Skip to main content
SpringerLink
Log in

How to Infer Ancestral Genome Features by Parsimony: Dynamic Programming over an Evolutionary Tree

  • Chapter
Models and Algorithms for Genome Evolution

Part of the book series: Computational Biology ((COBO,volume 19))

Abstract

We review mathematical and algorithmic problems of reconstructing evolutionary features at ancestors in a known phylogeny. In particular, we revisit a generic framework for the problem that was introduced by Sankoff and Rousseau (Math. Program. 9:240–246, 1975).

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 EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
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. Agnarsson, I., Miller, J.A.: Is ACCTRAN better than DELTRAN? Cladistics 24, 1–7 (2008)

    Article  Google Scholar 

  2. Ames, R.M., Money, D., Ghatge, V.P., Whelan, S., Lovell, S.C.: Determining the evolutionary history of gene families. Bioinformatics 28(1), 48–55 (2012)

    Article  Google Scholar 

  3. Bérard, S., Gallien, C., Boussau, B., Szöllősi, G.J., Daubin, V., Tannier, E.: Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics 28, i382–i388 (2012)

    Article  Google Scholar 

  4. Blanchette, M., Green, E.D., Miller, W., Haussler, D.: Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 12, 2412–2423 (2004)

    Article  Google Scholar 

  5. Blanchette, M., Schwikowski, B., Tompa, M.: Algorithms for phylogenetic footprinting. J. Comput. Biol. 9(2), 211–223 (2002)

    Article  Google Scholar 

  6. Caetano-Anollés, G.: Evolution of genome size in the grasses. Crop Sci. 45, 1809–1816 (2005)

    Article  Google Scholar 

  7. Camin, J.H., Sokal, R.R.: A method for deducing branching sequences in phylogeny. Evolution 19, 311–326 (1965)

    Article  Google Scholar 

  8. Capra, J.A., Williams, A.G., Pollard, K.S.: Proteinhistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput. Biol. 8(6), e1002567 (2011)

    Article  Google Scholar 

  9. Cavalli-Sforza, L.L., Edwards, A.W.H.: Phylogenetic analysis models and estimation procedures. Am. J. Hum. Genet. 19(3), 233–267 (1967)

    Google Scholar 

  10. Clemente, J.C., Ikeo, K., Valiente, G., Gojobori, T.: Optimized ancestral state reconstruction using Sankoff parsimony. BMC Bioinform. 10, 51 (2009)

    Article  Google Scholar 

  11. Csűrös, M.: Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26(15), 1910–1912 (2010)

    Article  Google Scholar 

  12. Csűrös, M.: Ancestral reconstruction by asymmetric Wagner parsimony over continuous characters and squared parsimony over distributions. In: Proc. Sixth RECOMB Comparative Genomics Satellite Workshop. Springer Lecture Notes in Bioinformatics, vol. 5267, pp. 72–86 (2008)

    Google Scholar 

  13. Darwin, C.: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London (1859)

    Google Scholar 

  14. Day, W.H.E.: Computationally difficult parsimony problems in phylogenetic systematics. J. Theor. Biol. 103, 429–438 (1983)

    Article  Google Scholar 

  15. Day, W.H.E., Johnson, D.S., Sankoff, D.: The computational complexity of inferring rooted phylogenies by parsimony. Math. Biosci. 81, 33–42 (1986)

    Article  MathSciNet  MATH  Google Scholar 

  16. Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Syst. Zool. 35, 224–229 (1986)

    Article  Google Scholar 

  17. Edwards, A.W.F., Cavalli-Sforza, L.L.: Reconstructing evolutionary trees. In: Heywood, V.H., McNeill, J. (eds.) Phenetic and Phylogenetic Classification, vol. 6, pp. 67–76. Systematics Association, London (1963)

    Google Scholar 

  18. Elias, I.: Settling the intractability of multiple alignment. J. Comput. Biol. 13(7), 1323–1339 (2006)

    Article  MathSciNet  Google Scholar 

  19. Farris, J.S.: Methods for computing Wagner trees. Syst. Zool. 19(1), 83–92 (1970)

    Article  Google Scholar 

  20. Farris, J.S.: Phylogenetic analysis under Dollo’s law. Syst. Zool. 26(1), 77–88 (1977)

    Article  MathSciNet  Google Scholar 

  21. Feijão, P., Meidanis, J.: SCJ: a breakpoint-like distance that simplifies several rearrangement problems. IEEE/ACM Trans. Comput. Biol. Bioinform. 8(5), 1318–1329 (2011)

    Article  Google Scholar 

  22. Felsenstein, J.: Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22(3), 240–249 (1973)

    Article  Google Scholar 

  23. Felsenstein, J.: Parsomony in systematics: biological and statistical issues. Annu. Rev. Ecol. Syst. 14, 313–333 (1983)

    Article  Google Scholar 

  24. Fitch, W.M.: Toward defining the course of evolution: minimum changes for a specific tree topology. Syst. Zool. 20, 406–416 (1971)

    Article  Google Scholar 

  25. Fitch, W.M., Farris, J.S.: Evolutionary trees with minimum nucleotide replacements from amino acid sequences. J. Mol. Evol. 3(4), 263–278 (1974)

    Article  Google Scholar 

  26. Gelfman, S., Burstein, D., Penn, O., Savchenko, A., Amit, M., Schwartz, S., Pupko, T., Ast, G.: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res. 22(1), 35–50 (2012)

