Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton

We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. These data enabled us to define 51 anciently-derived kinesin paralogs (including three new kinesin families) and 105 domain architectures. We then mapped these characters across eukaryotes, accounting for secondary loss within established eukaryotic groupings, and alternative tree topologies.We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell.The transition from prokaryote to eukaryote was a hugely important event in the evolutionary history of life and provided the foundations for the evolution of numerous complex organismal forms. Present day eukaryotes differ fundamentally from prokaryotes in having much higher complexity of cell organization. This complexity cannot have appeared fully-formed, but arose by stepwise elaborations of cell structure - implying that certain lineages of extant eukaryotes might have retained "simpler" ancestral features (see [1,2]). However, the order and relative importance of many of the acquisitions that must have occurred to allow the cellular features now seen in extant eukaryotes remain controversial. By comparing the genomes of a wide taxonomic range of eukaryotes, and including sufficient taxon sampling to account for secondary loss, we can reconstruct the likely genomic composition of the last commo