Comparisons Among Genes in Relative Rate, etc.
In order to compare the relative rates of several nuclear genes and to assess the utility of various data sets we developed a preliminary data set based on four nuclear genes: EF-1alpha, arginine kinase, LW opsin, and 28S(D2 region). We did this for a sample of 58 species spanning most families and subfamilies, with an emphasis on the LT bee family Apidae. A complete list of the taxa sampled for each gene can be obtained below in the form of an excel spreadsheet. We analyzed this data set by equal weights parsimony, assessed robustness using the bootstrap, and evaluated the relative rates of the different data partitions (codon positions and genes) using a Bayesian analysis with site-specific rates. Relative rates among genes and codon positions are shown below.
Our results indicate that EF-1alpha, arginine kinase, and LW opsin evolve at comparable rates with EF-1alpha and arginine kinase slightly slower in first and second positions than LW opsin. Third position rates are very similar across all three genes. The ribosomal gene (28S) evolves at roughly the rate of opsin first positions and slightly faster than EF-1alpha and arginine kinase first positions. Similar results were obtained in a study of the bee family Halictidae using EF-1alpha, wingless, and LW opsin (Danforth et al. 2004). EF-1alpha and wingless evolved at roughly comparable rates, with LW opsin showing an elevated first and second position rate. Leys et al. (2002) in a study of xylocopine bees, estimated relative rates among COI, cytB (both mitochondrial genes) as well as nuclear EF-1alpha (F1 copy) and PEPCK using maximum likelihood methods. We reproduce a figure from their Table 4 below (see figure). In this study PEPCK appears to show far more first and second position variation than EF-1alpha. Note also that the mitochondrial genes evolve at a high rate relative to the nuclear genes.
Of the five protein-coding genes that have been analyzed so far in bees (EF-1alpha, arginine kinase, LW opsin, PEPCK and wingless), it appears that PEPCK and LW opsin are among the fastest, and EF-1alpha, arginine kinase, and wingless are somewhat slower. We suspect from preliminary results that RNA pol II will be markedly slower than any of these other genes. It remains to be seen how CAD fits into this picture of relative rates. The combination of one or more protein-coding genes with 28S may be a good choice because 28S provides, overall, a much more slowly evolving marker. Alignments within families are reasonably clear, but alignments across several families are not very reliable. Introns within nuclear genes (e.g., PEPCK introns in the Leys et al. 2002 study) can provide additional information when these intron regions are alignable. Introns appear to show variable rates among genes as well. Introns within EF-1alpha, for example, are more easily aligned than introns in LW opsin. Introns in most nuclear genes analyzed appear to evolve at approximately the rate of third position sites (Leys et al. 2002, Lin & Danforth 2004).
Download
| Excel spreadsheet: |
Taxa included as part of the preliminary analysis of relative rates (.xls file) |