innovation. Pp 218-227 in B. K. Hall and W. Olson (Eds.) Keywords in Evolutionary Developmental Biology. Harvard University Press, Cambridge MA.

Hermisson, J., T. Hansen and G. P. Wagner 2003. Epistasis in polygenic trairs and the evolution of genetic architecture. Am. Nat, 161:708-734.

Wagner, G. P. and P. F. Stadler 2003 Quasi-independence, homology and the unity of type: a topological theory of characters. J. Theor. Biol., 220:505-527.

Bagheri-Chaichian, H., J., Hermisson, J. R. Vaisnys, and G. P. Wagner 2003 Effects of epistasis on phenotypic robustness in metabolic pathways. Math. Biosci. 184:27-51.

Schwenk, K., and G. P. Wagner 2003. The relativism of constraints on phenotypic evolution. In press in M. Pigliucci and K. Preston (eds.) The Evolutionary Biology of Complex Phenotypes.

Galis, F., G. P. Wagner and E. L. Jokusch 2003 Why is limb regeneration possible inamphibians but not in reptiles, birds and mammals? Evol. & Dev. 5:208-220.

de Visser J. A. G., M., J. Hermisson, G. P. Wagner, L. Ancel-Meyers, H. Bagheri-Chaichian, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, W. Fontana, G. Gibson, T. F. Hansen, D. Krakauer, R. C. Lewontin, C. Ofria, S. H. Rice, G. von Dassow, A. Wagner, and M. C. Whitlock 2003 Evolution and detection of genetic robustness. Evolution, 57: 1959-1972.

Larsson, HCE and GP Wagner 2003 Old morphologies misinterpreted. Trends in Ecology and Evolution 18(1): 10

Wagner, G. P., C. Amemiya, and F. Ruddle 2003: Hox cluster duplications and the opportunity for evolutionary novelties. Proc. Natl. Acad. Sci. 100: 14603-14606.

Wagner, G. P. and H. C. E. Larsson 2003 What is the promise of developmental evolution? III The crucible of developmental evolution. J. Exp. Zool. Part B: Mol Dev Evol. 300:1-4

Wagner, G. P. 2003 Evolutionary Genetics: the nature of hidden genetic variation unveiled. Current Biology 13:, R958-960.

Calabretta, R., A. DiFerdinando, G. P. Wagner and D. Parisi 2003: What does it take to evolve behaviorally complex organisms? Biosystems 69:245-262.

Wagner, W. and G. P. Wagner 2003. Examining the modularity concept in evolutionary psychology: the levels of genes, mind and culture. J. Cultural and Evolutionary Psychology, 3-4:135-165.

2002

Stadler, B. M. R., P. F. Stadler, M. Shpak, and G. P. Wagner 2002 Recombination spaces, metrics and pretopologies. Z Phys. Chem., 216: 1-18.

Wagner, G. P. 2002 Homology. Pp 497-501 in Mark Pagel (ed. in chief) The Oxford Encyclopedia of Evolution. Oxford University Press, Oxford and New York.

Wagner, G. P., 2002. Correlated selection response. Pp 469-471 in S. Brenner and J. H. Miller (eds.) Encyclopedia of Genetics, Academic Press, San Diego.

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). Evol & Dev., 4:1-6.

Wagner, G. P., and C.-h. Chiu 2002 Genetic and epigenetic factors in the origin of tetrapod limbs. Pp 265-285 in G. B. Müller and S. Newman (eds.) Origin of Form. MIT press, Cambridge MA.

Carter, A. J. R. and G. P. Wagner 2002 Evolution of functionally conserved enhancers can be accelerated in large populations: a population genetic model. Proc. Roy Soc., Biol. 169: 953-960.

Chiu, C.-h., C. Amemiya, K. Dewar, C.-B. Kim, F. Ruddle and G. P. Wagner 2002. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci., 99:5492-5497.

Larsson, C. E., and G. P. Wagner 2002 The pentadactyl ground state of the avian wing. J Exp Zool (Mol & Dev Evol) 294: 146-151.

