Skip to main content
SpringerLink
Log in

An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation

  • Conference paper
Algorithms in Bioinformatics (WABI 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6293))

Included in the following conference series:

Abstract

DNA-based species assignment and delimitation are two important problems in systematic biology. In a recent work of O’Meara, species delimitation is investigated through coupling it with species tree inference in the framework of gene tree and species tree reconciliation. We present a polynomial time algorithm for splitting individuals into species to minimize the deep coalescence cost of the gene tree and species tree reconciliation, a species assignment problem arises from species delimitation via gene tree and species tree reconciliation. How to incorporate this proposed algorithm into the heuristic search strategy of O’Meara for species delimitation is also discussed. The proposed algorithm is implemented in C++.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Agapow, P.M.: The impact of species concept on biodiversity studies. Q. Rev. Biol. 79, 161–179 (2004)

    Article  PubMed  Google Scholar 

  2. Bafna, V., Hannenhalli, S., Rice, K., Vawter, L.: Ligand-Receptor pairing via tree comparison. J. Comput. Biol. 7, 59–70 (2000)

    Article  CAS  PubMed  Google Scholar 

  3. Baum, D.A., Shaw, K.L.: Genealogical perspectives on the species problem. In: Hoch, P.C., Stephenson, A.C. (eds.) Experimental and molecular approaches to plant biosystematics, pp. 289–303. Missouri Botanical Garden, Saint Louis (1995)

    Google Scholar 

  4. Brockelman, W.Y., Gittins, S.P.: Natural hybridization in the Hylobates lar species group: implications for speciation in gibbons. In: Preushcoft, H., Chivers, D.J., Brockelman, W.Y., et al. (eds.) The Lesser Apes. Evolutionary and Behavioral Biology. Edinburgh University Press, Edinburgh (1984)

    Google Scholar 

  5. Burns, J.M., Janzen, D.H., Hajibabaei, M., Hallwachs, W., Hebert, P.D.: DNA barcodes and cryptic species of skipper butterflies in the genus Perichares in Area de Conservacion Guanacaste, Costa Rica. Proc. Nat’l. Acad. Sci. USA 105, 6350–6355 (2008)

    Article  CAS  Google Scholar 

  6. De Queiroz, K.: Species concepts and species delimitation. Syst. Biol. 56, 879–886 (2007)

    Article  PubMed  Google Scholar 

  7. Degnan, J.H., Rosenberg, N.A.: Discordance of species trees with their most likely gene trees. PLoS Genet. 2, e68 (2006)

    Article  Google Scholar 

  8. Doyle, J.J.: Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot. 17, 144–163 (1992)

    Article  Google Scholar 

  9. Fitch, W.: Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99–113 (1970)

    Article  CAS  PubMed  Google Scholar 

  10. Goodman, M., et al.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132–163 (1979)

    Article  CAS  Google Scholar 

  11. Guigó, R., Muchnik, I., Smith, T.: Reconstruction of ancient molecular phylogeny. Mol. Phylogenet Evol. 6, 189–213 (1996)

    Article  PubMed  Google Scholar 

  12. Hebert, P.D.N., Cywinska, A., Ball, S.L., DeWaard, J.R.: Biological identification through DNA barcodes. Proc. R. Soc. B 270, 313–321 (2003)

    Google Scholar 

  13. Hebert, P.D.N., Gregory, T.R.: The promise of DNA barcoding for taxonomy. Syst. Biol. 54, 852–859 (2005)

    Article  PubMed  Google Scholar 

  14. Knowles, L.L., Carstens, B.C.: Delimiting species without monophyletic gene trees. Syst. Biol. 56, 887–895 (2007)

    Article  PubMed  Google Scholar 

  15. Leaché, A.D., et al.: Quantifying ecological, morphological, and genetic variation to delimit speceis in the coast horned lizard speceis complex (Phrynosoma). Proc. Nat’l Acad. Sci. USA 106, 12418–12423 (2009)

    Article  Google Scholar 

  16. Leliaert, F., Verbruggen, H., Wysor, B., De Clerck, O.: DNA taxonomy in morphologically plastic taxa: algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales). Mol. Phylogenet. Evol. 53, 122–133 (2009)

    Article  CAS  PubMed  Google Scholar 

  17. Libeskind-Hadas, R., Charleston, M.A.: On the computational complexity of the reticulate cophylogeny reconstruction problem. J. Comput. Biol. 16, 105–117 (2009)

    Article  CAS  PubMed  Google Scholar 

  18. Ma, B., Li, M., Zhang, L.X.: From gene trees to species trees. SIAM J. Comput. 30, 729–752 (2000)

    Article  Google Scholar 

  19. Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46, 523–536 (1997)

    Article  Google Scholar 

  20. Mallet, J., Willmott, K.: Taxonomy: Renaissance or tower of babel? Trends Ecol. Evol. 18, 57–59 (2003)

    Article  Google Scholar 

  21. Matz, M.V., Nielsen, R.: A likelihood ratio test for species membership based on DNA sequence data. Phil. Trans. R. Soc. B 360, 1969–1974 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Nielsen, R., Matz, M.: Statistical approaches for DNA barcoding. Syst. Biol. 55, 162–169 (2006)

    Article  PubMed  Google Scholar 

  23. O’Meara, B.C.: New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59, 59–73 (2010)

    Article  PubMed  Google Scholar 

  24. Page, R.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58–77 (1994)

    Google Scholar 

  25. Pamilo, P., Nei, M.: Relationship between gene trees and species trees. Mol. Biol. Evol. 5, 568–583 (1988)

    CAS  PubMed  Google Scholar 

  26. Petit, J.R., Excoffier, L.: Gene flow and species delimitation. Trends Ecol. Evol. 24, 386–393 (2009)

    Article  PubMed  Google Scholar 

  27. Pons, J., et al.: Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55, 595–609 (2006)

    Article  PubMed  Google Scholar 

  28. Ronquist, F.: Three-dimensional cost matrix optimisation and maximum cospeciation. Cladistics 14, 167–172 (1998)

    Article  Google Scholar 

  29. Steinke, D., Vences, N., Salzburger, W., Meyer, A.: TaxI: a software tool for DNA barcoding using distance methods. Phil. Trans. R. Soc. B 360, 1975–1980 (2005)

    Google Scholar 

  30. Tautz, D., et al.: DNA points the way ahead in taxonomy. Nature 418, 479 (2002)

    Article  CAS  PubMed  Google Scholar 

  31. Will, K.W., Rubinoff, D.: Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classigication. Cladistics 20, 47–55 (2004)

    Article  Google Scholar 

  32. Xu, S.: Phylogenetic analysis under reticulate evolution. Mol. Biol. Evol. 17, 897–907 (2000)

    Article  CAS  PubMed  Google Scholar 

  33. Zhang, L.X.: From gene trees to species trees II: Species tree inference in the deep coalescence model. Manuscript (2010)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge Road, Singapore, 119076

    Louxin Zhang & Yun Cui

Authors
  1. Louxin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yun Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Computing Sciences, University of East Anglia, NR 7TJ, Norwich, UK

    Vincent Moulton

  2. Lewis-Sigler Institute for Integrative Genomics, Department of Computer Science, Princeton University, NJ 08544, Princeton, USA

    Mona Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Zhang, L., Cui, Y. (2010). An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation. In: Moulton, V., Singh, M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science(), vol 6293. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15294-8_25

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-15294-8_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15293-1

  • Online ISBN: 978-3-642-15294-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation