| Summary: | The eukaryotic translation elongation factor EFL (for EF-Like) is a paralogue of the better-known elongation factor 1-alpha (EF-1α), which brings aminoacyl-tRNAs to the ribosome during translation. This essential protein was thought to be ubiquitous in eukaryotes until the recent discovery of EFL in a small number of diverse, mainly unicellular, eukaryotic organisms that were found to lack EF-1α. Because of the great evolutionary distances between EFL-encoding lineages and the near mutual exclusivity of the two proteins, the observed complex distribution of EFL was initially attributed entirely to multiple lateral gene transfers. In the enclosed chapters, the distribution of EFL was characterized in more detail in four distantly related eukaryotic lineages at both fine and broad taxonomic scales in order to better understand the effects that endosymbiotic gene transfer, differential loss, and lateral gene transfer have had on the molecular evolution of EFL. Endosymbiotic transfer of EFL was detected in the chlorarachniophytes, a group of algae whose secondary plastids retain a vestigial nucleus, known as a nucleomorph, in their reduced eukaryotic cytoplasm, known as the periplastid compartment (PPC). The endosymbiotically transferred EFL carries a bipartite targeting sequence similar to those of plastid-targeted proteins in this group and to plastid- and PPC-targeting sequences in cryptomonads to direct it to the PPC, suggesting similarities in the way these two lineages have solved their shared challenge of targeting to complex plastids with nucleomorphs. No clear phylogenetic evidence for lateral transfer of EFL has yet emerged; rather, differential loss of EFL and EF-1α from an ancestral state of co-occurrence was characterized in euglenozoans and detected in publicly available data from heterokonts and opisthokonts, unexpectedly revealing a significant role for this process in shaping the complex distribution of EFL and EF-1α. This finding serves as a cautionary reminder that adequate taxon sampling and a robust organismal phylogenetic hypothesis are crucial in order to correctly infer lateral gene transfer. === Science, Faculty of === Botany, Department of === Graduate
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