Phylogenetic signal is the extent to which phenotypic expression is related to phylogenetic relationships between species, thus reflecting the effect of common ancestry. Signal loss occurs when some species obtain adaptation, regarding a given trait, to certain environmental conditions. Compartmentalization in processes leading to trait expression reduces dependence among them, thus favoring, up to some degree, their independent evolution. Compartmentalization may therefore lead to phylogenetic signal loss, but this effect has been overlooked. Compartmentalization in the expression of melanin-based color traits could exist, which first requires a biochemical process (melanin synthesis in melanocytes) and then a physical process consisting in the deposition of melanins in the integument. To test this hypothesis, the phylogenetic signal was estimated in the concentration of the four structural units of melanins (5,6-dihydroxyindole, 5,6-dihydroxyindole-2-carboxylic acid, benzothiazine and benzothiazole) and in the expression of color produced as a consequence of their deposition in feathers in 59 species of birds. While phylogenetic signal was low in all traits, it was not different from zero in melanin concentration but was considerably higher in color expression. This suggests that compartmentalization in the pigmentary system may allow a differential adaptability and phylogenetic signal loss in melanin synthesis. informacion[at]ebd.csic.es: Galván (2018) Physiological compartmentalization as a possible cause of phylogenetic signal loss: an example involving melanin-based pigmentation. Biol J Linn Soc. Doi 10.1093/biolinnean/bly164