Elongation factor-1 alpha
Elongation factor-1alpha (EF-1alpha) is a nuclear gene that encodes a protein involved in the GTP-dependent binding of charged tRNAs to the acceptor site of the ribosome during translation (Maroni 1993, pp. 126-134). EF-1alpha has proven to be a useful gene for studies of higher-level phylogenetic relationships, especially in insects (Cho et al. 1995; Friedlander et al. 1998; Mitchell et al. 1997, 2000; Moulton 2000; Regier et al. 2000; Caterino et al. 2000). Amino acid sequences of EF-1alpha have been used to resolve relationships among arthropod classes (Regier & Shultz 1997, 1998; Shultz & Regier 2000), worm phyla (Kojima et al. 1993; McHugh 1997, 2000; Eeckhaut et. al 2000), and among early eukaryotes (Hasegawa, et al. 1993; Kamaishi, et al. 1996). EF-1alpha occurs as two copies in bees (Danforth & Ji 1998), ants (T. Schultz, pers. comm.), and flies (Hovemann et al. 1988). We have developed primers that specifically amplify the F1 or the F2 copy in bees (Danforth et al. 1999, Danforth & Ji 2001, Sipes & Wolf 2001). Paralogs can be easily distinguished based on the positions of introns, which differ among copies (see attached pdf file with a map of both the F1 and F2 copies). We typically sequence nearly the entire F2 copy (roughly 1600 bp, with three introns) for most of our studies (primers for this paralog are listed below in the pdf file). Introns are difficult to align unambiguously at the family level and, while some conserved non-coding regions may be retained, most intron sequence may need to be excluded from the analysis.
A recent study (Brady & Danforth 2004) demonstrated that there is intron presence/absence variation in the F1 copy of EF-1alpha. All members of the family Colletidae that we sampled had an intron that was lacking in all other bees, sphecid wasps, and ants that we sampled. We interpreted this as a uniquely derived intron that supports the monophyly of the colletid bees and excludes the Stenotritidae from the Colletidae.
We have typically used the F2 copy of EF-1alpha (e.g., Danforth et al. 2004) because our primers (see pdf files below) can amplify a large and continuous fragment of approximately 1600 bp which includes two introns. However, a number of bee studies have used the F1 copy (e.g., Leys et al. 2002, Bull et al. 2003; Schwarz et al. 2003, 2004). The fragment analyzed in these studies is approximately 500 bp in length and includes only exon sequence (except in colletids in which there is an intron; Brady & Danforth 2004). We prefer the F2 copy because of its ease of amplification and because there is a substantial amount of data already available for this copy.
The honey bee (Apis mellifera) F2 copy is available on Genbank as accession number AF015267 (Danforth & Ji 1998). The honey bee (Apis mellifera) F1 copy is available on Genbank as accession number X52884 (Walldorf & Hovemann 1990).
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Gene Information: |
Map of EF-1alpha gene (.pdf file) |
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