Conclusion and a way forward

Abstract

Abstract This concluding chapter discusses the various issues raised in the course of the book and suggests a way forward for readers attempting ancestral sequence reconstruction. Ancestral sequence reconstruction can be used for testing general hypotheses about the environment and lifestyles of extinct species, general hypotheses about the processes driving gene and genome evolution, specific hypotheses about the evolution of gene function in individual gene families, and ultimately the it can be used for the generation of an understanding of the mapping between sequence (and substitution) to molecular function. A consideration of alternative phylogenetic tree topologies and their effects on ancestral sequence reconstruction is recommended. For smaller data-sets, integrated methods that combine multiple sequence alignment and phylogenetic tree construction in one step are slow, but may provide a better assessment of homology and the evolutionary history of any given amino acid position. Readers may also consider starting with precalculated gene families that already contain multiple sequence alignments and phylogenetic trees for families of interest. Such families can be modified with detailed knowledge and expanded to include new sequences, as available and desired.