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is a more “ecological” view that considers the genome as a set of genetic elements with potentially different kinds of interactions, ranging from cooperative (mutualistic), to neutral (commensal), to selfish (parasitic) (Avise, 2001). According to this paradigm, genetic conflict can arise among components of the genome that have different transmission patterns (e.g., transposons, nuclear genes, cytoplasmic genes), and therefore conflicting genetic interests. The basic idea is as follows: When components of the genome have different transmission patterns, selection can act on an element to increase its transmission even if that is detrimental to the organism and/or other heritable components of the genome. Genetic conflict within the genome will then result, because enhanced transmission of an SGE decreases transmission of other genetic elements. An evolutionary “arms race” can then occur among different components of the genome over basic biological processes.

Werren et al. (1988) raised three basic questions about SGEs that are still the subject of study today: (i) What are their origins, (ii) how are SGEs maintained, and (iii) are SGEs important in evolution? Regarding this last question, they concluded that “selfish elements, and the ‘intragenomic conflict’ they create, may be an important force promoting evolutionary change. However, this possibility has not been demonstrated conclusively in any system” (Werren et al., 1988). They further observed that the pace of understanding of SGEs “is expected to accelerate with the application of molecular cloning techniques” (Werren et al., 1988). Subsequent advances have eclipsed this expectation. What has occurred in the intervening years is the genomics revolution, a veritable explosion of information and techniques that have begun to open the “black box” of genome structure, function, and evolution. Today, there are over 1,000 bacterial genomes and over 100 eukaryote genomes sequenced, with the numbers growing almost daily (http://www.ebi.ac.uk/genomes/). These data and advances in genetic techniques have helped reveal how genomes evolve and function. The story that is emerging increasingly supports a central role of SGEs in shaping structure and function of genomes and in playing an important role in such fundamental biological processes as gene regulation, development, evolution of genetic novelty, and evolution of new species.

Here, I describe the conceptual framework for SGEs and genetic conflict as well as their types, and I then discuss developments that reveal the role of SGEs in important biological processes. There are several common themes to the topic that are briefly listed here and elaborated on below:



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