Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed. 1. Introduction Decades ago when researchers began purifying DNA from eukaryotes using cesium chloride gradients, they observed bands of DNA that were distinct from the major genomic bands. The sequences comprising these ancillary bands were named satellites—a term from Greek meaning “followers of a superior entity”—and were found to separate from the other sequences due to their adenosine- and thymine-rich base pair compositions. Since their discovery, satellites have proven to be one of the most intriguing parts of the genome, owing to their high abundance, rapid evolutionary change, and a growing body of evidence indicating that they can impact speciation. The abundance of satellites varies widely in eukaryotic genomes, from effectively 0% in yeast species such as Schizosaccharomyces pombe to 25–50% or more in Drosophila and mammalian species [2–4]. Individual satellite monomers also vary dramatically in their monomer length, from the D. melanogaster pentameric monomer, AATAT, to more complex monomers such as the 972-bp centromeric satellite in the Indian muntjac [5]. Satellite monomers such as these are organized into arrays, or blocks, of tens to thousands of tandem copies located in the centromeres, the telomeres, and their surrounding regions. Indeed, the Y chromosome in many higher eukaryotes consists almost entirely of satellites. Despite their abundance, satellites are nonprotein coding and were therefore hypothesized to be genomic “junk” [6] or even selfish genetic elements [7]. Contrary to the former idea, the chromosomal regions consisting of satellites are now
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