Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)

被引:62
作者
Kriegs, Jan Ole [1 ]
Matzke, Andreas [1 ]
Churakov, Gennady [1 ]
Kuritzin, Andrej [2 ]
Mayr, Gerald [3 ]
Brosius, Juergen [1 ]
Schmitz, Juergen [1 ]
机构
[1] Univ Munster, Inst Expt Pathol, ZMBE, D-48149 Munster, Germany
[2] St Petersburg State Inst Technol, Dept Math & Phys, St Petersburg 198013, Russia
[3] Forsch Inst Senckenberg, Div Ornithol, D-60325 Frankfurt, Germany
关键词
D O I
10.1186/1471-2148-7-190
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
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. Conclusion: 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.
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页数:11
相关论文
共 55 条
[1]   A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships [J].
Amrine-Madsen, H ;
Koepfli, KP ;
Wayne, RK ;
Springer, MS .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2003, 28 (02) :225-240
[2]  
Armstrong MH, 2001, AUK, V118, P799, DOI 10.1642/0004-8038(2001)118[0799:PUOAOI]2.0.CO
[3]  
2
[4]   A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences [J].
Birks, SM ;
Edwards, SV .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2002, 23 (03) :408-421
[5]   A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus) [J].
Churakov, G ;
Smit, AFA ;
Brosius, J ;
Schmitz, J .
MOLECULAR BIOLOGY AND EVOLUTION, 2005, 22 (04) :886-893
[6]  
CROWE T M, 1978, Annals of the South African Museum, V76, P43
[7]   Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes):: effects of character exclusion, data partitioning and missing data [J].
Crowe, Timothy M. ;
Bowie, Rauri C. K. ;
Bloomer, Paulette ;
Mandiwana, Tshifhiwa G. ;
Hedderson, Terry A. J. ;
Randi, Ettore ;
Pereira, Sergio L. ;
Wakeling, Julia .
CLADISTICS, 2006, 22 (06) :495-532
[8]   Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree [J].
de Jong, WW ;
van Dijk, MAM ;
Poux, C ;
Kappé, G ;
van Rheede, T ;
Madsen, O .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2003, 28 (02) :328-340
[9]   Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes [J].
Dimcheff, DE ;
Drovetski, SV ;
Mindell, DP .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2002, 24 (02) :203-215
[10]   Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters [J].
Dyke, GJ ;
Gulas, BE ;
Crowe, TM .
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, 2003, 137 (02) :227-244