What we do

Because discipline-oriented approaches can sometimes restrain imagination (see the ‘why’ section), I established a laboratory combining biologists, physicists and computer scientists, making our research highly multidisciplinary and integrative. Our central (but not exclusive) model is the development and evolution of the vertebrate skin, with special emphasis on skin appendages (scales, hairs, spines), skin colours (pigmentary and structural), and skin colour patterns. Our strategy is to tackle these topics from different angles by using multiple techniques (genomics, physical experiments, mathematical modelling and numerical simulations) and various concepts from different fields. We work at multiple spatial scales (genomes, cells, tissues, organisms) and use new model species of tetrapods (frogs, snakes, lizards, crocodiles, hedgehogs, tenrecs, spiny mice). The continuous importance of classical models (fruit fly, mouse, nematode, etc) is unquestionable, but we think that the development of new models is crucial for a better understanding of the processes generating the complexity and diversity of phenotypes.

Overall, the approaches that we use can be crudely separated into two categories: (1) Molecular Evolutionary Developmental biology (led by Dr. Athanasia C. Tzika since 2015) and (2) Physics of Biology (led by Prof. Michel C. Milinkovitch). These two lines of research use the same non-model species, meet at multiple time points during our research and feed one another with techniques, data and ideas.

Molecular Evo-Devo (MED)

Given that natural selection and physical constrains act on the phenotypes that originate from development, the merging of evolutionary and developmental biology helps to explicitly address the generative mechanisms underlying the evolution of organismal forms. Currently, we are focusing on the development of skin scales, skin colours, and skin colour patterns in new models (cf. the ‘How’ section) of snakes, lizards, and crocodiles; as well as on the convergent development and evolution of spines in tenrecs, hedgehogs, and spiny rodents. Much additional information can be found on our Reptilomics.org web site and in the following three chosen publications (all publications are available on the Publication Page).

Physics of Biology (PoB)

Many questions in development are conceptually similar to those investigated in soft-matter physics, statistical physics, and mechanics. It is becoming increasingly clear that the interactions between physical and biological processes generate and constrain the variety and complexity of evolved phenotypes. Our focus is on the development and evolution of skin scales in reptiles and hairs/spines in mammals, nanostructures with photonic properties (producing structural colours) in reptiles, and skin patterning (spatial distribution) of skin colour and appendages in tetrapods. Much additional information can be found in the following chosen publications (all publications are available on the Publication Page).

  • [PoB] A Living Mesoscopic Cellular Automaton Made of Skin Scales  

    Manukyan L., Montandon S.A., Fofonjka A., Smirnov S. & M.C. Milinkovitch

    Nature 544: 173-179 (2017) - doi:10.1038/nature22031

  • [MED] The Anatomical Placode in Reptile Scale Morphogenesis Indicates Shared Ancestry 
Among Skin Appendages in Amniotes
    Di-Poï N. & M. C. Milinkovitch
    Science Advances 2, e1600708 (2016)

  • [PoB] Photonic Crystals Cause Active Colour Change in Chameleons

    Teyssier J., Saenko S.V., van der Marel D. & M.C. Milinkovitch

    Nature Communications 6: 6368 (2015)

  • [MED] Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics
    Tzika A.C., Ullate-Agote A., Grbic D. & M. C. Milinkovitch
    Genome Biol. Evol. 7: 1827-1841 (2015)

  • [PoB] R2OBBIE-3D, a Fast Robotic High-Resolution System for Quantitative Phenotyping of Surface Geometry and Colour-Texture

    Martins A., Bessant M., Manukyan L. & M.C. Milinkovitch

    PLOS ONE 10(6): e0126740 (2015) - doi:10.1371/journal.pone.0126740

  • [MED] Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene 
    Saenko S.V., Lamichhaney S., Martinez Barrio A., Rafati N., Andersson L. & M. C. Milinkovitch
    Scientific Reports 5, 17118 (2015)

  • [MED] The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource 
for EvoDevo studies in squamates
    Ullate-Agote A., Milinkovitch M.C. & A.C. Tzika
    Int. J. Dev. Biol. 58: 881-888 (2014)

  • [PoB] 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.
    Science 339, 78-81 (2013)

Previous life

Prior to 2010, we have been actively involved in Molecular Phylogenetics as well as Population and Conservation Genetics. Here are links to our old website with lots of background information on our research results in those fields.

Molecular Phylogenetics/Phylogenomics



Conservation Genetics



EvoSimulator: a simple tool illustrating the power of ‘mutation + selection’