Natural selection acts as a filter, leaving out those forms that are less adapted to the environment. However, it is quite common to see distinct forms within the same species and living in the same population. For instance, you can see the three alternative male colour morphs (orange, yellow, and white) that naturally coexist in the same Pyrenean populations of the common lizard, Zootoca vivipara. Why is that? Is there no fittest form? What maintains such variation? I dedicate a large part of my research to answer these questions given that this may help us to understand how diversity is generated and maintained during evolution and how life may be able to respond to global threats such as habitat deterioration and climate change.

I combine different approaches including correlative studies in natural populations and experimental manipulations of semi-natural populations to investigate how colouration is associated with multiple fitness proxies and/or different ecological roles. More recently, I have started to address these questions using also population genetic models.

More in: San-Jose et al. 2014, and San-Jose et al. 2019.


Part of my research focuses on uncovering the genetic basis that underlies the variation in colouration that we can observed within many species. My main goal is to comprehend the reciprocal interactions between genetics and the evolution of colouration. In other words, how the genetic basis of colouration influences the evolution of colour traits and, in turn, how selection on coloration shapes the genetic architecture for colouration.

I study species that show continuous variation in colouration (for instance, like in the barn owls shown in the picture) but also species that have a few discrete colour forms like lizards and snakes, trying to unravel the potential parallelisms driving these distinct forms of variation. I use multiple approaches including quantitative genetics, wide-genome transcriptomics, the candidate gene approach, and likelihood models of Mendelian inheritance. Additionally, I dedicate part of my research to contribute developing the theory around the genetics of colouration, which translates into reviews or synthesis articles.

More in: San-Jose and Roulin 2017, 2018, San-Jose et al. 2017a, San-Jose et al. 2017b, San-Jose et al. 2015.

Credit: Isabelle Henry


In addition to any genetic factors controlling the development of coloration, environmental factors can induce colour changes by altering pigment deposition in the skin, for instance. A common type of colouration to study how the environment affects an animal’s coloration are those based on carotenoid pigments (e.g., those responsible for the typical red combs of hens and roosters). These are very interesting pigments. Most animals cannot synthesize them and must acquire them from the diet and, additionally, they may play an important role as antioxidants.

I study colouration based on carotenoids in lizards because, contrarily to birds and fishes, the carotenoid-based colouration of lizards is not limited by the quantity of carotenoids they obtain from the diet. Nevertheless, carotenoid-based colourations in lizards still changes with the environment, raising the question of what mechanisms drive colour changes in this group of animals and why their carotenoid-based colourations differ from what we know in fish and birds.

More in: San-Jose and Fitze, 2013a, San-Jose et al. 2013b, and San-Jose et al. 2012.