New theory contends that long-lived, quiescent retroelements are a major driving force in human genome evolution

“Alu elements are short, 300-nucleotide-long DNA sequences capable of copying themselves, mobilizing through an RNA intermediate, and inserting into another location in the genome. Over evolutionary time, this retrotransposition activity has led to the generation of over one million copies of Alu elements in the human genome, making them the most abundant type of sequence present. Because Alu elements are so abundant, comprising approximately 10% of the total human genome, they have been thoroughly characterized in terms of their origin and sequence composition. What has remained elusive to scientists, however, are the actual mechanisms by which these elements persist and propagate over time to influence human evolution.”

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“To date, the most widely accepted theory of Alu retrotransposition is called the "master gene" theory, which asserts that the majority of Alu retrotransposition activity is driven by a small number of hyperactive "master" sequences. In this model, mutations occurring in the "master" copies have rendered themselves capable of substantial propagation and persistence over time. However, prior evidence from the Ya5 subfamily indicated that at least some "master" Alu elements may persist in low-copy numbers for long periods of evolutionary time without retrotranspositional activity, suggesting that the mechanisms of Alu expansion may be much more complex. These observations led Dr. Batzer and his co-workers to examine the Yb subfamily of Alu elements, to demonstrate that the Yb subfamily has a similar evolutionary pattern to that of AluYa5, and to formulate the "stealth driver" hypothesis for the evolution of these Alu elements.

"In contrast to 'master' genes, 'stealth drivers' are not responsible for generating the majority of new Alu copies, but rather for maintaining genomic retrotransposition capacity over extended periods of time," Batzer explains. "By generating new Alu copies at a slow rate, a 'stealth driver' may occasionally spawn progeny elements that are capable of much higher retrotransposition rates. These hyperactive progeny elements may act as 'master' genes for the amplification of Alu subfamilies and are responsible for producing the majority of the subfamily members. Due to their high retrotransposition levels, however, they are likely to be rapidly purged from human populations through natural selection."”