Evolutionary properties of sequences and ancestral state reconstruction
A number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral sequences. Coevolution of interacting partners is seen as important, first in directing the evolution of proteins, and second in explaining why structural constraints may become lineage-specific while function remains the same. Although the concept of heterotachy and covarion evolution in the literature is most often restricted to describing the evolution of orthologs, the same or similar principles of sequence divergence apply to proteins related by gene duplication (paralogs), and which have different functions and functional constraints. This chapter discusses heterotachy and gene finding, gene finding with ancestral sequences, and heterotachy and ancestral state reconstruction.
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