Phylogenetic information in inter-SINE and inter-SSR fingerprints of the Artiodactyla and evolution of the Bov-tA SINE

Various interspersed repeated sequences and elements (IRSs) can be utilized to generate PCR-based multilocus fingerprint profiles by amplifying the in terelement segments, using primers matching the elements themselves. We ass essed the utility of inter-IRS fingerprinting in phylogenetic comparisons a mong six artiodactyl species using several primers derived from two abundan t genomic components: the Bov-tA short interspersed nuclear elements (SINEs ) and simple sequence repeats or microsatellites (SSRs). Character- and dis tance-based analyses of the fingerprint data produced trees conforming to t he established phylogenetic relationships of species. The strength of phylo genetic signal from different primers varied; combining data from different experiments resulted in robust trees. Within the Cervidae, the hierarchica l relationship [(Odocoileus, Rangifer) Alces] was strongly supported. Both methods appear useful tools for systematic studies at time scales < 30 Myr. To elucidate the material basis of inter-SINE fingerprints, we obtained th e first sequences of the 'bovid' Bov-tA element also from two cervids (rein deer and white-tailed deer) and analysed their relationship to a number of paralogous bovid elements. The differences among sequences, both intra- and interspecific, were relatively high (mean 18.5%); the sequences showed no clear clustering with the species from which they had been isolated. Most i ndividual elements probably date back to the cervid-bovid ancestor > 25 Myr ago, which is in line with the observed fingerprint distributions.