AMPLIFICATION OF DISTINCT SUBFAMILIES OF SHORT INTERSPERSED ELEMENTS DURING EVOLUTION OF THE SALMONIDAE

There are at least three different kinds of short interspersed repetit ive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfam ily Salmoninae, such as salmon, trout and charr. In order to determine whether the amplification of the Hpa sequence occurred rapidly within a short evolutionary period or gradually, over the long term, a searc h was made for Hpa sequences in primitive salmonids; namely, grayling and whitefish. A grayling species has fivefold fewer copies of these s equences than the Salmoninae species, whereas several whitefish specie s have 200-fold to 20-fold fewer copies than the Salmoninae species. C haracterization of the Hpa sequences in these species allowed us to re cognize two distinct Hpa subfamilies on the basis of diagnostic substi tutions as well as a new short interspersed element with an Hpa-relate d sequence. The distribution of these sequences revealed that distinct members of the HpaI or Hpa-related family were amplified during estab lishment of each subfamily lineage in a manner very similar to the amp lification of the human Alu family. We provide evidence for the validi ty of a model that involves ''multiple source genes'' to explain diagn ostic substitutions of the Hpa subfamilies and the timing of their app earance during evolution.