Wagner, G. P. 2002 To Epistasis and Beyond! Review of: Wolf et al. (eds) Epistasis and the Evolutionary Process. Evolution 56: 852-855.

Wagner, G. P. 2002 Die Rolle der Homologa als Bausteine der Anpassung – eine Hypothese. Pp 219-228 in G. Schlosser and M. Weingarten (eds.) Formen der Erklärung in der Biologie. Vol 2, Studien zur Theorie der Biologie. Verlag für Wissenschaft und Bildung, Berlin (translation of Wagner 1995, Jb. Geol. & Paläont., 195, 279-288).

2001

Laubichler and Wagner, 2001 How molecular is molecular developmental biology? A reply to Alex Rosenberg’s reductionism redux: computing the embryo. Biol. and Phil., 16:53-68.

Hansen, T. F., and G. P. Wagner 2001. Modeling genetic architecture: a multilinear theory of gene interaction. Theor. Pop. Biol., 59:61-86.

Wagner, G. P.(Ed.) 2001 The Character Concept in Evolutionary Biology. Academic Press, San Diego, CA.

Hansen, T. F., and G. P. Wagner 2001 Epistasis and the mutation load: a measurement-theoretical approach. Genetics, 158:477-485.

Stadler, B. M. R., Staler, P., Wagner, G. P., and Fontana, W. 2001. The topology of the possible: formal spaces underlying pattern of evolutionary change. J theor Biol., 213:241-274.

Wagner, G. P. and Chiu, Chi-hua 2001. The tetrapod limb: a hypothesis on its origin. J exp Zool (Mol Dev Evol), 291, 226-240.

Schwenk, K, and Wagner, G. P. 2001 Function and the evolution of phenotypic stability: connecting pattern with process. Am. Zool., 41, 552-563.

Wagner, G. P. 2001. What is the promise of developmental evolution? Part II: a causal explanantion of evolutionary innovations may be impossible. J. Exp. Zool. (Mol. Dev. Evol.) 291, 305-309

2000

Wagner, G. P., and K. Schwenk 2000. Evolutionarily stable configurations: functional integration and the evolution of phenotypic stability. Evolutionary Biology, 31, 155-217.

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

Laubichler, M. D. nd G. P. Wagner 2000. Organism and character decomposition: steps towards an integrative theory of biology. Phil Sci: 67(Proceedings). S289-S300,.

Chiu, C., C. T. Amemiya. J. Carr, J. Bhargava, J. K. Hwang, C. S. Shashikant, F. H. Ruddle and G. P. Wagner 2000. A recombinogenic targeting method to modify large inserts for Cis-regulatory analysis in transgenic mice: Construction and expression of a 100 kb, zebrafish Hoxa-11b-lacZ reporter gene. Dev. Genes and Evol. 210, 105-109.

Shpak,, M., and G. P. Wagner 2000. Asymmetry of configuration space induce by unequal crossover: implications for a mathematical theory of evolutionary innovation. Artificial Life, 6: 25-43.

Stadler, P. F., R. Seitz, and G. P. Wagner 2000. Population dependent Fourier decomposition of fitness landscapes over recombination spaces. Bull. Math. Biol., 62: 399-428.

Wagner, G. P., and M. D. Laubichler 2000: Character identification in evolutionary biology: the role of the organism. Theory in Biosciences, 119:20-40.

Gibson, G. and G. P. Wagner 2000: Canalization in Evolutionary Genetics: a Stabilizing Theory? BioEssays, 22:372-380.

Calabretta, R., S. Nolfi, D. Parisi, and G. P. Wagner 2000. Duplication of modules facilitates the evolution of functional specialization . Artificial Life, 6: 69-84.

Mezey, J., J. Cheverud and G. P. Wagner 2000. Is the genotype-phenotype map modular? A statistical approach using mouse QTL data. Genetics, 156:305-311.

