Molecular Systematics of Bees (genes and primers)
Standard protocols for DNA extraction, PCR, gel electrophoresis and sequencing are available in the pdf file below.
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DNA extraction, PCR, gel electrophoresis and sequencing protocols (.pdf file) |
Ribosomal Genes
Insect molecular systematists interested in reconstructing deeper (i.e., Mesozoic and older) divergences are presented with a choice of using nuclear ribosomal genes or nuclear single-copy, protein-coding genes. Mitochondrial genes are generally considered too rapidly evolving for these deep divergences and show substitution patterns that are problematic for reconstructing ancient divergences (Lin & Danforth 2004). We do not recommend using mitochondrial genes for higher-level studies in bees.
Nuclear ribosomal genes are by far the most common nuclear markers for higher-level studies in insects. A cursory search on Biosis in April 2003 revealed nearly 100 papers on insect phylogeny using one or more nuclear ribosomal genes. Reviews of the utility of ribsomal gene data in phylogenetic analysis include Hillis & Dixon (1991), Simon et al. (1994), and Caterino et al. (2000). While nuclear ribosomal genes (e.g., 5.8S, 18S, and 28S) have been the most common choice for deep divergences in insects (Whiting et al. 1997, Wiegmann et al. 2000, Giribet et al. 2001, Kjer et al. 2001, Wheeler et al. 2001, Belshaw & Quicke 2002, Dietrich et al. 2001, Hovmöller et al. 2002 [but see Ogden & Whiting 2003]), these genes also present alignment problems (see Hickson et al. 2000 for a comparison of various methods), and in some cases these genes have been shown to recover phylogenetic relationships totally at odds with reality (Schmitz & Moritz 1998).
Nuclear Protein Coding Genes
Slowly-evolving, nuclear, protein-coding genes have recently become available for phylogenetic analysis in many groups of insects. These genes have a number of advantages over ribosomal genes. Most obviously, they are easily alignable. Many of these genes have been demonstrated to be capable of recovering Creteaceous age divergences in insects (Friedlander et al. 1992, 1994, 1996, 1997, 2000; Moulton & Wiegmann 2004; Wiegmann et al. 2000).