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UNITED LIVING COLOURS “dot CH”: Integrating Evolutionary Developmental Genetics, 3D Computer Graphics, and Natural Photonics for deciphering variation & complexity in reptilian colour traits

English title UNITED LIVING COLOURS “dot CH”: Integrating Evolutionary Developmental Genetics, 3D Computer Graphics, and Natural Photonics for deciphering variation & complexity in reptilian colour traits
Applicant Milinkovitch Michel
Number 132430
Funding scheme Sinergia
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.01.2011 - 30.06.2014
Approved amount 1'200'000.00
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All Disciplines (4)

Discipline
Genetics
Mathematics
Condensed Matter Physics
Information Technology

Keywords (8)

Pigmentary and structural colors; Evolutionary functional genomics; Evo-Devo; Computer Graphics; Reaction-diffusion mechanisms; Optical physics; Mathematics; New model organisms

Lay Summary (French)

Lead
Lay summary
Notre projet de recherche intègre l'expertise de généticiens du développement, d'informaticiens, de physiciens, et de mathématiciens pour une meilleure compréhension des mécanismes fondamentaux générant la variation, la complexité, et la convergence des traits de coloration chez les reptiles. Notre analyse porte sur des espèces de laboratoire ainsi que sur des populations échantillonnées dans la nature de manière non-invasive (photographies à haute résolution et échantillons de sang). Plus spécifiquement, nous (1) développons l'équipement et les logiciels informatiques permettant la reconstruction simultanée de la géométrie en 3 dimensions et de la texture colorée d'animaux vivants; (2) caractérisons les pigments et les structures responsables de la coloration; (3) identifions les gènes impliqués dans l'évolution de ces traits de coloration, et (4) effectuons des modélisations mathématiques des processus d'établissement de la coloration lors du développement de l'animal.L'étude implique trois groupes de recherche de l'Université de Genève et de l'Université de Berne. Nous utilisons nos exceptionnelles populations captives de reptiles ainsi que de nombreux échantillons biologiques et acquisition de données visuelles à haute résolution sur des populations naturelles.Notre étude permettra d'identifier les gènes impliqués dans l'évolution des traits spectaculaires de coloration chez les reptiles et de développer des méthodes informatiques nouvelles utilisables dans l'industrie de l'image (imagerie médicale, cinéma, jeux vidéo, etc).
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking
Milinkovitch M.C. Manukyan L. Debry A. Di-Poï N. Martin S. Singh D. Lambert D. Zwicker M. (2013), Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking, in Science, 339, 78-81.
Crocodilians evolved scattered multi-sensory micro-organs
Di-Poï Nicolas, Milinkovitch Michel C. (2013), Crocodilians evolved scattered multi-sensory micro-organs, in EvoDevo, 2013(4), 19.
Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards
Teyssier Jeremie, Saenko Suzanne V., van der Marel Dirk, Milinkovitch Michel C. (2013), Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards, in BMC Biology, 2013(11), 105.
Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles
Tzika A.C. Helaers R. Schramm G. & M. C. Milinkovitch (2011), Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles, in EvoDevo, 2011(2), 19.
Interactive Diffraction from Biological Nanostructures
Dhillon Daljit S., Teyssier Jeremie, Single Michael, Milinkovitch Michel C., Zwicker Matthias, Interactive Diffraction from Biological Nanostructures, in Computer Graphics Forum, 1.

Communication with the public

Communication Title Media Place Year
Media relations: radio, television FR3 nouvelles du soir FR3 International 2013
Media relations: print media, online media Gepanzertes Sensibelchen 20Minuten German-speaking Switzerland 2013
Media relations: print media, online media La sensibilité à fleur de peau du crocodile Science et Avenir International 2013
Media relations: print media, online media Le gecko, quantique de la tête au pieds Campus Western Switzerland 2013
Media relations: print media, online media Les crocodiles: blindés mais sensibles Campus Western Switzerland 2013
Media relations: print media, online media Les crocos ont une sensibilité à fleur de peau Le matin dimanche Western Switzerland 2013
Media relations: radio, television O Positif RTBF la Première International 2013
Media relations: print media, online media Articles in various newspapers Blogs, newspapers in France, Russia, ... International 2012
Media relations: radio, television Emission CQFD TSR Western Switzerland 2012
Media relations: radio, television Journal (19:30) TSR TSR Western Switzerland 2012
Media relations: print media, online media Nature features: Crocodile head scales result from cracking BBC International 2012

