Ancestral sequence, reconstructed

Hein, J. (1989). A tree reconstruction method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6, 649-668. 

Unfortunately, we cannot access specific sequence information about enzymes from the LUCA to allow resurrection of very ancient enzymes and evaluation of their properties. Phylogenetic reconstruction of ancestral protein sequences does not allow us to look back billions of years beyond a certain point, there is too much ambiguity due to sequence divergence to allow a trustworthy estimation of the ancestral sequence. 

With tree analysis it is possible to infer sequences of ancestral proteins and probable evolutionary pathways to their modern descendants.1 The advent of site-directed mutagenesis makes possible the recreation of evolutionary intermediates based on these predictions. One may then compare the properties of reconstructed intermediates with one another and with proteins from contemporary creatures. These comparisons provide a way of testing theories about the mechanism of molecular evolution. For example, this approach has provided a new criterion for distinguishing between neutral and nonneutral events.2 This chapter describes the use of site-directed mutagenesis to recreate ancestral lysozymes and presents methods of evaluating their properties. 

Ancestral reconstruction of a long protein sequence can be a tedious task. Fortunately, it may not always be necessary to analyze the entire protein sequence cladistically. Functional characteristics often are thought to be determined by limited regions in a protein molecule if so, the analysis can be limited to these regions. 

Attention is attracted to the possibility of reconstructing the amino-acid sequence of ancestral polypeptide chains W virtue of a comparison between the amino-acid sequences of related polypeptide chains foimd in contemporary organisms. A tentative partial structure is proposed for two ancestral hemoglobin polypeptide chains. Some perspectives of paleobio-chemistry are outlined. 

The objectives of this chapter are several first, to resolve phylogenetic relationships within the Ptychomniales using DNA sequence data second, to reconstruct ancestral character states within the Ptychomniales and third, to test whether the presence of dwarf males correlates to morphological characters and the epiphytic habitat. 

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