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Morphological Characters from the Genome: SINE Insertion Polymorphism and Phylogenies

  • Agnès DettaïEmail author
  • Jean-Nicolas Volff
Chapter
Part of the Genome Dynamics and Stability book series (GENOME, volume 4)

Abstract

For the last fifteen years, researchers have been using SINE (short interspersed elements; non-autonomous retroposons) insertion polymorphism as characters for phylogeny. Although the collection of these characters is much less straightforward and much more work intensive than for classical sequence data, they are subject to very little homoplasy, and therefore allow more reliable determination of the phylogeny of species. As reversions are very rare, and the ancestral state (absence of the insertion) is known, these characters are orientated a priori. They are also good markers for population genetics. Because of their almost complete lack of homoplasy, character conflict in these characters is a better indicator of incomplete lineage sorting and hybridization than other types of data, even for ancient divergences. Only a few examples of convergencies and reversions have been identified, and after looking through hundreds of characters; moreover, most instances of homoplasy are identifiable as such, so SINE insertion polymorphism can still be regarded as very high quality characters. Constant progress has been made through the years for the isolation of new SINEs as well as for the isolation of new insertion loci, both by bioinformatic methods and by benchwork. Numerous dedicated computer programs are available, and the newly sequenced complete genomes allow their full scale utilization. SINE insertion polymorphism data has proved its interest on complex phylogenetic problems where morphological and sequence data were not resolutive. The improvements in its portability encourage an enlargement of its application to new taxa, where it will provide novel and high quality phylogenetic information.

Keywords

Transposable Element Southern Blot Hybridization Incomplete Lineage Sorting Insertion Polymorphism Insertion Locus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Notes

Acknowledgments

Agnes Dettaï was supported by an Alexander von Humboldt postdoctoral Fellowship. The Volff group is funded by the Biofuture program of the German Bundesministerium für Bildung und Forschung (BMBF). We received helpful comments on this manuscript from Gael Lancelot, Matthieu Andro, and Julien Lorion.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  1. 1.Département Systématique et EvolutionMuséum National d'Histoire NaturelleParisFrance
  2. 2.Physiologische Chemie I, BiozentrumUniversity of WürzburgWürzburgGermany

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