Adaptive evolution can occur when genetic change affects traits subject to natural selection. Although selection is a deterministic process, adaptation can be difficult to predict in finite populations because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these connections using a combination of field and laboratory experiments. We conduct a large-scale manipulative field experiment with wild populations of deer mice in distinct habitats to directly estimate natural selection on pigmentation traits and next test whether this selection drives changes in allele frequency at an underlying pigment locus. We find that divergent cryptic phenotypes are repeatedly favoured in each habitat, leaving footprints of selection in the Agouti gene. Next, using transgenic experiments in Mus, we functionally test one of the Agouti mutations associated with survival, a Serine deletion in exon 2, and find that it causes lighter coat colour via changes in its protein binding properties. Finally, we show significant change in the frequency of this mutation in our field experiment. Together, our findings demonstrate how a sequence variant alters phenotype and show the ensuing ecological consequences that drive changes in population allele frequency, thereby revealing the full process of evolution by natural selection.. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/383240 doi: bioRxiv preprint first posted online Aug. 2, 2018; 2 While a growing number of genomic studies have pinpointed genes that contribute to phenotypic evolution [1][2][3][4][5][6] , often the ecological mechanisms driving trait evolution remain untested. On the other hand, many elegant field studies have documented the action of natural selection on traits 7-13 , but the underlying molecular mechanisms are unclear. Here, we combine a large-scale manipulative field experiment with laboratory-based genetic and biochemical tests to identify both the ecological and molecular mechanisms that cause trait adaptation in a single study of a wild vertebrate. Forging these precise mechanistic connections will aid in predicting the evolutionary consequences of environmental change in natural populations 14,15 .We took advantage of recently evolved, cryptically coloured populations of deer mice to investigate the evolutionary and genetic consequences of divergent natural selection. The Sand Hills of Nebraska were formed from light-coloured quartz ~8-10,000 years ago 16 . This dune habitat differs from the surrounding habitat in physical properties, most notably the soil colour 17 (Fig. 1
Divergent selection on pigmentation in experimental enclosuresTo explicitly test for divergent natural selection that favours locally adapted pigment phenotypes, we collected 481 wild mice from the ancestral "dark" and derived "light"...