Bioinformatics pp 365-383 | Cite as

Inferring Ancestral Gene Order

  • Julian M. Catchen
  • John S. Conery
  • John H. Postlethwait
Part of the Methods in Molecular Biology™ book series (MIMB, volume 452)


To explain the evolutionary mechanisms by which populations of organisms change over time, it is necessary to first understand the pathways by which genomes have changed over time. Understanding genome evolution requires comparing modern genomes with ancestral genomes, which thus necessitates the reconstruction of those ancestral genomes. This chapter describes automated approaches to infer the nature of ancestral genomes from modern sequenced genomes. Because several rounds of whole genome duplication have punctuated the evolution of animals with backbones, and current methods for ortholog calling do not adequately account for such events, we developed ways to infer the nature of ancestral chromosomes after genome duplication. We apply this method here to reconstruct the ancestors of a specific chromosome in the zebrafish Danio rerio.

Key words

Ancestral reconstruction chromosome evolution genome duplication automated workflow 



This project was supported by grant no. 5R01RR020833-02 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCRR or NIH. J. Catchen was supported in part by an IGERT grant from NSF in Evolution, Development, and Genomics (DGE 9972830).


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Julian M. Catchen
    • 1
  • John S. Conery
    • 1
  • John H. Postlethwait
    • 1
  1. 1.Department of Computer and Information Science and Institute of NeuroscienceUniversity of OregonEugene

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