Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.

Centre for Life's Origins and Evolution Department of Genetics Evolution and the Environment University College London Darwin Building Gower Street London WC1E 6BT UK

Division of Infectious Diseases Department of Medicine University of Alberta 1 124 Clinical Sciences Building 11350 83 Avenue Edmonton T6G 2R3 Alberta Canada

Faculty of Science University of South Bohemia Branišovská 1160 31 České Budějovice 37005 Czech Republic

Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 1160 31 České Budějovice 37005 Czech Republic

Life Science Research Centre Faculty of Science University of Ostrava Chittussiho 983 10 Ostrava 71000 Czech Republic

Medical Biochemistry Amsterdam UMC University of Amsterdam Meibergdreef 15 Amsterdam 1105 AZ The Netherlands

School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK

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