title: Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes).
abstract: BACKGROUND
  The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades.
  
  
  RESULTS
  We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae.
  
  
  CONCLUSIONS
  The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.
authors.affiliation: Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str, 56, D-48149 Münster, Germany. kriegs@uni-muenster.de
authors.forename: Jan Ole
authors.initials: JO
authors.lastname: Kriegs
authors.forename: Andreas
authors.initials: A
authors.lastname: Matzke
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.forename: Andrej
authors.initials: A
authors.lastname: Kuritzin
authors.forename: Gerald
authors.initials: G
authors.lastname: Mayr
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D046094:Galliformes / Q000235:genetics*; D016678:Genome; D054643:INDEL Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements