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Biochemical Genetics

, Volume 50, Issue 11–12, pp 959–966 | Cite as

Polyphyletic Origin of the Genus Amaurornis Inferred from Molecular Phylogenetic Analysis of Rails

  • Luzhang RuanEmail author
  • Yushi Wang
  • Jinrun Hu
  • Yi Ouyang
Note

Introduction

The Rallidae (a family of wading birds) are distributed worldwide and occupy diverse habitats (Slikas et al. 2002). Apart from the coots and some moorhens, most of these birds live on the ground in dense vegetation and are very difficult to observe (Wang 2006). About 15 endemic rail species are distributed in eastern Asia (Wang 2006), but unfortunately, most of the habitats for these taxa are disappearing rapidly and some species are becoming endangered. Previous phylogenetic studies of some Asian rails were unable to resolve some of the deeper relationship patterns (Livezey 1998; Sibley and Ahlquist 1990; Slikas et al. 2002). In this study, we took a molecular approach, using mitochondrial DNA sequences to examine the relationships among these species.

Materials and Methods

DNA Extraction, PCR Amplification, and Sequencing

Cytochrome c oxidase subunit I (COI) and cytochrome b (CYTB) sequences were obtained from 10 of the 15 extant rail species (Table  1; Wang 2006)...

Keywords

Codon Position Much Recent Common Ancestor Parsimony Informative Character Substantial Node Potential Scale Reduction Factor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank the Chinese Natural Science Foundations (No. 30960052 and 31260510) and the Jiangxi Province Education Foundation (GJJ12002) for their financial support to this study.

References

  1. Archer M, Arena DA, Bassarova M, Beck RMD, Black K, Boles WE, Brewer P, Cooke BN, Crosby K, Gillespie A, Godthelp H, Hand SJ, Kear BP, Louys J, Morrell A, Muirhead J, Roberts K, Scanlon JD, Travouillon KJ, Muirhead S (2006) Current status of species-level representation in faunas from selected fossil localities in the Riversleigh World Heritage Area, northwestern Queensland. Alcheringa 1(Special Issue):1–17Google Scholar
  2. Drummond AJ, Rambaut A (2007) Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214PubMedCrossRefGoogle Scholar
  3. Edwards SV, Arctander P, Wilson AC (1991) Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc Royal Soc London Series B 243:99–107CrossRefGoogle Scholar
  4. Fain MG, Krajewski C, Houde P (2007) Phylogeny of “core Gruiformes” (Aves: Grues) and resolution of the Limpkin–Sungrebe problem. Mol Phylogen Evol 43(2):515–529CrossRefGoogle Scholar
  5. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1–15CrossRefGoogle Scholar
  6. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  7. Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–6200PubMedCrossRefGoogle Scholar
  8. Krajewski C, Sipiorski JT, Anderson FE (2010) Complete mitochondrial genome sequences and the phylogeny of cranes (Gruiformes: Gruidae). Auk 127:440–452CrossRefGoogle Scholar
  9. Livezey BC (1998) A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae). Philos Trans Royal Soc Lond B 353:2077–2151CrossRefGoogle Scholar
  10. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
  11. Nylander J, Ronquist F, Huelsenbeck JP, Nieves-Aldrey J (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53:47–67PubMedCrossRefGoogle Scholar
  12. Olson SL (1973) A classification of the Rallidae. Wilson Bull 85:381–416Google Scholar
  13. Ozaki K, Yamamoto Y, Yamagishi S (2010) Genetic diversity and phylogeny of the endangered Okinawa rail, Gallirallus okinawae. Genes Genet Syst 85:55–63PubMedCrossRefGoogle Scholar
  14. Rambaut A (2007) FigTree [online]. Website last modified 9 Aug 2007. http://beast.bio.ed.ac.uk/FigTree. Accessed 12 Oct 2011
  15. Ruan LZ, Zhang LX, Wen LY, Sun QW, Liu NF (2005) Phylogeny and molecular evolution of Tetraogallus in China. Biochem Genet 43:507–518CrossRefGoogle Scholar
  16. Sibley CG, Ahlquist J (1990) Phylogeny and classification of birds. Yale University Press, New HavenGoogle Scholar
  17. Slikas B, Olson SL, Fleischer RC (2002) Rapid, independent evolution of flightlessness in four species of Pacific island rails (Rallidae): an analysis based on mitochondrial sequence data. J Avian Biol 33:5–14CrossRefGoogle Scholar
  18. Stamatakis A (2006) RA × ML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690PubMedCrossRefGoogle Scholar
  19. Swofford DL (1998) PAUP: phylogenetic analysis using parsimony (and other methods). Sinauer Associates, SunderlandGoogle Scholar
  20. Taira A (2001) Tectonic evolution of the Japanese island arc system. Annu Rev Earth Planet Sci 29:109–134CrossRefGoogle Scholar
  21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCrossRefGoogle Scholar
  22. Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol Biol 8:81PubMedCrossRefGoogle Scholar
  23. Taylor B, van Perlo B (1998) Rails: a guide to the rails, crakes, gallinules and coots of the world. Pica Press, RobertsbridgeGoogle Scholar
  24. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment though sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  25. Wang QS (2006) Fauna Sinica: Aves Gruiformes. Science Press, Beijing, pp 57–125Google Scholar
  26. Yang R, Xb Wu, Yan P, Su X, Yang BH (2010) Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences. Mol Biol Reports 37:3057–3066CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Luzhang Ruan
    • 1
    Email author
  • Yushi Wang
    • 1
  • Jinrun Hu
    • 1
  • Yi Ouyang
    • 1
  1. 1.School of Life Sciences and Food Engineering, Nanchang UniversityNanchangChina

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