Phylogenetic Utility and Evidence for Multiple Copies of Elongation Factor-1α in the Spider Genus Habronattus (Araneae: Salticidae)

Abstract

In the continuing quest for informative genes for use in molecular systematics, the protein-coding gene Elongation factor-1␣ (EF-1␣) has rapidly become one of the most prevalent ''single-copy'' nuclear genes utilized, particularly in arthropods. This paper explores the molecular evolutionary dynamics and phylogenetic utility of EF-1␣ in the salticid spider genus Habronattus. As has been reported for other arthropod lineages, our studies indicate that multiple (two) copies of EF-1␣ exist in Habronattus. These copies differ in intron structure and thus in size, making it possible to easily separate PCR amplification products. We present data for an intronless EF-1␣ copy for three Habronattus species. The presence of nonsense mutations and generally elevated rates of amino acid change suggest that this copy is evolving under relaxed functional constraints in Habronattus. A larger taxon sample (50 species plus outgroups) is presented for an EF-1␣ copy that includes both intron and exon regions. Characteristics of both regions suggest that this is a functional, orthologous copy in the species sampled. Maximum-likelihood relativerate comparisons show that exon third codon sites are evolving more than 100 times as fast as second codon sites in these sequences and that intron sites are evolving about twice as fast as exon third sites. In combination, the EF-1␣ data provide robust, species-level phylogenetic signal that is largely congruent with morphologically well supported areas of Habronattus phylogeny. The recovery of some novel clades, and the unexpected fragmentation of others, suggests areas requiring further phylogenetic attention.

Phylogeny of Habronattus jumping spiders (Araneae: Salticidae), with consideration of genital and courtship evolution

“…The monophyly of the agilis, amicus, dorotheae and americanus groups (Fig. 1) are supported by both mitochondrial and nuclear data using various analyses (see also Hedin & Maddison, 2001b). The tranquillus group, for which we have only mitochondrial data, is also well supported, as is its relationship with the amicus group.…”

“…Specimens from which DNA sequences were obtained. In square brackets are names used by Hedin & Maddison (2001b) that differ from those used here. For Havaika sp., only the 16S portion of the mitochondrial sequence was obtained.…”

“…For Havaika sp., only the 16S portion of the mitochondrial sequence was obtained. Nuclear DNA accession numbers AF359058±AF359111 were previously reported in Hedin & Maddison (2001b Habronattus spider phylogeny 21…”

Identifying and Removing Fast-Evolving Sites Using Compatibility Analysis: An Example from the Arthropoda

“…Evidence for the presence of multiple copies of the EF-1α gene within Arthropoda exists (Hovemann et al, 1988;Danforth and Ji, 1998;Hedin and Maddison, 2001). However, based on the paralog intron-structure (Hedin and Maddison, 2001) and phylogenetic analyses (Danforth and Ji, 1998), these EF-1α paralogs appear to be the result of independent duplications in specific lineages rather than of ancient duplication events (Hedin and Maddison, 2001). Accordingly, neither base composition bias nor paralogy can explain the misplacement of S. tulumensis in Figure 2, leaving LBA as the most likely explanation.…”

Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups

“…The RPB2 gene has been found to be multicopy in certain taxa in plants and trypanosomes [33], and multiple copies of EF1α have been reported in humans and in the spider genus Habronattus [34–36]. Multicopy genes are assumed to evolve under the mechanism of concerted evolution to maintain homogeneity of all copies [37].…”