Field data from mouse enclosure experimentSampling, phenotype, and survival data from mouse enclosure experiment conducted in Nebraska, USA. Column IDs as follows: id: Individual mouse identification number date: Date that mouse was introduced to enclosures type: Habitat type that mouse was sampled from. Light = light substrate, Dark = dark substrate. location: Sampling location for mouse. site: Experimental treatment of enclosure that mouse was introduced to. D = dark substrate, L = light substrate. enc: Enclosure that mouse was introduced to. sex: Sex of mouse age: Age of mouse. A = adult, S = subadult, J = juvenile. DF_BriCon: Principal component score corresponding to the brightness and contrast of dorsal/flank pigmentation. DF_ChrHue: Principal component score corresponding to the chroma and hue of dorsal/flank pigmentation. V_BriCon: Principal component score corresponding to the brightness and contrast of ventral pigmentation. DF_Hue: Principal component score corresponding to the hue of dorsal/flank pigmentation. V_ChrHue: Principal component score corresponding to the chroma and hue of ventral pigmentation. DV: Dorsal ventral pigmentation boundary. TP: Tail pigmentation pattern. surv1: Survival of mouse from time point 0 to time point 1. 0 = dead. 1 = alive. surv2: Survival of mouse from time point 1 to time point 2. 0 = dead. 1 = alive. surv3: Survival of mouse from time point 2 to time point 3. 0 = dead. 1 = alive.Mouse.csv

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.