DNA fingerprinting of fishes using tandemly repeated and interspersed DNA sequences

We examined the application of DNA fingerprinting in fishes, emphasizing fishes in the family Salmonidae. Established DNA fingerprinting probes that detect tandemly repeated DNA sequences were used to genetically differentiate geographically isolated populations of steelhead trout (Oncorhynchus mykiss). We demonstrated that population-specific bands could be identified by examining several individuals from different populations. The use of DNA mixtures was also evaluated. Using this technique, bands that vary at the individual level were diluted into the background, highlighting those bands found only in a majority of the individuals in a population.; We also demonstrated the utility of previously described, salmonid-specific short interspersed elements (SINEs) as probes for DNA fingerprinting. These probes are individual-specific, inherited in a Mendelian manner, and reflect the phylogenetic relationships among salmonids. However, our results indicate that the distribution and structure of these elements is more complex than has been reported. Specifically, a probe homologous to the 5{dollar}spprime{dollar} end of one element reported to be found only in the genus Salvelinus is found in all salmonids. Further, probes homologous to different regions of the same SINE element do not detect identical patterns in Southern blot analysis.; We have also examined the DNA fingerprint patterns detected in a diverse subset of 23 species of fishes. Fishes are extremely variable in their genome size and base composition. This diversity is reflected in variation in the DNA fingerprint patterns detected by any given probe. The number of bands detected by different probes can vary dramatically among species. Probes that are more similar to the GC composition of the target species tend to detect more bands than probes with a different GC composition.