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 interelement segments, using primers matching the elements themselves. We assessed the utility of inter‐IRS fingerprinting in phylogenetic comparisons among six artiodactyl species using several primers derived from two abundant genomic components: the Bov‐tA short interspersed nuclear elements (SINEs) and simple sequence repeats or microsatellites (SSRs). Character‐ and distance‐based analyses of the fingerprint data produced trees conforming to the established phylogenetic relationships of species. The strength of phylogenetic signal from different primers varied; combining data from different experiments resulted in robust trees. Within the Cervidae, the hierarchical 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 the first sequences of the ‘bovid’ Bov‐tA element also from two cervids (reindeer 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 individual elements probably date back to the cervid–bovid ancestor >25 Myr ago, which is in line with the observed fingerprint distributions.