Mosaic retroposon insertion patterns in placental mammals
Gennady Churakov1,3,5, Jan Ole Kriegs1,3,4, Robert Baertsch2, Anja Zemann1, Jürgen Brosius1 and
Jürgen Schmitz1,5
-Author Affiliations
1 Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany;
2 Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
↵3 These authors contributed equally to this work.
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 have 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 ∼2 million potentially phylogenetically 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 hypothesis (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 sister group 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.
Footnotes
↵4 Present address: LWL-Museum für Naturkunde, 48161 Münster, Germany.
↵5 Corresponding authors.
E-mail jueschm@uni-muenster.de; fax 49-251-8352134.
E-mail churakov@uni-muenster.de; fax 49-251-8352134.
[Supplemental material is available online at www.genome.org.]
Received December 19, 2008.
Accepted March 3, 2009.
Copyright © 2009 by Cold Spring Harbor Laboratory Press
E-mail churakov@uni-muenster.de; fax 49-251-8352134.
[Supplemental material is available online at www.genome.org.]
Received December 19, 2008.
Accepted March 3, 2009.
Copyright © 2009 by Cold Spring Harbor Laboratory Press
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Excerpt/Excerto:
"We believe that the most parsimonious interpretation of the current data is that the ancestral placental populations were characterized by severe ancestral subdivisions and rejoinings, leading to a complex mosaic of phylogenetic relationships in recent species. Effects of alternating divergence, hybridization, introgression, and incomplete lineage sorting might complicate our search for a clear dichotomy at the base of this tree and leave us with an indistinct, effective “soft” polytomy, leading sometimes to one or the other solution depending on the size of the data set and the particular markers examined."
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