M. A. Félix, Evolution in developmental phenotype space, Curr Opin Genet Dev, vol.22, p.22925969, 2012.

M. Barkoulas, J. S. Van-zon, J. Milloz, A. Van-oudenaarden, and M. A. Félix, Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation, Dev Cell, vol.24, p.23328399, 2013.

S. B. Carroll, Evolution at two levels: on genes and form, PLoS Biol, vol.3, 2005.
DOI : 10.1371/journal.pbio.0030245
URL : https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0030245&type=printable

C. I. Swanson, N. C. Evans, and S. Barolo, Structural rules and complex regulatory circuitry constrain expression of a Notch-and EGFR-regulated eye enhancer, Dev Cell, vol.18, p.20230745, 2010.
DOI : 10.1016/j.devcel.2009.12.026
URL : https://doi.org/10.1016/j.devcel.2009.12.026

C. I. Swanson, D. B. Schwimmer, and S. Barolo, Rapid evolutionary rewiring of a structurally constrained eye enhancer, Curr Biol, vol.21, p.21737276, 2011.

J. Erceg, T. E. Saunders, C. Girardot, D. P. Devos, L. Hufnagel et al., Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity, PLoS Genet, vol.10, p.1004060, 2014.

D. L. Stern, Evolutionary developmental biology and the problem of variation, Evolution, vol.54, p.11005278, 2000.

M. D. Shapiro, M. E. Marks, C. L. Peichel, B. K. Blackman, K. S. Nereng et al., Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks, Nature, vol.428, p.15085123, 2004.

N. Gompel, B. Prud'homme, P. J. Wittkopp, V. A. Kassner, and S. B. Carroll, Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila, Nature, vol.433, p.15690032, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00310898

A. P. Mcgregor, V. Orgogozo, I. Delon, J. Zanet, D. G. Srinivasan et al., Morphological evolution through multiple cis-regulatory mutations at a single gene, Nature, vol.448, p.17632547, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00169725

B. B. Tuch, D. J. Galgoczy, A. D. Hernday, H. Li, and A. D. Johnson, The evolution of combinatorial gene regulation in fungi, PLoS Biol, vol.6, p.38, 2008.

H. Chung, D. W. Loehlin, H. D. Dufour, K. Vaccarro, J. G. Millar et al., A single gene affects both ecological divergence and mate choice in Drosophila, Science, vol.343, p.24526311, 2014.

A. P. Gasch, A. M. Moses, D. Y. Chiang, H. B. Fraser, M. Berardini et al., Conservation and evolution of cis-regulatory systems in ascomycete fungi, PLoS Biol, vol.2, 2004.

A. Tanay, A. Regev, and R. Shamir, Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast, Proc Natl Acad Sci U S A, vol.102, p.15883364, 2005.

L. Arnoult, K. F. Su, D. Manoel, C. Minervino, J. Magrina et al., Emergence and diversification of fly pigmentation through evolution of a gene regulatory module, Science, vol.339, pp.1423-1426, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00862170

P. J. Wittkopp, Variable gene expression in eukaryotes: a network perspective, J Exp Biol, vol.210, p.17449821, 2007.

E. Hoyos, K. Kim, J. Milloz, M. Barkoulas, J. B. Pénigault et al., Quantitative variation in autocrine signaling and pathway crosstalk in the Caenorhabditis vulval network, Curr Biol, vol.21, p.21458263, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00587094

X. Wang and H. Chamberlin, Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-28 ovo gene, Genes Dev, vol.16, p.12231624, 2002.

X. Wang and H. M. Chamberlin, Evolutionary innovation of the excretory system in Caenorhabditis elegans, Nat Genet, vol.36, p.14758362, 2004.

M. Félix, Evolution of developmental mechanisms in nematodes, J Exp Zool (Mol Dev Evol), vol.28, pp.3-18, 1999.

I. Nuez and M. Félix, Evolution of susceptibility to ingested double-stranded RNAs in Caenorhabditis nematodes, PLoS One, vol.7, p.22253787, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00666012

Q. Wei, Y. Shen, X. Chen, Y. Shifman, and R. E. Ellis, Rapid creation of forward-genetics tools for C. briggsae using TALENs: lessons for nonmodel organisms, Mol Biol Evol, vol.31, pp.468-473, 2014.

C. Frokjaer-jensen, Exciting prospects for precise engineering of Caenorhabditis elegans genomes with CRISPR/Cas9, Genetics, vol.195, p.24190921, 2013.

D. J. Dickinson, J. D. Ward, D. J. Reiner, and B. Goldstein, Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination, Nat Methods, vol.10, p.23995389, 2013.