    Article  Google Scholar 

  27. Han, M.V., Hahn, M.W.: Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony. Genetics 190, 813–825 (2012)

    Article  Google Scholar 

  28. Hartigan, J.: Minimum mutation fits to a given tree. Biometrics 29, 53–65 (1973)

    Article  Google Scholar 

  29. Hwang, F.K., Richards, D.S.: Steiner tree problems. Networks 22, 55–89 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  30. Kannan, L., Wheeler, W.C.: Maximum parsimony on phylogenetic networks. Algorithms Mol. Biol. 7, 9 (2012)

    Article  Google Scholar 

  31. Kasap, S., Benkrid, K.: High performance phylogenetic analysis with maximum parsimony on reconfigurable hardware. IEEE Trans. VLSI Syst. 19(5) (2011)

    Google Scholar 

  32. Kluge, A.R., Farris, J.S.: Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1–32 (1969)

    Article  Google Scholar 

  33. Koonin, E.V.: Comparative genomics, minimal gene sets and the last universal common ancestor. Nat. Rev. Microbiol. 1, 127–136 (2003)

    Article  Google Scholar 

  34. Le Quesne, W.J.: The uniquely evolved character concept and its cladistic application. Syst. Zool. 23, 513–517 (1974)

    Article  Google Scholar 

  35. Maddison, W.P.: Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Syst. Zool. 40(3), 304–314 (1991)

    Article  Google Scholar 

  36. Makarova, K.S., Sorokin, A.V., Novichkov, P.S., Wolf, Y.I., Koonin, E.V.: Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol. Direct 2, 33 (2007)

    Article  Google Scholar 

  37. Mirkin, B.G., Fenner, T.I., Galperin, M.Y., Koonin, E.V.: Algorithms for computing evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3, 2 (2003)

    Article  Google Scholar 

  38. Moret, B.M.E., Lin, Y., Tang, J.: Rearrangements in phylogenetic inference: compare or encode? In: Chauve, C. et al. (eds.) Models and Algorithms for Genome Evolution. Computational Biology, vol. 19. Springer, Berlin (2014). In this volume

    Google Scholar 

  39. Narushima, H., Misheva, N.: On characteristics of ancestral-state reconstructions under the accelerated transformation optimization. Discrete Appl. Math. 122, 195–209 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  40. Needleman, S.B., Wunsch, C.B.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)

    Article  Google Scholar 

  41. Pauling, L., Zuckerkandl, E.: Chemical paleogenetics: molecular “restoration studies” of extinct forms of life. Acta Chem. Scand. 17, 9–16 (1963)

    Article  Google Scholar 

  42. Rogers, J.S.: Deriving phylogenetic trees from allele frequencies. Syst. Zool., 52–63 (1984)

    Google Scholar 

  43. Sankoff, D.: Minimal mutation trees of sequences. SIAM J. Appl. Math. 28(1) (1975)

    Google Scholar 

  44. Sankoff, D.: The early introduction of dynamic programming into computational biology. Bioinformatics 16(1), 41–47 (2000)

    Article  Google Scholar 

  45. Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., Cedergren, R.: Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. USA 89, 6575–6579 (1992)

    Article  Google Scholar 

  46. Sankoff, D., Morel, C., Cedergren, R.J.: Evolution of 5S RNA and the non-randomness of base replacement. Nat., New Biol. 245, 232–234 (1973)

    Article  Google Scholar 

  47. Sankoff, D., Rousseau, P.: Locating the vertices of a Steiner tree in arbitrary metric space. Math. Program. 9, 240–246 (1975)

    Article  MathSciNet  MATH  Google Scholar 

  48. Schwartz, S., Silva, J., Burstein, D., Pupko, T., Eyras, E., Ast, G.: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 18, 88–103 (2008)

    Article  Google Scholar 

  49. Swofford, D.L., Maddison, W.P.: Reconstructing ancestral states using Wagner parsimony. Math. Biosci. 87, 199–229 (1987)

    Article  MathSciNet  MATH  Google Scholar 

  50. Tang, J., Wang, L.-S.: Improving genome rearrangement phylogeny using sequence-style parsimony. In: Proceedings of the IEEE Fifth Symposium on Bioinformatics and Bioengineering (BIBE’05), pp. 137–144 (2005)

    Chapter  Google Scholar 

  51. Witmer, P.D., Doheny, K.F., Adams, M.K., Boehm, C.D., Dizon, J.S., Goldstein, J.L., Templeton, T.M., Wheaton, A.M., Dong, P.N., Pugh, E.W., Nussbaum, R.L., Hunter, K., Kelmenson, J.A., Rowe, L.B., Brownstein, M.J.: The development of a highly informative mouse simple sequence length polymorphism (SSLP) marker set and construction of a mouse family tree using parsimony analysis. Genome Res. 13, 485–491 (2003)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science and Operations Research, University of Montréal, Montreal, QC, Canada

    Miklós Csűrös

Authors
  1. Miklós Csűrös
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Miklós Csűrös .

Editor information

Editors and Affiliations

  1. Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada

    Cedric Chauve

  2. Computer Science and Operations Research, University of Montreal, Montreal, Québec, Canada

    Nadia El-Mabrouk

  3. Biometry and Evolutionary Biology, INRIA Rhône-Alpes, University of Lyon, Villeurbanne, France

    Eric Tannier

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag London

About this chapter

Cite this chapter

Csűrös, M. (2013). How to Infer Ancestral Genome Features by Parsimony: Dynamic Programming over an Evolutionary Tree. In: Chauve, C., El-Mabrouk, N., Tannier, E. (eds) Models and Algorithms for Genome Evolution. Computational Biology, vol 19. Springer, London. https://doi.org/10.1007/978-1-4471-5298-9_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4471-5298-9_3

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-4471-5297-2

  • Online ISBN: 978-1-4471-5298-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation