title: Phylogenetic information in inter-SINE and inter-SSR fingerprints of the artiodactyla and evolution of the bov-tA SINE.
abstract: 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.
authors.affiliation: Department of Biosciences, Division of Genetics, PO Box 56, FIN-00014 University of Helsinki, Finland. silja.kostia@helsinki.fi
authors.forename: S
authors.initials: S
authors.lastname: Kostia
authors.forename: M
authors.initials: M
authors.lastname: Ruohonen-Lehto
authors.forename: R
authors.initials: R
authors.lastname: Väinölä
authors.forename: S L
authors.initials: SL
authors.lastname: Varvio
mesh_terms: D000818:Animals; D001188:Artiodactyla / Q000235:genetics* / Q000502:physiology; D001483:Base Sequence; D002417:Cattle; D016172:DNA Fingerprinting / Q000379:methods*; D019143:Evolution, Molecular; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012343:RNA, Transfer / Q000235:genetics; D012756:Sheep / Q000235:genetics; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*; D013552:Swine / Q000235:genetics
chemical_list: D012343:RNA, Transfer