C. Chen, L. A. Fenk, and M. De-bono, Efficient genome editing in Caenorhabditis elegans by CRISPRtargeted homologous recombination, Nucleic Acids Res, vol.41, p.193, 2013.

J. A. Arribere, R. T. Bell, B. X. Fu, K. L. Artiles, P. S. Hartman et al., Efficient marker-free recovery of custom genetic modifications with CRISPR/Cas9 in Caenorhabditis elegans, Genetics, vol.198, pp.837-846, 2014.

C. Mello and A. Fire, Caenorhabditis elegans Modern Biological Analysis of an Organism, Epstein HF, Shakes DC, pp.451-482, 1995.

A. Paix, Y. Wang, H. E. Smith, C. Y. Lee, D. Calidas et al., Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 Sites in Caenorhabditis elegans, Genetics, vol.198, p.25249454, 2014.

C. Frokjaer-jensen, M. W. Davis, C. E. Hopkins, B. J. Newman, J. M. Thummel et al., Single-copy insertion of transgenes in Caenorhabditis elegans, Nat Genet, vol.40, pp.1375-1383, 2008.

L. D. Stein, Z. Bao, D. Blasiar, T. Blumenthal, and M. R. Brent, The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics, PLoS Biol, vol.1, pp.166-192, 2003.

K. Kiontke, N. P. Gavin, Y. Raynes, C. Roehrig, F. Piano et al., Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss, Proc Natl Acad Sci, vol.101, p.15184656, 2004.

M. Félix, Genomes: a helpful cousin for our favourite worm, Curr Biol, vol.14, p.14738755, 2004.

K. Kiontke, M. Félix, M. Ailion, M. V. Rockman, C. Braendle et al., A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits, BMC Evol Biol, vol.11, p.339, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00654214

A. Mortazavi, E. M. Schwarz, B. Williams, L. Schaeffer, I. Antoshechkin et al., Scaffolding a Caenorhabditis nematode genome with RNA-seq, Genome Res, vol.20, pp.1740-1747, 2010.

A. Raj, S. A. Rifkin, E. Andersen, and A. Van-oudenaarden, Variability in gene expression underlies incomplete penetrance, Nature, vol.463, pp.913-918, 2010.

T. Gregor, H. G. Garcia, and S. C. Little, The embryo as a laboratory: quantifying transcription in Drosophila, Trends Genet, vol.30, p.25005921, 2014.

P. W. Sternberg, Vulval development, WormBook, The C. elegans Research Community, 2005.

M. Félix and M. Barkoulas, Robustness and flexibility in nematode vulva development, TIG, vol.28, pp.185-195, 2012.

B. J. Hwang and P. W. Sternberg, A cell-specific enhancer that specifies lin-3 expression in the C. elegans anchor cell for vulval development, Development, vol.131, p.14660442, 2004.

A. M. Saffer, D. H. Kim, A. Van-oudenaarden, and H. R. Horvitz, The Caenorhabditis elegans synthetic multivulva genes prevent ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF, PLoS Genet, vol.7, 2011.

J. Liu, P. Tzou, R. J. Hill, and P. W. Sternberg, Structural requirements for the tissue-specific and tissuegeneral functions of the C. elegans epidermal growth factor LIN-3, Genetics, vol.153, p.10545457, 1999.

K. Kiontke, A. Barrière, I. Kolotuev, B. Podbilewicz, R. J. Sommer et al., Trends, stasis and drift in the evolution of nematode vulva development, Curr Biol, vol.17, p.18024125, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00200635

M. Félix, Cryptic quantitative evolution of the vulva intercellular signaling network in Caenorhabditis, Curr Biol, vol.17, p.17240335, 2007.

H. Tian, B. Schlager, H. Xiao, and R. J. Sommer, Wnt signaling induces vulva development in the nematode Pristionchus pacificus, Curr Biol, vol.18, pp.142-146, 2008.

X. Wang and R. J. Sommer, Antagonism of LIN-17/Frizzled and LIN-18/Ryk in nematode vulva induction reveals evolutionary alterations in core developmental pathways, PLoS Biol, vol.9, p.1001110, 2011.

W. M. Winston, C. Molodowitch, and C. P. Hunter, Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1, Science, vol.295, pp.2456-2459, 2000.

M. Dichtel-danjoy and M. Félix, The two steps of vulval induction in Oscheius tipulae CEW1 recruit common regulators including a MEK kinase, Dev Biol, vol.265, p.14697357, 2004.

A. E. Friedland, Y. B. Tzur, K. M. Esvelt, M. P. Colaiacovo, G. M. Church et al., Heritable genome editing in C. elegans via a CRISPR-Cas9 system, Nat Methods, vol.10, p.23817069, 2013.

