Genetics is an interesting, if mind numbingly complicated, subject. As you all know genes are composed of four nucleotides that form pair bonds with each other (to be simplistic). Adenine pairs with thymine and guanine pairs with cytosine. Three base pairs form a codon, etc. Traditionally, a gene is defined as a segment (i.e. series of codons) that code for a polypeptide chain or specifies a functional RNA molecule. This brings us to repetitive DNA. Repetitive DNA consists of nucleotide sequences that occur several times, either in tandem or are dispersed. For example, the genome of the kangaroo rat contains over 50% repetitive DNA in the form of three, localized, repeated sequences. These are AAG, TTAGGG and ACACAGCGGG. Each sequence is repeated from one-two billion times. Another type of repetitive DNA is dispersed throughout the genome and are divided into two major types: short interspersed repeated sequences and long interspersed repeated sequences (of which their is only one in the human genome). A number of mechanisms have been suggested for the creation of repetitive DNA including gene duplication, transposition, unequal crossing-over and replication slippage. The problem is, however, what function the repetitive sequences serve. Four possibilities have been suggested:
1) They perform essential functions, such as global regulation of gene expression. This implies that removal of repetitive DNA will have a deleterious effect.
2) Repetitive DNA is useless "junk" DNA and it's loss will have no effect of fitness.
3) It is a fucntionless parasite
4) It has a structural function unrelated to carrying genetic information. For example, it may affect chromosomal architecture such as curvature.
Recently, a study was done which seems to support the first possibility. Here is a little more background:
“Sequencing of the complete genome in humans, fruit flies, nematodes and plants has revealed that the number of protein-coding genes is much more similar among these species than expected,” he says. “Curiously, the largest differences between major species groups appear to be the amount of ‘junk’ DNA rather than the number of genes.”
Using a recently developed population genetic approach, Andolfatto showed in his study that these expansive regions of “junk” DNA—which in Drosophila accounts for about 80 percent of the fly’s total genome—are evolving more slowly than expected due to natural selection pressures on the non-protein-coding DNA to remain the same over time.
“This pattern most likely reflects resistance to the incorporation of new mutations,” he says. “In fact, 40 to 70 percent of new mutations that arise in non-coding DNA fail to be incorporated by this species, which suggests that these non-protein-coding regions are not ‘junk,’ but are somehow functionally important to the organism.”
The research found that a large amount of the functional divergence between Drosophila species was exhibited in the "junk" regions.
(The info on repetitive sequeces came from Li and Graur's 1991 book "Fundamentals of Molecular Evolution")