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.

Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives

“…Our initial analysis of several of these loci indicates that it is possible to amplify most of these loci also in other carnivoran species. Using a similar strategy, Farwick et al have recovered 232 putatively informative loci in the mouse genome (Farwick et al, 2006). These automated strategies are much more efficient than traditional PCR-based methods for SINE isolation, where only a few reliable and informative loci are identified (e.g.…”

“…However, their use for phylogenetic analyses has been limited due to the difficult, time-consuming, and cost-intensive work to establish SINE loci in non-model organisms (Borodulina and Kramerov, 2005;Treplin and Tiedemann, 2007). Farwick et al (2006) have demonstrated for Rodentia the usefulness of an automatic screening strategy to find phylogenetically informative transposed elements flanked by highly conserved regions.…”

“…As such, they can accumulate retrotransposon insertions, which comprise additional phylogenetic markers, which have been successfully employed in several studies of vertebrate relationships and have proved to be a reliable apomorphic character (e.g. Farwick et al, 2006;Kriegs et al, 2006 andNishihara et al, 2005;Schmitz et al, 2001;Shimamura et al, 1997). Retrotransposons, such as short interspersed elements (SINEs) occur in high copy numbers in many mammals (Wang and Kirkness 2005) and offer two important advantages when used as phylogenetic marker: (1) they are regarded as being nearly homoplasy-free and (2) they are polarized characters such that the absence of a retrotransposon at a given locus is usually the ancestral state (e.g.…”

Two New Taxa (Caviomorpha, Rodentia) from the Early Oligocene Tinguiririca Fauna (Chile)

“…The venerable notion of caviomorph monophyly (Wood and Patterson, 1959) has been corroborated repeatedly by molecular analyses (Nedbal et al, 1994;Huchon and Douzery, 2001;Opazo, 2005;Farwick et al, 2006;Poux et al, 2006;Huchon et al, 2007;Blanga-Kanfi et al, 2009;Churakov et al, 2010), but morphological evidence has remained more ambiguous. Auditory (Meng, 1990) and dental (Marivaux et al, 2004;Sallam et al, 2009) features have been interpreted as indicative of caviomorph monophyly, as has a recent combined molecular and morphological dataset (Horovitz et al, 2006).…”

Multiple molecular evidences for a living mammalian fossil

“…We recently conducted an exhaustive, automated search for phylogenetic informative SINE markers in rodents, revealing 31 diagnostic SINEs from 16 genomic loci in representatives of all major rodent lineages (29). Using these as templates for PCR, in the present study we amplified the orthologous loci in samples of Laonastes DNA.…”