Transposon signatures: species‐specific molecular markers that utilize a class of multiple‐copy nuclear DNA

Transposable elements are mobile sequences found in nuclear genomes and can potentially serve as molecular markers in various phylogenetic and population genetic investigations. A PCR‐based method that utilizes restriction site variation of element copies within a genome is developed. These patterns of site variation, referred to as transposon signatures, are useful in differentiating between closely related groups. Signature data using the magellan retrotransposon, for example, is useful in examining relationships within the genus Zea and Tripsacum. This method allows transposable elements, or even other multiple‐copy nuclear DNA sequences, to be generally utilized as molecular markers in discriminating between other closely related species and subspecies.