The gene elongation factor 1 alpha (EF1a) has had a complicated and somewhat unclear evolutionary history; however, it still remains a useful tool in the reconstruction of organismal phylogeny at varying levels in eukaryotic species. In this study, the relationship is explored between EF1a and a seemingly-related protein, elongation factor-like (EFL), that sometimes isfound to have replaced the function of EF1a. We found evidence that EF1a and EFL are ancient paralogs, possibly of the archaeal version of EF1a, that have also undergone more recent events of horizontal gene transfer (HGT) in certain eukaryotic lineages. Although some members of the euglenozoan (Excavata) lineage, the diplonemids, seem to have completely lost EF1a theremaining lineages and sister group to the euglenozoans were clarified with both EF1a and small subunit ribosomal DNA (18S). The discicristates clade was supported with the Heterolobosea found as sister to the Euglenozoa. The recently described Discoba clade was also supported with the Jakobida recovered as sister to the discicristates. The Euglenida lineage was further analyzed with EF1a, 18S and large subunit ribosomal DNA (28S) to recover supported clades. However, it was determined that within the Euglenida there have been multiple independent gene duplication events of EF1a, which are useful for the genus and species-level clarification of the Euglenida organisms, but can obscure the true species history of the group at deeper levels if used inappropriately. EF1a is still considered useful in phylogenetic reconstruction since it is such a conserved gene, but the study and understanding of the gene within the context of the lineage to be studied must be determined prior to analyses.
