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Systematic Biology 2006 55(6):936-948; doi:10.1080/10635150601064806
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© 2006 Society of Systematic Biologists

Automated Scanning for Phylogenetically Informative Transposed Elements in Rodents

Astrid Farwick1, Ursula Jordan1, Georg Fuellen2,3,4, Dorothée Huchon5, François Catzeflis6, Jürgen Brosius1 and Jürgen Schmitz1

1 Institute of Experimental Pathology, ZMBE, University of Münster Von-Esmarch-Str. 56, 48149 Münster, Germany E-mail: jueschm{at}uni-muenster.de (J.S.)
2 Department of Medicine, AG Bioinformatics, University of Müunster Domagkstr. 3, 48149 Münster, Germany
3 Department of Biology, AG Bioinformatics, University of Müunster Schlossplatz 4, 48149 Münster, Germany
4 Institute for Mathematics and Computer Science, University Greifswald Jahnstr. 15a, 17487 Greifswald, Germany
5 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978, Israel
6 Institut des Sciences de l'Evolution, Université Montpellier 2 34095 Montpellier, France

Edited by Andrew Shedlock: Associate Editor


  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.

Keywords: Automated scanning; CPAL; mouse; phylogeny; rodents; SINE

Received November 4, 2005; Revised December 31, 2005; Accepted May 10, 2006
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