Neutral Evolution and the Shape of Our Genome

Finding: There is a growing body of evidence which shows that many of the genetic bits and pieces that drive evolutionary changes do not confer any advantages or disadvantages to humans or other animals.

The conventional view
The basic belief of evolution was that all random genetic changes that manage to stick around have some selective advantage on the species.

But a study concludes that we are what we are largely due to random changes that are completely neutral. This study reinforces and highlights the equal, and in some cases greater, importance of neutral genetic drift.

Repeat Elements
Repeat elements are fragments of DNA containing the same repetitive sequence of chemical base pairs several hundred times. Experiments demonstrate that repeat elements rose to prominence without offering any benefits to the organism it inhabits. They are one of the major architectural markers of the human genome, and they make up over 40 percent of our genome,

Numts or Copies of mitochondrial sequences found in DNA portions

One type of repeat element was found while looking at genes associated with Bardet Biedl syndrome, a rare disorder. Researchers found portions of DNA that had been copied from the mitochondria, the energy-making apparatus of human cells that has its own small genome. These mitochondrial sequences are known as numts.

More Numts as the species gets more sophisticated
The whole human genome, has more than 1200 such pieces of mitochondrial DNA of various lengths embedded into chromosomes. While chimps have a comparable number, mice and rats only have around 600 numts. Since they increase in frequency as species advance, it suggested there was some evolutionary purpose to keeping them around.

But none of these numts contained an actual gene to make a protein that does anything, nor did they seem to control the function of any nearby genes. These numts are a neutral part of our genome. If anything, they may be mildly negative since long repeat sequences can be unstable or get inserted inside genes and disrupt them.

The researchers believe they have uncovered a possible reason why these potentially damaging but mostly neutral bits of DNA accumulate over time by comparing the sequences of human numts with those in different animals. How closely the different species' sequences match can provide an estimate of when that particular sequence got inserted into the ancestor of the human genome.

Numts became embedded roughly when primates emerged: 54 Million years ago
Calculations made about the location and structure of the numts revealed that most numts became embedded in our genome over a 10-million-year period centered roughly 54 million years ago -- right around the time when the first primates emerged. When new species emerge, their numbers and therefore their genetic differences are very small. The consequences are that this creates a genetic bottleneck during which any changes in the genome will either get eliminated quickly or spread to the whole population quickly.

Numts expanded because they were not eliminated - they were not detrimental

Numts, being "neutral," were generally at low levels in ancient mammals, but during the primate emergence 54 million years ago, they accumulated and spread through the small early primate populations precisely because they were not detrimental enough to be eliminated. Then, as these populations expanded, numts reached stable but higher frequencies.