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MBE Advance Access published online on October 31, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl164
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 24, 2006

Research Article

Insertion Events of CR1 Retrotransposable Elements Elucidate the Phylogenetic Branching Order in Galliform Birds

Vera B. Kaiser 1, Marcel van Tuinen 2, and Hans Ellegren 1 *

1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
2 Department of Ornithology and Mammalogy, California Academy of Sciences, San Francisco, CA 94103

* To whom correspondence should be addressed.
Hans Ellegren, E-mail: Hans.Ellegren{at}ebc.uu.se


  Abstract

Using standard phylogenetic methods, it can be hard to resolve the order in which speciation events took place when new lineages evolved in the distant past and within a short time frame. As an example, phylogenies of galliform birds (including well-known species such as chicken, turkey and quail) usually show low bootstrap support values at short internal branches, reflecting the rapid diversification of these birds in the Eocene. However, given the key role of chicken and related poultry species in agricultural, evolutionary, general biological and disease studies, it is important to know their internal relationships. Recently, insertion patterns of transposable elements such as SINE and LINE markers have proved powerful in revealing branching orders of difficult phylogenies. Here we decipher the order of speciation events in a group of 27 galliform species based on insertion events of CR1 transposable elements. Forty-four CR1 marker loci were identified from the draft sequence of the chicken genome, and from turkey BAC clone sequence, and the presence or absence of markers across species was investigated via electrophoretic size separation of amplification products and subsequent confirmation by DNA sequencing. Thirty markers proved possible to type with electrophoresis of which 20 were phylogenetically informative. The distribution of these repeat elements supported a single homoplasy-free cladogram which confirmed that megapodes, cracids, New World quail, and guineafowl form outgroups to Phasianidae, and that quails, pheasants and partridges are each polyphyletic groups. Importantly, we show that chicken is an outgroup to turkey and quail, an observation which does not have significant support from previous DNA sequence- and DNA-DNA hybridisation-based trees and has important implications for evolutionary studies based on sequence or karyotype data from galliforms. We discuss the potential and limitations of using a genome-based retrotransposon approach in resolving problematic phylogenies among birds.

Keywords: Retrotransposon; cladogram; phylogenetics; birds; genomics.
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