Chiu, C.-H., D. Nonaka, L. Xue, C. T. Amemiya and G. P. Wagner 2000. Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition. Mol. Phyl. Evol., .17, 305-316.

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

Kim, C.-B., C. Amemiya, W. Bailey, K. Kawasaki, J. Mezey, W. MillerII, S. Minoshima, N. Shimizu, G. P. Wagner, and F. Ruddle 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proc. Natl. Acad. Sci. USA, 97, 1655-1660.

Wagner, G. P. 2000. What is the promise of developmental evolution? Part I: Why is developmental biology necessary to explain evolutionary innovations? J Exp. Zool. (Mol. Dev. Evol), 288, 95-98.

1999

Wagner, G. P. 1999: The quantitative genetic theory of evolvability. In A. S. Wu (ed.) Proceeding of the �99 Genetic and Evolutionary Computation Conference. Workshop Prog. Pp 47-50.

Wagner. G. P. 1999. A research program for testing the biological homology concept. Pp 125-134 In: B. K. Hall (ed.) Homology. Novartis Symposium # 222. J Wiley, Chichester.

Wagner, G. P., and J. Gauthier 1999. 1,2,3 = 2,3,4: a solution to the problem of the homology of the digits in the avian hand. PNAS, 96, 5111-5116.

Wagner, G. P., C. Chiu, and T. F. Hansen 1999. Is Hsp-90 a regulator of evolvability? J. Exp. Zool. (Mol. Dev. Evol.), 285:116-118.

Wagner, G. P., P. A. Kahn, M. J. Blanco, B. Y. Misof, and R. A. Liversage 1999. Evolution of Hoxa-11 expression in amphibians: is the urodele autopodium an innovation? Am. Zool., 39:686-694.

Wagner G.P. and P.F. Stadler 1999. Complex Adaptations and the Structure of Recombination Spaces. In: C.L. Nehaniv and M. Ito, eds., Algebraic Engineering, World Scientific Press, pp. 96–115.

1998

Blanco, M. J., B. Y. Misof, and G. P. Wagner 1998. Heterochronic differences of Hoxa-11 expression of Xenopus fore- and hind limb development: evidence for lower limb identity for the anuran ankle bones. Development Genes and Evolution, 208:175-187.

Calabretta, R., Nolfi, S., Parisi, D., and Wagner, G. P. 1998a. Emergence of functional modularity in robots. In Pfeifer, R., Blumberg, B., Meyer, J.-A., and Wilson, S.W. eds. From Animals to Animats 5, pp. 497-504. Cambridge, Mass.: MIT Press.

Calabretta, R., Nolfi, S., Parisi, D., and Wagner, G. P. 1998b. A case study of the evolution of modularity: towards a bridge between evolutionary biology, artificial life, neuro- and cognitive science. In Adami, C., Belew, R. Kitano, H., and Taylor, C. eds. Proceedings of the Sixth International Conference on Artificial Life, pp. 275-284. Cambridge, Mass.: MIT Press.

Stadler, P. F. and G. P. Wagner 1998. The algebraic theory of recombination spaces. Evolutionary Computation, 5, 241-275.

Wagner, G. P. 1998 Complexity Matters. Science 279, 1158-1159.

Wagner, G. P., M. D. Laubichler, and H. Bagheri-Chaichian 1998. Genetic measurement theory of epistatic effects. Genetica, 102/103: 569-580.

1997

Baatz, M. and G. P. Wagner 1997. Adaptive inertia caused by hidden pleiotroic effects. Theor. Population Biology, 51, 49-66.

Bagheri-Chaichian, H., G. P. Wagner 1997. Representational issues in the evolution of physiological adaptations. S European Journal for Semiotic Studies 9, 321-353.

Bailey, W., J. Kim, G. P. Wagner, and F. Ruddle 1997: Phylgenetic reconstruction of Hox Cluster duplications. Molecular Biology and Evolution, 14, 843-853.

