Evolution is the change in gene frequency within a population. Over a long period of time, evolution can generate new species. Processes like speciation generally take millions of years, but evolution is happening all the time, especially at the level of local populations, such as that changing allele frequencies and coat color in gray squirrels. Natural selection is the key mechanism of evolution.
Natural selection is a process that involves heritable traits that permit an organism to leave more offspring than those who lack those traits thereby enabling those traits to become more common in a population over successive generations. What is the genetic difference between black and gray squirrels?
Black and gray squirrels are only different based on one gene. Alleles are variations on DNA sequences at a specific location on a chromosome (usually different forms of the same gene). The allele for squirrel fur color has two different possible sequences – one that codes for gray fur and one that codes for black fur. Each squirrel has two copies of this allele. If a squirrel has two copies of the gray allele, then it will be gray, but if it has either one copy of the gray and one of the black or if it has two copies of the black allele, then it will be black. The gray type is actually genetically recessive, which is somewhat counterintuitive since it is the more common genotype these days!
Most dark pigmentation in mammals is associated with the MC1R gene. The MC1R gene regulates how much brown/black pigment (eumelanin) versus pale red/yellow pigment (phaeomelanin) is added to hairs as they grow. When the alpha melanocyte-stimulating stimulating hormone (αMSH) binds to the MC1R gene, eumelanin (dark pigment) is produced; otherwise phaeomelanin (light pigment) is produced. In black squirrels, the MC1R gene has undergone a small deletion (24 base pairs of DNA) that corresponds to just 8 amino acids. This deletion hastens binding of the αMSH to the MC1R gene increasing production of eumelanin (the mechanism is not yet known). This is known as the EB allele. In the gray squirrel a complete MC1R gene (lacking the deletion) blocks binding of αMSH increasing production of phaeomelanin. This is known as the E+ allele. The EB allele is incompletely dominant to the E+ allele. So E+/E+ is the genotype of the gray squirrel, EB/EB is the genotype of the black squirrel, and EB/E+ (or E+/EB) is the genotype of the brown-black squirrel. In the field it’s hard to distinguish a black EB/EB from a black EB/E+ squirrel but look carefully: the EB/EB is jet black all over but and EB/E+ squirrel have mostly brown-black backs but a distinctly lighter-colored (often orange-colored) belly. It’s quite likely that there are other genes and alleles at work but at present this is our best understanding of the genetic mechanism at work. (See FAQ; Literature)
Because squirrels are so visible and recognizable they are a great way to get non-scientists interested in evolution and involved in scientific studies. The simple genetic difference between black and gray squirrels also provides an easy way (relatively speaking!) to watch how our rapidly changing environment is affecting evolutionary processes within our own lifetimes. You don’t need a fancy machine to sequence DNA to watch this bit of evolution in action, just your own two eyes.