Associated projects

Number Title Start Funding scheme
140785 Evolutionary developmental genetics of ?phenotypic novelties and convergences 01.06.2012 Project funding (Div. I-III)

Abstract

One key issue in evolution is to understand how morphology and physiology are altered to produce new forms serving novel functions. The pigmentation system in reptiles is promising for exploring the connection between genotype and phenotype in an ecological and phylogenetic framework because: (i) reptilian species and populations exhibit astonishing variation in multiple ecologically-relevant pigmentary and structural colours and colour patterns; and (ii) colour traits are, in principle, amenable to objective quantification and modelling. Investigation of the mechanisms generating variation in colours and patterns will require developing three major transdisciplinary bridges: (i) biologists have neglected the mathematical analyses of self-organisation phenomena (such as reaction-diffusion mechanisms, RDM) whereas mathematicians, engineers, and computer scientists have extensively used RDM, but in contexts of little relevance to real biological phenomena; (ii) mathematicians and computer graphics scientists have known for many years that 3D geometry, border effects, and growth heavily influence RDM solutions but they have poorly investigated these complex phenomena because they were irrelevant outside of the biology framework (e.g., for developing video games and artificial life applications); and (iii) most physicists interested into biological structural colours (due to wave interferences through light scattering in submicron structures) do not study these structures in an evolutionary/developmental framework, and biologists interested in structural colours usually lack the required skills in physics. Clearly, investigation of biologically-relevant colours (pigmentary and structural) and colour pattern variation is in its infancy and did not yet expand to adaptive variation beyond “simple” levels of melanism. Breakthroughs will require a transdisciplinary approach in terms both of concepts and techniques.Here, we propose integrating the expertise of three high-profile research groups in Switzerland (evolutionary and developmental geneticists, 3D computer graphics scientists, and condense matter physicists) for a truly improved understanding of the mechanisms generating variation and complexity at ecologically-relevant colour traits in reptiles. Our analyses will encompass multiple models (from recently-established laboratory model species to natural populations) and multiple scientific disciplines. More specifically, we propose to (i) develop the equipment and computer graphics pipeline for the simultaneous and high-resolution acquisition of both 3D geometry and colour texture on living animals, (ii) characterise the optical properties of pigmentary and structural (surface gratings, photonic crystals) colours in our reptilian species, (iii) apply molecular ecology analyses to data collected in the field from species characterised by large variation in pigmentary and structural coloration / colour patterns, (iv) perform developmental genetics experiments and QTL analyses of captive and natural reptilian populations selected for various pigmentary and structural colours and patterns, and (v) perform mathematical analysis of acquired phenotypes as well as mathematical simulations of both colour selection mechanisms in nanoscopic structures and RDM on 3D geometries acquired from real animals. Many steps in the study will involve the three Swiss research groups, and several junior researchers will be co-supervised by PIs from different disciplines. We will use both our exceptional captive population of corn snakes (including all known colour and colour-pattern mutations) and samples from a large number of individuals from two Malagasy lizard species. The highly novel and original integration of skills and expertise of the three Swiss research groups will allow for a truly improved understanding of the molecular developmental and self-organisation mechanisms generating spectacular intra-specific variation in reptilian colour and colour patterns associated with variance in fitness.The project will not only benefit to biology as it will also advance the state-of-the-art in computer graphics by contributing novel algorithms for registering deformable shapes, in particular from partial and time varying data. It will also lead to novel models for realistic, biologically plausible colour textures, and for approximate (but physically-based) reflection models of structural colours suitable for computer graphics rendering.
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