Calabretta, R. C., G. P. Wagner, S. Nolfi, and D. Parisi 1997. Evolutionary mechanisms for the origin of modular design in arificial neural networks. Proceedings of the Int. Conf. On Complex Systems, Nashua, NH 21-26 September 1997.

Wagner, G. P. 1997. The structure of biological concepts and its relation to the dynamics of biological organizations. S European Journal for Semiotic Studies, 9, 299-320.

Wagner, G. P., G. Booth and H. Homayoun-Chaichian 1997. A Population Genetic Theory of Canalization. Evolution, 51, 329-347.

1996

Gitchoff, P. and G. P. Wagner 1996. Recombination induced hypergraphs: A new approach to mutation-recombination isomorphism. Complexity, 2, 37-43.

Misof, B. Y., M. J. Blanco and G. P. Wagner 1996. A PCR-survey of Hox genes of the zebrafish: new sequences and evolutionary implications. J. Exp. Zool., 274, 193-206.

Misof, B. Y. And G. P. Wagner 1996: Evidence for four Hox Clusters in the killifish, Fundulus heteroclitus. Molecular Phylogenetics and Evolution, 5, 309-322.

Müller, G. B. and G. P. Wagner 1996. Homolgy, Hox genes, and developmental integration. Am. Zool., 36, 4-13.

Wagner, G. P. 1996. Apparent stabilizing selection and the maintenance of neutral genetic variation. Genetics, 143, 617-619.

Wagner, G. P. 1996: Homologues, natural kinds and the evolution of modularity. Am. Zool., 36, 36-43.

Wagner, G.P. and L. Altenberg 1996. Complex adaptations and the evolution of evolvability. Evolution, 50, 967-976.

1995

Wagner, G. P. 1995. Adaptation and the modular design of organisms. pp 317-328 in F. Mor�n, A. Mor�n, J. J. Merelo and P. Chac�n (eds.) Advances in Artificial Life. Berlin. Springer Verl.

Wagner, G. P. 1995. The biological role of homologues: A building block hypothesis. Jb. Geol. & Paläont., 195, 279-288.

1994

Krall, P. And G. P. Wagner 1994. Accumulation of unconditionally conservative characters in organismal evolution. Center for Computational Ecology-Tech Report # 21.

Fontana, W, G. P. Wagner, and L. W. Buss 1994: Beyond digital naturalism. Artificial Life, 1, 211-227.

Wagner, A. and G. P. Wagner 1994: Epistasis can facilitate the evolution of reproductive isolation by peak shifts: A two-locus two-allele model. Genetics, 138, 533-545.

Wagner, G. P. 1994. The dialog between evolutionary biology and computer science. In: W. Wieser, “Die Evolution der Evolutionstheorie”, Spectrum Verlag, Munich, Germany, pp 221-233.

Wagner, G. P. 1994: Evolution and function of the chitin system. In: B. Schierwater, B. Streit, G. P. Wagner and R. DeSalle (Eds.) “Molecular Approaches in Ecology and Evolution.” Birkhäuser Verl., Basel, pp 559-577.

Wagner, G. P. 1994: Homology and the mechanisms of development. In: B. K. Hall (ed.) “Homology: The Hierarchical Basis of Comparative Biology.” Academic Press, San Diego, pp 273-299.

Wagner, A., Blackstone, N., Cartwright, P., Dick, M., Misof, B., Snow, P., Wagner, G. P., Bartels, J., Murtha, M., Pendelton, J., 1994: Surveys of gene families using Polymerase Chain Reaction: PCR selection and PCR drift. System. Biol., 43, 250-261.

Wagner, G. P. and Laubichler, 1994: Kontext und Organisation: Commentary on E. Mayr: Evolution – Grundfragen und Mißverständnisse. Ethik und Sozialwissenschaften, 261-263.

1993

Wagner, G. P. and P. Krall 1993: What is the difference between models of error thresholds and Muller’s ratchet? J. Math. Biol., 32, 33-44.

