Automated scanning for phylogenetically informative transposed elements in rodents

Astrid Farwick, Ursula Jordan, Georg Fuellen, Dorothée Huchon, François Catzeflis, Jürgen Brosius, Jürgen Schmitz

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)936-948
Number of pages13
JournalSystematic Biology
Volume55
Issue number6
DOIs
StatePublished - Dec 2006

Keywords

  • Automated scanning
  • CPAL
  • Mouse
  • Phylogeny
  • Rodents
  • SINE

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