Skip to main content
SpringerLink
Log in

Ancestral Genome Reconstruction

  • Chapter
  • First Online:
Bioinformatics and Phylogenetics

Part of the book series: Computational Biology ((COBO,volume 29))

Abstract

Reconstruction of extinct ancestral genomes is an important topic in comparative genomics and has a wide range of applications. By comparing a current-day species against its ancestor, we can deduce how it differs from the ancestor and infer detailed information about the evolution of species. With more and more fully sequenced genomes becoming available, we are able to reconstruct ancestors at the whole genome level by using evolutionary events such as genome rearrangements, gene insertions, deletions and duplications. In this chapter, we will present the concepts related to whole genome evolution and ancestral reconstruction. We will review evolutionary models and algorithms in pairwise comparison of genomes, computing of the median problem and optimizations in inferring phylogenies and ancestors from multiple genomes.

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

Access this chapter

Log in via an institution
eBook
USD 16.99
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. Avdeyev, P., Jiang, S., Aganezov, S., Hu, F., Alekseyev, M.A.: Reconstruction of ancestral genomes in presence of gene gain and loss. J. Comput. Biol. 23(3), 150–164 (2016)

    Article  MathSciNet  Google Scholar 

  2. Bader, D., Moret, B., Yan, M.: A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8(5), 483–491 (2001)

    Article  Google Scholar 

  3. Bader, M.: Genome rearrangements with duplications. BMC Bioinform. 11(Supple 1), S27 (2010)

    Google Scholar 

  4. Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI’06). Lecture Notes in Computer Science, vol. 4175, pp. 163–173. Springer Verlag, Berlin (2006)

    Google Scholar 

  5. Biller, P., Feijao, P., Meidanis, J.: Rearrangement-based phylogeny using the single-cut-or-join operation. IEEE/ACM Trans. Comput. Biol. Bioinform. (TCBB) 10(1), 122–134 (2013)

    Article  Google Scholar 

  6. Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. Genome Inform. 8, 25–34 (1997)

    Google Scholar 

  7. Braga, M., Stoye, J.: Counting all DCJ sorting scenarios. In: Proceedings of RECOMB International Workshop on Comparative Genomics (RECOMB-CG’09), pp. 36–47. Springer Verlag, Berlin (2009)

    Chapter  Google Scholar 

  8. Caprara, A.: On the practical solution of the reversal median problem. In: Proceedings of the 1st International Workshop Algorithms in Bioinformatics (WABI’01). Lecture Notes in Computer Science, vol. 2149, pp. 238–251 (2001)

    Google Scholar 

  9. Compeau, P.: A simplified view of DCJ-Indel distance. In: Proceedings of the 12th Workshop Algorithms in Bioinformatics (WABI’12). Lecture Notes in Computer Science, vol. 7534, pp. 365–377. Springer Verlag, Berlin (2012)

    Google Scholar 

  10. Cosner, M., Jansen, R., Moret, B., Raubeson, L., Wang, L.S., Warnow, T., Wyman, S.: A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes. In: Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB’00), pp. 104–115 (2000)

    Google Scholar 

  11. Feijão, P., Meidanis, J.: SCJ: a variant of breakpoint distance for which sorting, genome median and genome halving problems are easy. In: International Workshop on Algorithms in Bioinformatics, pp. 85–96. Springer (2009)

    Google Scholar 

  12. Feng, B., Lin, Y., Zhou, L., Guo, Y., Friedman, R., Xia, R., Hu, F., Liu, C., Tang, J.: Reconstructing yeasts phylogenies and ancestors from whole genome data. Sci. Rep. 7(1), 15,209 (2017)

    Google Scholar 

  13. Fertin, G., Labarre, A., Rusu, I., Vialette, S., Tannier, E.: Combinatorics of Genome Rearrangements. MIT press (2009)

    Google Scholar 

  14. Fitch, W.M.: Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Biol. 20(4), 406–416 (1971)

    Article  Google Scholar 

  15. Gagnon, Y., Blanchette, M., El-Mabrouk, N.: A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinform. 13(Suppl 19), S4 (2012)

