Automated scanning for phylogenetically informative transposed elements in rodents.
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.
Farwick
Astrid
A
Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany.
Jordan
Ursula
U
Fuellen
Georg
G
Huchon
Dorothée
D
Catzeflis
François
F
Brosius
Jürgen
J
Schmitz
Jürgen
J
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
D005819:Genetic Markers