Wagner, G. P., J. Lo, R. Laine, and M. Almeder, 1993: Chitin in the epidermal cuticle of a vertebrate (Paralipophrys trigloides, Blenniidae, Teleostei). Experientia, 49, 317-319.

Wagner, G. P., and B. Y. Misof 1993: How can a character be developmentally constrained despite variation in developmental pathways? J. evol. Biol., 6, 449-455.

1992

Misof, B. Y. and G. P. Wagner 1992: Regeneration in Salaria pavo (Blenniidae, Teleostei): Histogenesis of the regenerating pectoral fin suggests different mechanisms for morphogenesis and structural maintenance. Anatomy and Embryology, 186, 153-165.

Rienesl, J. and G. P. Wagner 1992: Constancy and change of basipodial variation patterns: a comparative study of crested and marbled newts and their natural hybrids. J. Evol. Biol., 5, 307-324.

Wagner, G. P. and K. W. Kratky 1992: A probabilistic model for the discrimination between periodic and non-periodic series of events and its relevance for the problem of inductive support. Evolution and Cognition, 2, 1-21.

Wagner, G. P. and B. Y. Misof 1992: Evolutionary modification of regenerative capability in vertebrates: a comparative study on Teleost pectoral fin regeneration. J. exp. Zool., 261, 62-78.

1991

Müller, G. B. and G. P. Wagner 1991: Novelty in evolution: restructuring the concept. Ann. Rev. Ecol. System., 22, 229-256.

Wagner, G. P. and M. Almeder 1991: Epigenetic control of pectoral fin web shape in Lipophrys canevae (Blenniidae, Telseostei). Experientia, 47, 737-738.

1990

Brandstätter, R., B. Misof, C. Pazmandi, and G. P. Wagner 1990: Micro-anatomy of the pectoral fin in blennies (Blenniini, Blennioidea, Teleostei). J. Fish Biology, 37, 729-743.

Vogl, C., and G. P. Wagner 1990: Interspecific variability in randomly evolving clades: Models for testing hypotheses on the relative evolutionary flexibility of quantitative traits. Syst. Zool., 39, 715-731.

Wagner, G.P. 1990: A comparative study of morphological integration in Apis mellifera. Zeitschrift für zoologische Systematik und Evolutionsforschung, 28, 48-61.

Wagner, G. P. 1990: Der Gen-Selektionismus: Grundlagen, Grenzen und Alternativen. Wiener Studien zur Wissenschaftstheorie 3, 222-223.

Wagner, G. P. 1990: The domestication of replicators: a neo-Darwinian commentary on the concept of replicator selection. Evolutionary Trends in Plants 4, 71-73.

Wagner, G. P., and W. Gabriel 1990: Quantitative variation in finite parthenogenetic populations: what stops Muller’s ratchet in the absence of recombination? Evolution, 44, 715-731.

1989

Arnold, S. J., P. Alberch, V. Csanyi, R. C. Dawkins, S. B. Emerson, B. Fritzsch, T. J. Horder, J. Maynard-Smith, M. J. Starck, E. S. Vrba, G. P. Wagner, and D. B. Wake 1989: How do complex Organisms Evolve? In: D. B. Wake and G. Roth (eds.) Complex organismal Functions: Integration and Evolution in Vertebrates. Dahlem Konferenzen, J. Wiley & Sons, pp 403-433.

Bürger, R., G.P.Wagner, und F. Stettinger 1989: How much heritable variation can be maintained in finite populations by mutation selection balance? Evolution, 43, 1748-1766.

Cheverud, J. M., G. P. Wagner, and M. M. Dow 1989: Methods for the comparative analysis of variation patterns. Syst. Zool. 38, 201-213.

Rienesl, J., und G. P. Wagner 1989: The basipodial variation patterns in sympatric crested and marbled newts (Triturus c. cristatus, Triturus m. marmoratus) and their natural hybrid. Verh. d. Dtsch. Zool. Ges. 82, 264.

Wagner, G. P. 1989: The biological homology concept. Annual Reviews in Ecology and Systematics, 20, 51-69.

