Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation

  • Kristina Straub
  • Rainer MerklEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)


Ancestral sequence reconstruction (ASR) is a powerful tool to infer primordial sequences from contemporary, i.e., extant ones. An essential element of ASR is the computation of a phylogenetic tree whose leaves are the chosen extant sequences. Most often, the reconstructed sequence related to the root of this tree is of greatest interest: It represents the common ancestor (CA) of the sequences under study. If this sequence encodes a protein, one can “resurrect” the CA by means of gene synthesis technology and study biochemical properties of this extinct predecessor with the help of wet-lab experiments.

However, ASR deduces also sequences for all internal nodes of the tree, and the well-considered analysis of these “intermediates” can help to elucidate evolutionary processes. Moreover, one can identify key mutations that alter proteins or protein complexes and are responsible for the differing properties of extant proteins. As an illustrative example, we describe the protocol for the rapid identification of hotspots determining the binding of the two subunits within the heteromeric complex imidazole glycerol phosphate synthase.

Key words

Ancestral sequence reconstruction Vertical analysis Evolutionary biochemistry In silico mutagenesis Protein–protein interaction 



This work was supported by the Deutsche Forschungsgemeinschaft (ME2259/2-1). Calculations were facilitated by using advanced computational infrastructure provided by the Leibniz Supercomputing Center of the Bavarian Academy of Sciences and Humanities ( ) under grant pr48fu. We thank Samuel Blanquart for continuous support, many helpful hints, and fruitful discussions.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Biophysics and Physical BiochemistryUniversity of RegensburgRegensburgGermany

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