New instruments combined with DNA intercalating dyes that can be used at saturating concentrations allow the discrimination of sequence changes in PCR amplicons without manual handling of PCR products.
Researchers looked at the egg genes across a variety of species, and used novel statistical tools developed by Dr. Ziheng Yang of University College in London that compared different types of sequence changes in different regions of each gene.
For empirical data, trees were inferred using two models of sequence change: JTT, and a variant ("equalin", EQ) of the F81 model of Felsenstein [ 1].
Two tests were used to detect the patterns of sequence change using dN/dS ratios in the gene families of this study.
Particularly in simulations where a single branch was differentially lengthened (Table 2), using the wrong model of sequence change sometimes improved some aspects of performance.
Furthermore, when the divergence of nonfunctional DNA has not reached saturation, those sequences can be used to normalize rates of sequence change thereby allowing tests for adaptive evolution to be performed (Yang 2007).
There are three outcomes of using dN/dS as an indicator of sequence change.
The explosion of protein sequences deduced from genetic code has led to both a problem and a potential resource: Efficient data use requires interpreting the functional impact of sequence change without experimentally characterizing each protein variant.
For MGGLS, MGLLS, SGGLS, and SGLLS methods, gene- or supergene-specific rates of sequence change were estimated using linear regression (y-intercept fixed through the origin) from one or more calibrations and applied to the intergroup distance estimates to produce gene- or supergene-specific times.
SE, standard error; Signif, significance (probability level that estimate >|t|); y-Intcpt, y-intercept; Mult R, multiple R; Adj R, adjusted R. From our data, it is not possible to reject the hypothesis that the relationship between BP and PP has the same slope whether the Bayesian inference is conducted using JTT, or EQ, as the model of sequence change.
