Retroposon insertion patterns of neoavian birds: Strong evidence for an extensive incomplete lineage sorting era

Molecular Biology and Evolution

Volumn 29, Issue 6, 2012, Pages 1497-1501

  Matzke, Andreas ^a   Churakov, Gennady ^a   Berkes, Petra ^a   Arms, Erin M ^a   Kelsey, Denise ^a   Brosius, Jürgen ^a   Kriegs, Jan Ole ^a,b   Schmitz, Jürgen ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b Landschaftsverband Westfalen Lippe   (Germany)

Author keywords

Bird orders; Cumulative retroposon fixation probability; Incomplete lineage sorting; Neoaves; Phylogeny; Retroposons

Indexed keywords

ARTICLE; BIRD; CRETACEOUS; EVOLUTION; GENETIC POLYMORPHISM; NONHUMAN; PHYLOGENY; PROBABILITY; RETROPOSON;

ANIMALS; BIRDS; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENETIC SPECIATION; MUTAGENESIS, INSERTIONAL; PHYLOGENY; POLYMORPHISM, GENETIC; RETROELEMENTS;

AVES; DINOSAURIA;

EID: 84861358284     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr319     Document Type: Article

References (19)

1. Bashir A, Ye C, Price AL, Bafna V. 2005. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 15:998-1006. (Pubitemid 40994220)
2. Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J. 2010. A novel web-based TinT application and the chronology of the Primate Alu retroposon activity. BMC Evol Biol. 10:376.
3. Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J. 2009. Mosaic retroposon insertion patterns in placental mammals. Genome Res. 19:868-875.
4. Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J. 2010. Rodent evolution: back to the root. Mol Biol Evol. 27:1315-1326.
5. Hackett SJ, Kimball RT, Reddy S, et al. (18 co-authors). 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768. (Pubitemid 351931288)
6. Han KL, Braun EL, Kimball RT, et al. (17 co-authors). 2011. Are transposable element insertions homoplasy free?: an examination using the avian tree of life. Syst Biol. 60:375-386.
7. Kaiser VB, van Tuinen M, Ellegren H. 2007. Insertion events of CR1 retrotransposable elements elucidate the phylogenetic branching order in galliform birds. Mol Biol Evol. 24:338-347. (Pubitemid 46026306)
8. Kimura M, Ohta T. 1969. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61:763-771.
9. Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J. 2007. Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). BMC Evol Biol. 7:190.
10. Mayr G. 2011. Metaves, Mirandornithes, Strisores and other novelties-a critical review of the higher-level phylogeny of neornithine birds. J Zool Syst Evol Res. 49:58-76.
11. Nishihara H, Maruyama S, Okada N. 2009. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc Natl Acad Sci USA. 106:5235-5240.
12. Poe S, Chubb AL. 2004. Birds in a bush: five genes indicate explosive evolution of avian orders. Evolution 58:404-415. (Pubitemid 38362384)
13. Schmitz J, Zischler H. 2002. Molecular cladistic markers and the infraordinal phylogenetic relationships of primates. In: Kay RF, Ross C, editors. In anthropoid origins: new visions. New York: Kluwer Academic Press.
14. Shedlock AM, Takahashi K, Okada N. 2004. SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol. 19:545-553. (Pubitemid 39234761)
15. Steel M, Penny D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol Biol Evol. 17:839-850. (Pubitemid 30346543)
16. Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, Brosius J, Kriegs JO, Schmitz J. 2011. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat Commun. 2:443.
17. Takahashi K, Terai Y, Nishida M, Okada N. 2001. Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol. 18:2057-2066. (Pubitemid 33026777)
18. Treplin S, Tiedemann R. 2007. Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae). Mol Phylogenet Evol. 43:328-337. (Pubitemid 46484354)
19. Watanabe M, Nikaido M, Tsuda TT, Inoko H, Mindell DP, Murata K, Okada N. 2006. The rise and fall of the CR1 subfamily in the lineage leading to penguins. Gene 365:57-66. (Pubitemid 43185224)