C. Braendle, C. F. Baer, and M. A. Félix, Bias and evolution of the mutationally accessible phenotypic space in a developmental system, PLoS Genet, vol.6, p.20300655, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00497202

A. J. Walhout, P. C. Van-der-vliet, and H. T. Timmers, Sequences flanking the E-box contribute to cooperative binding by c-Myc/Max heterodimers to adjacent binding sites, Biochim Biophys Acta, vol.1397, p.9565685, 1998.

C. A. Grove, D. Masi, F. Barrasa, M. I. Newburger, D. E. Alkema et al., A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors, Cell, vol.138, pp.314-327, 2009.

E. K. Farley, K. M. Olson, W. Zhang, A. J. Brandt, D. S. Rokhsar et al., Suboptimization of developmental enhancers, Science, vol.350, pp.325-328, 2015.
DOI : 10.1126/science.aac6948
URL : https://science.sciencemag.org/content/sci/350/6258/325.full.pdf

M. Z. Ludwig, C. Bergmann, N. H. Patel, and M. Kreitman, Evidence for stabilizing selection in a eukaryotic enhancer element, Nature, vol.403, p.10676967, 2000.

S. Fisher, E. A. Grice, R. M. Vinton, and S. L. Bessling, Conservation of RET regulatory function from human to zebrafish without sequence similarity, Science, vol.312, p.16556802, 2006.

E. E. Hare, B. K. Peterson, V. N. Iyer, R. Meier, and M. B. Eisen, Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation, PLoS Genet, vol.4, p.1000106, 2008.

M. Paris, T. Kaplan, X. Y. Li, J. E. Villalta, S. E. Lott et al., Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression, PLoS Genet, vol.9, p.24068946, 2013.

J. R. True and E. S. Haag, Developmental system drift and flexibility in evolutionary trajectories, Evol Dev, vol.3, p.11341673, 2001.
DOI : 10.1046/j.1525-142x.2001.003002109.x
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1525-142x.2001.003002109.x

S. Small, A. Blair, and M. Levine, Regulation of even-skipped stripe 2 in the Drosophila embryo, EMBO J, vol.11, p.1327756, 1992.

M. Z. Ludwig, A. Palsson, E. Alekseeva, C. M. Bergman, J. Nathan et al., Functional evolution of a cis-regulatory module, PLoS Biol, vol.3, 2005.

X. Wang, J. F. Greenberg, and H. M. Chamberlin, Evolution of regulatory elements producing a conserved gene expression pattern in Caenorhabditis, Evol Dev, vol.6, p.15230964, 2004.

A. Barrière, K. L. Gordon, and I. Ruvinsky, Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration, PLoS Genet, vol.8, p.23028368, 2012.

A. Barrière and I. Ruvinsky, Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes, PLoS Genet, vol.10, p.24968346, 2014.

M. Z. Ludwig, . Manu, R. Kittler, K. P. White, and M. Kreitman, Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness, PLoS Genet, vol.7, p.22102826, 2011.

A. Barrière, K. L. Gordon, and I. Ruvinsky, Distinct functional constraints partition sequence conservation in a cis-regulatory element, PLoS Genet, vol.7, 2011.

C. D. Arnold, D. Gerlach, D. Spies, J. A. Matts, Y. A. Sytnikova et al., Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution, Nat Genet, vol.46, pp.685-692, 2014.

M. Lynch, The evolution of genetic networks by non-adaptive processes, Nat Rev Genetics, vol.8, p.17878896, 2007.

T. R. Sorrells and A. D. Johnson, Making sense of transcription networks, Cell, vol.161, pp.714-723, 2015.

S. Brenner, The genetics of Caenorhabditis elegans, Genetics, vol.77, p.4366476, 1974.

A. Mathelier, X. Zhao, A. W. Zhang, F. Parcy, and R. Worsley-hunt, JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles, Nucleic Acids Res, vol.42, pp.142-147, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00943558

J. V. Turatsinze, M. Thomas-chollier, M. Defrance, and J. Van-helden, Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules, Nat Protoc, vol.3, pp.1578-1588, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01624305

A. Medina-rivera, M. Defrance, O. Sand, C. Herrmann, and J. A. Castro-mondragon, RSAT 2015: Regulatory Sequence Analysis Tools, vol.43, pp.50-56, 2015.
DOI : 10.1093/nar/gkv362
URL : https://hal.archives-ouvertes.fr/hal-01624369

W. S. Katz, R. J. Hill, T. R. Clandinin, and P. W. Sternberg, Different levels of the C. elegans growth factor LIN-3 promote distinct vulval precursor fates, Cell, vol.82, p.7628018, 1995.