According to a study that 'deep sequenced' the genomes of 236 individuals from 125 human populations, these DNA deletions have been driven by natural selection during the migration of our species out of Africa.
In addition to sequencing the genomes of modern people, the scientists also delved into the DNA of archaic populations such as Neanderthals and Denisovans to reconstruct our ancestral genome of 200,000 years ago. In particular they looked at copy number variations (CNVs), which are classified as either duplications (more copy numbers) or deletions (fewer copy numbers). These have been more difficult to sequence than traditional single nucleotide variations (SNVs), and so have not been greatly studied before.
The researchers found CNVs were the source of seven times more genetic variation than SNVs, and by using CNV data the researchers were able to identify patterns of ancestry and migration. '[During] the last 80,000 years, the genomes of our ancestors that left Africa have gone through much more remodelling by CNVs compared to SNVs,' Professor Eichler told The Scientist. Duplications in gene copy number were four times more likely to affect gene function than deletions.
Since the origins of our species in Africa 200,000 years ago, humans have lost around 15.8 million base-pairs. The remaining 24.9 million base-pairs were lost in chunks as humans migrated around the world, allowing the scientists to create a map of human migration using this data. The entire human genome contains around three billion base-pairs, so these figures represent a very small proportion of the total, and losing unnecessary DNA is a key component of natural selection.
The scientists now hope to use this information to see how these CNVs might affect disease risk. For example, it is known that certain African populations carry gene duplications that may protect against sleeping sickness caused by trypanosome parasites.