Generating molecular markers from zooxanthellate cnidarians

Genetic techniques are providing tools that are necessary to answer questions concerning the ecology and evolution of cnidarians that, until recently, could not be easily addressed. In developing molecular markers for cnidarians with algal symbionts (zooxanthellae), however, caution must be used to ensure the markers in question are derived from the cnidarian host and not zooxanthellae. Unless the DNA template is from asymbiotic tissue, both host and symbiont genomes are present in the DNA template and zooxanthella-specific markers are often inadvertently generated. Steps should be taken to minimize the contamination by zooxanthella DNA in the template, and the origin of the molecular marker (host or symbiont) must be verified. Including zooxanthella-specific markers in analyses for cnidarians will confound interpretations of the results as biogeographic and phylogeographic patterns of zooxanthellae do not necessarily reflect those of the host.