Wagner, G.P. 1989: Multivariate mutation-selection balance with constrained pleiotropic effects. Genetics, 122, 223-234.

Wagner, G.P. 1989: The origin of morphological characters and the biological basis of homology. Evolution, 43, 1157-1171.

Wagner, G. P. 1989: Pectoral fin regeneration in ground fish. Verh. d. Dtsch. Zool. Ges. 82, 255-256.

Wagner, G.P. 1989: The variance allocation hypothesis of stasis and punctuation. In: P.Hoyningen-Huene/F.M.Wuketits (eds.) Molecular Biology and Organisms. Problems of reductionisms and system theory in the life sciences. Dortrecht and Boston: D.Reidel, pp 161-185.

1988

Dammasch, I.E., G.P. Wagner und J.R. Wolff 1988: Selfstabilization of neuronal networks II. Stability conditions for synaptogenesis. Biol. Cybern. 58, 149-158.

Gabriel, W., G.P. Wagner 1988: Parthenogenetic populations can remain stable in spite of high mutation rate and random drift. Naturwiss. 75, 204-205.

Wagner, G.P. 1988: Der Realitätsanspruch des Genkonzepts. In: E.Oeser, und E. Bonnet (Eds.) Das Realismusproblem. Wien: Edition S, pp 239-250.

Wagner, G.P. 1988: The gene and its phenotype. Biol. and Phil. 3, 105-115.

Wagner, G.P. 1988: The influence of variation and of developmental constraints on the rate of multivariate phenotypic evolution. J.Evol.Biol. 1, 45-66.

Wagner, G.P. 1988: The significance of developmental constraints for phenotypic evolution by natural selection. In: G.de Jong (Ed.) Population genetics and evolution, Heidelberg-Berlin-New York: Springer, 222-229.

Wagner, G.P. 1988: The vexing role of replicators in evolutionary change. Biol. and Phil. 3, 232-236.

1987

Wagner, G.P. 1987: Der Passungsbegriff und die logische Struktur der evolutionären Erkenntnistheorie. In: R.Riedl und F.M.Wuketits (Hg.) Die Evolutionäre Erkenntnistheorie. Berlin-Hamburg: Parey Verl., pp 64-72.

Wagner, G.P. 1987: Über die begrenzte Steuerbarkeit historischer Prozesse: Ein Argument aus der Systemtheorie der Evolution. In: R.Ellermann, U.Opolka (Eds.) Was bringen uns die Theorien selbstorganisierender Prozesse? COMDOK-Verlagsabteilung, pp. 41-54.

Wagner, G.P. und G.Ackermann 1987: Der Beitrag der Wahrscheinlichkeitstheorie zur Begründung der Evolutionären Erkenntnistheorie. In: R.Riedl und E.Bonnet (Eds.) Entwicklung der Evolution�ren Erkenntnistheorie. Wien: Edition S, pp 113-124.

1986

Dammasch, I.E., G.P. Wagner, und J.R.Wolff 1986: Selfstabilization of neuronal networks I. The compensation algorithm for synaptogenesis. Biol.Cybern. 54, 211-222. Wagner, G.P. 1986: Evolution der Evolutionsfähigkeit. In: Dress, A., H. Hendrichs, G. Küppers (Eds.): Selbstorganisation. München-Zürich: Piper, pp. 121-147.

Wagner, G.P. 1986: The systems approach: An interface between developmental and population genetic aspects of evolution. In: Patterns and Processes in the history of life. Dahlem Workshop Report, Life Sci. 36, Springer Verl., pp. 149-165.

Wagner, G.P., S. Eins und J.R. Wolff 1986: Tangential oragnization of infragranular fiber-plexus in rat cerebral cortex. Acta Anatomica 126, 1-12.

1985

Wagner, G.P. 1985: The adaptive significance of developmental constraints. Proc. of the International Symposium on Evolution and Morphogenesis. Prag: Academia Verl., pp 97-103.

