title: Automated scanning for phylogenetically informative transposed elements in rodents.
abstract: Transposed elements constitute an attractive, useful source of phylogenetic markers to elucidate the evolutionary history of their hosts. Frequent and successive amplifications over evolutionary time are important requirements for utilizing their presence or absence as landmarks of evolution. Although transposed elements are well distributed in rodent taxa, the generally high degree of genomic sequence divergence among species complicates our access to presence/absence data. With this in mind we developed a novel, high-throughput computational strategy, called CPAL (Conserved Presence/Absence Locus-finder), to identify genome-wide distributed, phylogenetically informative transposed elements flanked by highly conserved regions. From a total of 232 extracted chromosomal mouse loci we randomly selected 14 of these plus 2 others from previous test screens and attempted to amplify them via PCR in representative rodent species. All loci were amplifiable and ultimately contributed 31 phylogenetically informative markers distributed throughout the major groups of Rodentia.
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany.
authors.forename: Astrid
authors.initials: A
authors.lastname: Farwick
authors.forename: Ursula
authors.initials: U
authors.lastname: Jordan
authors.forename: Georg
authors.initials: G
authors.lastname: Fuellen
authors.forename: Dorothée
authors.initials: D
authors.lastname: Huchon
authors.forename: François
authors.initials: F
authors.lastname: Catzeflis
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D019295:Computational Biology; D005819:Genetic Markers; D008969:Molecular Sequence Data; D010802:Phylogeny; D012377:Rodentia / Q000235:genetics*; D016415:Sequence Alignment; D020086:Short Interspersed Nucleotide Elements
chemical_list: D005819:Genetic Markers