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Museum Collections
Databasing and Mapping
DNA Sequencing
Choice of Gene Loci
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Choice of Gene Loci

Because alternative data sources are implicitly excluded when a particular data source (e.g., a particular set of morphological characters or a particular gene) is selected for a given study (Nixon & Carpenter 1996; Swofford et al. 1996), data source selection should be conducted on the basis of reasoned expectations of the value (in time and money) of the data (Nixon & Carpenter 1996). Regrettably, such decisions are seldom made. For example, although the choice of gene loci (genome samples of 500–1000 or more base-pairs that can be sequenced as single pieces in both directions) is a critical step in any molecular phylogenetic analysis, too many investigators make their selections on the basis of primers that are available and/or capable of amplifying the DNA of their study organisms, without regard for the phylogenetic utility of those loci at their level of interest (Brower & DeSalle 1994; Soltis & Soltis 1998).           
     It is generally accepted that more than one gene locus should be used for phylogenetic reconstruction and that at least one locus should be acquired from the recombinant nuclear genome (Avise 1989; Doyle 1992; Degnan 1993; Brower & DeSalle 1994; Brower et al. 1996; Maddison 1997; Doyle & Davis 1998).
     Six gene loci, collectively summing to ca. 5.6 kilobases, are being sequenced for all vaejovid species for this project. These loci were chosen not only because of the availability of primers that could consistently amplify sufficiently large, phylogenetically informative fragments, but also because they have been reported to evolve at different rates and would thus be expected to provide phylogenetic resolution at different, overlapping taxonomic levels (e.g., Simon et al. 1994; Wahlberg & Zimmermann 2000; Giribet et al. 2001b; Prendini et al. 2003).
     The three nuclear gene loci being sequenced are considered sufficiently conserved to be informative for resolving the major clades of Vaejovidae, testing monophyly of the vaejovid genera, placing the family in the broader context of scorpion phylogeny and testing the contentious hypothesis that Uroctonus is a chactid and not a basal vaejovid (Soleglad & Fet 2003, 2004). Complete sequence of the small-subunit ribosomal RNA gene (18S rDNA), a variable fragment (D3 region) of the large-subunit ribosomal RNA gene (28S rDNA), and a variable fragment of the Histone H3 protein-coding gene, are being amplified. These fragments have been used in various studies of arthropod phylogeny at higher and lower levels (e.g., Turbeville et al. 1991; Carmean et al. 1992; Wheeler et al. 1993a,b; Wheeler 1997, 1998a; Colgan et al.1998; Wheeler & Hayashi 1998; Zrzavý et al. 1998, 2001; Edgecombe et al. 1999, 2000; Giribet et al. 1999a,b, 2001b, 2002; Giribet & Ribera 2000; Wheeler et al. 2001; Prendini et al. 2003).
     In order to provide resolution among the terminal taxa, and within the vaejovid genera, three gene loci were selected from the more labile mitochondrial genome. Comparatively labile fragments of the mitochondrial homologs of the nuclear small-subunit ribosomal RNA gene (12S rDNA) and the nuclear large-subunit ribosomal RNA gene (16S rDNA), both of which also contain conserved regions, were chosen, together with a more conserved fragment of the Cytochrome c Oxidase subunit I (CO I) protein-coding gene. The 12S fragment has been used in studies of the internal relationships of arthropods, scorpions and insects (e.g., Ballard et al. 1992; Simon et al. 1994; Wägele & Stanjek 1995; Zrzavý et al. 1998; Prendini et al. 2003). The 16S fragment has been employed in studies of interspecific and intraspecific variation within insects (Xiong and Kocher 1991; Vogler & DeSalle 1993; Vogler et al. 1993a,b; Simon et al. 1994; Fang et al. 1995; Wahlberg & Zimmermann 2000; Zimmermann et al. 2000), scorpions (Gantenbein et al. 1999a,b, 2000a,b, 2001a,b; Scherabon et al. 2000; Fet et al. 2001; Prendini et al. 2003) and spiders (Arnedo et al. 2002), and was also recently used in studies of arthropod phylogeny (Zrzavý et al. 1998; Giribet et al. 2001b). The CO I fragment has been used to determine relationships within Coleoptera, Lepidoptera, Orthoptera and other insect groups (Harrison et al. 1987; Simon et al. 1994; Wahlberg & Zimmermann 2000; Zimmermann et al. 2000), as well as among spiders (Arnedo et al. 2002), scorpions (Prendini et al. 2003), and in a study of arthropod higher phylogeny (Giribet et al. 2001b).           
     The following additional loci, Elongation Factor 1-α and Polymerase II (nuclear genome) and NADH dehydrogenase subunit I and Cytochrome Oxidase II (mitochondrial genome), may be added to the existing sample if found to contain sufficient variation and be reasonably easy to amplify.

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