In the beginning, according to professor Hans Eiberg, we all had brown eyes. There was later a genetic mutation that affected the OCA2 gene over 6,000 years ago, which ceased the ability to make brown-eyed babies. The mutation created a “switch” (HERC2) that switched off the ability to produce brown eyes, but not shut off the OCA2 gene completely. Those with the OCA2 gene completely shut off have a condition called albinism.
The blue eyes are created from a small lack of melanin in the iris. This slight variation of melanin led researchers to study the DNA of people with blue eyes from all over the world. They all inherited the same switch (HERC2) at the exact same spot of the DNA. This is different from people with brown eyes, as they have individual variation in the area of melanin production. From this data, Eiberg concluded that people with blue eyes share a common ancestor; the first person to have this genetic mutation.
If you would like to read more information about this, head over to Science Daily to read the official press release.