Automated Scanning for Phylogenetically Informative Transposed Elements in Rodents

• Published in: Systematic biology Vol. 55; no. 6; pp. 936 - 948
• Main Authors: Farwick, Astrid, Jordan, Ursula, Fuellen, Georg, Huchon, Dorothée, Catzeflis, François, Brosius, Jürgen, Schmitz, Jürgen, Shedlock, Andrew
• Format: Journal Article
• Language: English
• Published: England Society of Systematic Zoology 01.12.2006; Taylor & Francis; Oxford University Press; Oxford University Press (OUP)
• Subjects: Animals; Automated scanning; Base Sequence; Biodiversity and Ecology; Biological Evolution; Biological taxonomies; Computational Biology; CPAL; Environmental Sciences; Evolution; Genetic loci; Genetic Markers; Genetic transposition; Genetics; Genome Analysis and the Molecular Systematics of Retroelements Symposium; Genomes; Molecular Sequence Data; Monophyly; mouse; Phylogenetics; Phylogeny; Polymerase chain reaction; Rodentia - genetics; Rodents; Sequence Alignment; Short Interspersed Nucleotide Elements; SINE; mouse; phylogeny; SINE; Automated scanning; rodents; CPAL
• ISSN: 1063-5157; 1076-836X
• DOI: 10.1080/10635150601064806

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.