Mosaic Retroposon Insertion Patterns in Placental Mammals

Mosaic Retroposon Insertion Patterns in Placental Mammals

1. Gennady Churakov1,
2. Jan Ole Kriegs1,
3. Robert Baertsch2,
4. Anja Zemann1,
5. Juergen Brosius3 and
6. Juergen Schmitz1,4

Author Affiliations

1. E-mail: jueschm@uni-muenster.de

Abstract

One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals has so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The presence of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its absence in more distant species. To resolve the placental origin controversy we extracted approximately 2 million potentially phylogenetic informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sistergroup to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a soft polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.

Keywords:

Darwin issue ancestral hybridization lineage sorting placental origin retroelements

Footnotes

Received December 19, 2008.
Accepted March 3, 2009.

Copyright © 2009, Cold Spring Harbor Laboratory Press