Wagner, G.P. 1985: Evolution of morphological integration at the subspecific level in Apis mellifera. Verh. Dtsch. Zool. Ges. 78, 270.

Wagner, G.P. 1985: Über die populationsgenetischen Grundlagen einer Systemtheorie der Evolution. In: J.Ott, G.P.Wagner und F.M.Wuketits (Eds.): Evolution, Ordnung und Erkenntnis. Hamburg-Berlin: Parey, pp 97-111.

Wagner, G.P. und R. Bürger 1985: On the evolution of dominance modifiers II: A non-equilibrium approach to the evolution of genetic systems. J.theor.Biol. 113, 475-500.

Wagner, G.P. und J.R. Wolff 1985: Small lesions in the primary visual cortex of rats cause a specific reorganization of associational connections. Cell Tissue Res. 242, 357-364.

1984

Dammasch, I.E. und G.P.Wagner 1984: On the properties of randomly connected McCulloch-Pitts networks: Differences between input-constant and input-variant networks. Cybernetics and Systems 15, 91-117.

Wagner, G.P. 1984: Coevolution of functionally constrained characters: Prerequisites for adaptive versatility. BioSystems 17, 51-55.

Wagner, G.P. 1984: The logical basis of evolutionary epistemology. In: Wuketits, F.M. (Ed.): Concepts and Approaches in Evolutionary Epistemology. Boston: D. Reidel: pp 285-307. Wagner, G.P. 1984: On the eigenvalue distribution of genetic and phenotypic dispersion matrices: Evidence for a nonrandom organization of quantitative character variation. J.Math.Biol. 21, 77-95.

1983

Wagner, G.P. 1983: On the necessity of a systems theory of evolution and its population genetic foundation: Comments on Dr. Regelmann’s article. Acta Biotheor. 32, 223-226.

Wagner, G.P. 1983: Über die logischen Grundlagen der evolutionären Erkenntnistheorie. In: Lorenz, K. und F.M.Wuketits (Eds.) Die Evolution des Denkens. München: Piper Verl. pp 199-214.

Wagner, G.P., W.H. Oertel und J.R. Wolff 1983: Entorhinal lesions result in shrinkage of the outer molecular layer of rat dentate gyrus leading subsequently to an apparent increase of glutamate decarboxylase and cytochome oxidase activities. Neuroscience Letters 39, 255-260.

Wolff, J.R. und G.P.Wagner 1983: Selforganization in synaptogenesis: Interaction between the formation of excitatory and inhibitory synapses. In: Basar, E., H. Flohr, H.Haken und A.J. Mandell (Eds.): Synergetics of the Brain. Berlin- Heidelberg-New York: Springer. pp. 50-59.

1982

Wagner, G.P. 1982: The logical structure of irreversible systems-transformations: A theorem concerning Dollo’s law and chaotic movement. J. theor. Biol. 96, 337-346.

Wagner, G.P. 1982: On the evolution of multistability in the genome. Prog. Cybern. Systemsres. 9, 283-388.

Wagner, G.P., U.H. Wiese und J.R. Wolff 1982: Antinoradrenergic drugs do not interfere with the development of callosal connections in the rat. Experientia 38, 1218-1219.

Wagner, G.P., und J.R. Wolff 1982: Topography orientation and density of intracortical connections in the adult rat. Verh. Anat. Ges. 76, 451-452.

1981

Wagner, G.P. 1981: Feedback-selection and the evolution of modifiers. Acta Biotheoretica 30, 79-102.

Wagner, G.P. 1981: Komponenten des Informationsbegriffs. Phil. Nat. 18, 301-313.

1980

Wagner, G.P. 1980: Empirical information about the mechanism of typogenetic evolution. Naturwiss. 67, 258-259.

Wagner, G.P. 1980: Gerichtete Selektion erzeugt Instabilitäten in der strukturellen Organisation des Genoms. In: Jensen, H.J. (Ed.): Kybernetik 1980, München-Wien: Oldenburg. pp 31-34.