Retrotransposon Marker

Encyclopedia : R : RE : RET : Retrotransposon Marker

The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data. The reason for this is that Retrotransposons are assumed to represent powerful noise-free synapomorphies (Shedlock and Okada, 2000). The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is negligible even over evolutionary time scales. Retrotransposon integrations are assumed to be irreversible events since no eminent biological mechanisms have yet been described for the precise re-excision of class I transposons (but see van de Lagemaat et al., 2005). A clear differentiation between ancestral and derived character state at the respective locus thus becomes possible.

In combination, the virtual lack of homoplasy together with a clear character polarity make Retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived transpositional event (Hamdi et al., 1999; Shedlock and Okada, 2000). The “presence” of a given Retrotransposon in related taxa implies their orthologues integration, a derived condition acquired via a common ancestry, while the “absence” of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of Retrotransposons that were actively integrating before the divergence of a particular species.

Examples for phylogenetic studies based on Retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the Strepsirrhine tree (Roos et al., 2004) and the placental mammalian evolution (Kriegs et al., 2006).

References

Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (1999) Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 289: 861–871. [GS]
Shedlock AM, Okada N (2000) SINE insertions: Powerful tools for molecular systematics. Bioessays 22: 148–160. [GS]
van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 15: 1243–1249. [GS]
Nikaido M, Rooney AP, Okada N (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A 96: 10261–10266. [GS]
Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA (2003) Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A 100: 12787–12791. [GS]
Roos C, Schmitz J, Zischler H (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci U S A 101: 10650–10654. [GS]
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biol 4(4): e91.[link]

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