    Google Scholar 

  16. Hannenhalli, S., Pevzner, P.: Transforming mice into men (polynomial algorithm for genomic distance problems). In: Proceedings of the 36th Annual IEEE Symposium on Foundations of Computer Science (FOCS’95), pp. 581–592 (1995)

    Google Scholar 

  17. Hu, F., Lin, Y., Tang, J.: MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinform. 15(1), 1 (2014)

    Article  Google Scholar 

  18. Hu, F., Zhou, J., Zhou, L., Tang, J.: Probabilistic reconstruction of ancestral gene orders with insertions and deletions. IEEE/ACM Trans. Comput. Biol. Bioinform. 11(4), 667–672 (2014)

    Article  Google Scholar 

  19. Hu, F., Zhou, L., Tang, J.: Reconstructing ancestral genomic orders using binary encoding and probabilistic models. In: Bioinformatics Research and Applications, pp. 17–27. Springer (2013)

    Google Scholar 

  20. Huson, D., Vawter, L., Warnow, T.: Solving large scale phylogenetic problems using DCM-2. In: Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB’99) (1999)

    Google Scholar 

  21. Jones, B.R., Rajaraman, A., Tannier, E., Chauve, C.: ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics 28(18), 2388–2390 (2012)

    Article  Google Scholar 

  22. Kirkpatrick, S., Gelatt, C., Vecchi, M.: Optimization by simulated annealing. Science 220(4598), 671–680 (1983)

    Article  MathSciNet  Google Scholar 

  23. Lin, Y., Hu, F., Tang, J., Moret, B.: Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes. In: Pacific Symposium on Biocomputing, pp. 357–366. World Scientific (2013)

    Google Scholar 

  24. Lin, Y., Moret, B.: Estimating true evolutionary distances under the DCJ model. In: Proceedings of the 16th International Conference on Intelligent Systems for Molecular Biology (ISMB’08) (2008)

    Article  Google Scholar 

  25. Lin, Y., Rajan, V., Swenson, K., Moret, B.: Estimating true evolutionary distances under rearrangements, duplications, and losses. In: Proceedings of the 8th Asia Pacific Bioinformatics Conference (APBC’10). BMC Bioinform. 11(Suppl 1), S54 (2010)

    Google Scholar 

  26. Ma, J.: A probabilistic framework for inferring ancestral genomic orders. In: 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 179–184. IEEE (2010)

    Google Scholar 

  27. Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, W.J., Blanchette, M., Haussler, D., Miller, W.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16(12), 1557–1565 (2006)

    Article  Google Scholar 

  28. Marron, M., Swenson, K., Moret, B.: Genomic distances under deletions and insertions. In: Proceedings of the 9th International Conference Computing and Combinatorics (COCOON’03). Lecture Notes in Computer Science, vol. 2697, pp. 537–547. Springer Verlag, Berlin (2003)

    Google Scholar 

  29. Metropolis, N., Rosenbluth, A., Rosenbluth, M.: Equation of state calculations by fast computing machines. J. Chem. Phys. 21(6), 1087–1092 (1953)

    Article  Google Scholar 

  30. Moret, B., Lin, Y., Tang, J.: Rearrangements in phylogenetic inference: compare, model, or encode? In: Models and Algorithms for Genome Evolution, pp. 147–171. Springer (2013)

    Google Scholar 

  31. Moret, B., Siepel, A., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI’02). Lecture Notes in Computer Science, vol. 2452, pp. 521–536. Springer Verlag, Berlin (2002)

    MATH  Google Scholar 

  32. Moret, B., Tang, J., Wang, L.S., Warnow, T.: Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65(3), 508–525 (2002)

    Article  MathSciNet  Google Scholar 

  33. Moret, B., Warnow, T.: Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics. In: Fleischer, R., Moret, B., Schmidt, E. (eds.) Experimental Algorithmics. Lecture Notes in Computer Science, vol. 2547, pp. 163–180. Springer Verlag, Berlin (2002)

    Chapter  Google Scholar 

  34. Moret, B., Wyman, S., Bader, D., Warnow, T., Yan, M.: A new implementation and detailed study of breakpoint analysis. In: Proceedings of the 6th Pacific Symposium on Biocomputing (PSB’01), pp. 583–594. World Scientific Pub. (2001)

