Skip to main content
SpringerLink
Log in

Computational Reconstruction of Ancestral DNA Sequences

  • Protocol
Phylogenomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 422))

Abstract

This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
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 EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover 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

References

  1. Blanchette, M., Green, E. D., Webb, M., and Haussler, D. (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 14, 2412–2423.

    Article  CAS  PubMed  Google Scholar 

  2. International Human Genome Sequencing Consortium, Lander, E., et al. (2001) Initial sequencing and analysis of the human genome. Nature 5, 409(6822), 860–921 (PMID: 12466850).

    Article  CAS  PubMed  Google Scholar 

  3. International Mouse Genome Sequencing Consortium, Waterston, R. H., Lindblad-Toh, K., Birney, E., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 5, 420(6915), 520–562 (PMID: 12466850).

    Article  CAS  PubMed  Google Scholar 

  4. Rat Genome Sequencing Project Consortium, Gibbs, R. A., Weinstock, G. M., Metzker, M. L., et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521.

    Article  CAS  PubMed  Google Scholar 

  5. Margulies, E. H., Blanchette, M., NISC Comparative Sequencing Program, Haussler, D., and Green, E. (2003) Identification and characterization of multi-species conserved sequences. Genome Res. 13(12), 2507–2518 (PMID: 14656959).

    Article  CAS  PubMed  Google Scholar 

  6. Cooper, G. M., Brudno, M., Green, E. D., Batzoglou, S., and Sidow, A. (2003) Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13(5), 813–820.

    Article  CAS  PubMed  Google Scholar 

  7. Bejerano, G., Pheasant, M., Makunin, I., et al. (2004) Ultraconserved elements in the human genome. Science 304(5675), 1321–1325.

    Article  CAS  PubMed  Google Scholar 

  8. Goodman, M., Barnabas, J., Matsuda, G., and Moore, G. W. (1971) Molecular evolution in the descent of man. Nature 233, 604–613.

    Article  CAS  PubMed  Google Scholar 

  9. Enard, W., Przeworski, M., Fisher, S. E., et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418(6900), 869–872.

    Article  CAS  PubMed  Google Scholar 

  10. Eizirik, E., Murphy, W. J., and O’Brien, S. J. (2001) Molecular dating and biogeography of the early placental mammal radiation. J. Hered. 92(2), 212–219 (PMID: 11396581).

    Article  CAS  PubMed  Google Scholar 

  11. Springer, M. S., Murphy, W. J., Eizirik, E., and O’Brien, S. J. (2003). Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl Acad. Sci. U. S A 4, 100(3), 1056–1060 (PMID: 12552136).

    Article  CAS  PubMed  Google Scholar 

  12. Thomas, J., Touchman, J. W., Blakesley, R. W., et al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788–793.

    Article  CAS  PubMed  Google Scholar 

  13. Karolchick, D., Baertsch, R., Diekhans, M., et al. (2003) The UCSC genome browser database. Nucleic Acids Res. 31, 51–54.

    Article  Google Scholar 

  14. Maddison, D. R. and Schulz K.-S. (ed.) (2004) The Tree of Life Web Project. http://tolweb.org

  15. Felsenstein, J. (1989) PHYLIP-Phylogeny inference package (Version 3.2). Cladistics 5, 164–166.

    Google Scholar 

  16. Swofford, D. L. (2003) PAUP: Phylogenetic Analysis Using Parsimony. Sinauer, Sunderland, MA.

    Google Scholar 

  17. Huelsenbeck, J. P. and Ronquist, F. (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17, 754–755.

    Article  CAS  PubMed  Google Scholar 

  18. Bray, N. and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693–699.

    Article  CAS  PubMed  Google Scholar 

  19. Cooper, G. M., Stone, E. A., Asimenos, G., et al. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15(7), 901–913.

    Article  CAS  PubMed  Google Scholar 

  20. Blanchette, M., Kent, W. J., Riemer, C., et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708–715 (PMID: 15060014).

    Article  CAS  PubMed  Google Scholar 

  21. Schwartz, S., Kent, W. J., Smith, A., et al. (2003) Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103–107.

    Article  CAS  PubMed  Google Scholar 

  22. Chindelevitch, L., Li, Z., Blais, E., and Blanchette, M. (2006) On the inference of parsimonious indel evolutionary scenarios. J. Bioinformatics Comput. Biol. in press.

    Google Scholar 

  23. Fredslund, J., Hein, J., and Scharling, T. (2003) A large version of the small parsimony problem. Lecture Notes in Bioinformatics, Proceedings of WABI’03. 2812, 417–432.

    Google Scholar 

  24. Yang, Z., Kumar, S., and Nei, M. (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641–1650.

    CAS  PubMed  Google Scholar 

  25. Siepel, A. and Haussler, D. (2003) Combining phylogenetic and hidden Markov models in biosequence analysis. Proceedings of the 7th Annual International. Conference on Research in Computational Molecular Biology. pp. 277–286.

    Google Scholar 

  26. Bourque, G. and Pevzner, P. (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12(1), 26–36.

    CAS  PubMed  Google Scholar 

  27. Stoye, J., Evers, D., and Meyer, F. (1997) Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5, 303–204 (PMID: 9322053).

    CAS  PubMed  Google Scholar 

  28. Hasegawa, M., Kishino, H., and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22(2), 160–174.

    Article  CAS  PubMed  Google Scholar 

  29. Kent, J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. (2003). Evolution’s cauldron: duplication, deletion and rearrangement in the mouse and human genomes, Proc. Natl Acad. Sci. USA 100(20), 11,848–11,489.

    Article  Google Scholar 

  30. Jurka, J. (2002) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16(9), 418–420 (PMID: 10973072).

    Article  Google Scholar 

  31. Smit, A. and Green, P. (1999) RepeatMasker, http://ftp.genome.washington.edu/RM/RepeatMasker.html

  32. Hoeffding, W. (1963) Probability inequalities for sums of bounded random variables. J. Am. Stat. Assoc. 58, 13–27.

    Article  Google Scholar 

  33. Le Cam, L. (1986) Asymptotic Methods in Statistical Decision Theory, Springer, New York.

    Google Scholar 

  34. Lucena, B. and Haussler, D. (2005) Counterexample to a claim about the reconstruction of an ancestral character states. Syst Biol. 54(4), 693–695.

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. McGill Centre for Bioinformatics, McGill University, Montreal, Canada

    Mathauieu Blanchette & Abdoulaye Baniré Diallo

  2. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD

    Eric D. Green

  3. Center for Comparative Genomics and Bioinformatics, Penn State, University Park, PA

    Webb Miller

  4. Howard Hughes Medical Institute, University of California, Santa Cruz, CA

    David Haussler

Authors
  1. Mathauieu Blanchette
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Abdoulaye Baniré Diallo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eric D. Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Webb Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. David Haussler
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Mail Stop 4458, Texas A&M University, Raymond Stotzer Parkway, Rm 107 VMA, College Station, TX, 77843-4458, USA

    William J. Murphy PhD

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Blanchette, M., Diallo, A.B., Green, E.D., Miller, W., Haussler, D. (2008). Computational Reconstruction of Ancestral DNA Sequences. In: Murphy, W.J. (eds) Phylogenomics. Methods in Molecular Biology™, vol 422. Humana Press. https://doi.org/10.1007/978-1-59745-581-7_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-581-7_11

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-764-8

  • Online ISBN: 978-1-59745-581-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation