Reconstruction of ancestral proteomes
The process of inferring the set of proteins that was likely encoded in the genome of an extinct organism is called Ancestral Proteome Reconstruction. This process usually involves the comparison of proteomes of extant species and the reconstruction of their ancestors by using different methods that range from parsimonius reconstruction over a species-phylogeny to the reconstruction and analysis of complete phylomes. Although still in its infancy, Ancestral Proteome Reconstruction has proven to be a very useful tool to test hypotheses on extant organisms and past evolutionary events. This chapter provides an overview of the methodology involved and surveys recent studies that deal with the origin and evolution of the Last Universal Common Ancestor (LUCA), and eukaryotic organelles such as mitochondria and peroxisomes.
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