    Google Scholar 

  35. Pe’er, I., Shamir, R.: The median problems for breakpoints are NP-complete. Elec. Colloq. Comput. Complex. 71 (1998)

    Google Scholar 

  36. Perrin, A., Varré, J.S., Blanquart, S., Ouangraoua, A.: Procars: progressive reconstruction of ancestral gene orders. BMC Genomics 16(Suppl 5), S6 (2015)

    Article  Google Scholar 

  37. Rajan, V., Xu, W., Lin, Y., Swenson, K., Moret, B.: Heuristics for the inversion median problem. In: Proceedings of the 8th Asia Pacific Bioinformatics Conference (APBC’10). BMC Bioinform. 11(Suppl 1), S30 (2010)

    Google Scholar 

  38. Shao, M., Lin, Y.: Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. BMC Bioinform. 13(Suppl 19), S13 (2012)

    Article  Google Scholar 

  39. Shao, M., Lin, Y., Moret, B.: An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes. J. Comput. Biol. 22(5), 425–435 (2015)

    Article  MathSciNet  Google Scholar 

  40. Siepel, A., Moret, B.: Finding an optimal inversion median: experimental results. In: Proceedings of the 1st International Workshop Algorithms Bioinformatics (WABI’01). Lecture Notes in Computer Science, vol. 2149, pp. 189–203. Springer Verlag, Berlin (2001)

    Google Scholar 

  41. Silva, P., Braga, M., Machado, R., Dantas, S.: DCJ-indel distance with distinct operation costs. In: Proceedings of the 12th Workshop on Algorithms in Bioinformatics (WABI’12). Lecture Notes in Computer Science, vol. 7534, pp. 378–390. Springer Verlag, Berlin (2012)

    Google Scholar 

  42. Swenson, K., Arndt, W., Tang, J., Moret, B.: Phylogenetic reconstruction from complete gene orders of whole genomes. In: Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC’08), pp. 241–250 (2008)

    Google Scholar 

  43. Tang, J., Moret, B.: Scaling up accurate phylogenetic reconstruction from gene-order data. In: Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB’03). Bioinformatics, vol. 19, pp. i305–i312. Oxford U. Press (2003)

    Google Scholar 

  44. Tang, J., Moret, B., Cui, L., dePamphilis, C.: Phylogenetic reconstruction from arbitrary gene-order data. In: Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering BIBE’04, pp. 592–599. IEEE Press, Piscataway, NJ (2004)

    Google Scholar 

  45. Xia, R., Lin, Y., Zhou, J., Feng, B., Tang, J.: A median solver and phylogenetic inference based on double-cut-and-join sorting. J. Comput. Biol. 25(3), 302–312 (2018)

    Article  MathSciNet  Google Scholar 

  46. Xu, A., Moret, B.: GASTS: parsimony scoring under rearrangements. In: Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI’11). Lecture Notes in Computer Science, vol. 6833, pp. 351–363. Springer Verlag, Berlin (2011)

    Google Scholar 

  47. Xu, W.: DCJ median problems on linear multichromosomal genomes: graph representation and fast exact solutions. In: RECOMB International Workshop on Comparative Genomics, pp. 70–83. Springer (2009)

    Google Scholar 

  48. Xu, W., Sankoff, D.: Decompositions of multiple breakpoint graphs and rapid exact solutions to the median problem. In: Proceedings of the 8th International Workshop Algorithms in Bioinformatics (WABI’08). Lecture Notes in Computer Science, vol. 5251, pp. 25–37 (2008)

    Google Scholar 

  49. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)

    Article  Google Scholar 

Download references

Acknowledgements

JT was supported by the National Science Foundation of US (grant number IIS 1161586).

Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA

    Jijun Tang

Authors
  1. Jijun Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jijun Tang .

Editor information

Editors and Affiliations

  1. University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Tandy Warnow

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Tang, J. (2019). Ancestral Genome Reconstruction. In: Warnow, T. (eds) Bioinformatics and Phylogenetics. Computational Biology, vol 29. Springer, Cham. https://doi.org/10.1007/978-3-030-10837-3_9

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-10837-3_9

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-10836-6

  • Online ISBN: 978-3-030-10837-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation