The GAF domain of phytochrome is essential for photoconversion and signal transduction. In gymnosperms, it exists in all members of the phytochrome family that experience gene duplication. Maximum-likelihood models of codon substitution can provide a framework for constructing likelihood ratio tests of changes in selective pressure and make clear predictions about patterns of genetic change following gene duplication. In this study, 68 gymnosperm GAF sequences were analyzed to identify lineages and sites under positive selection. Our results indicate that (1) positive selection at a few sites (3.6%), rather than relaxation of selective constraints, has played a major role in the evolution of the gymnosperm GAF domain; (2) strong positive selective pressure tends to occur in the recent PHYP lineages of cogeneric species, but is absent in old lineages consisting of distantly related species; and (3) the selective pressure indicated by the omega ratio varies greatly among lineages and sites in the GAF domain.
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Article Synopsis
- Terahertz (THz) technology is gaining attention for its potential in bio-detection, but there's limited research on its use in mixtures.
- Traditional 1D spectral analysis is not sensitive enough due to overlapping and distortions, so this study used the Gramian angular field (GAF) method to create 2D images from THz spectra.
- The new approach, which combines histogram of oriented gradients (HOGs) and gray level histograms (GLHs) with a support vector regression (SVR) model, showed improved accuracy and stability over traditional methods, making it more effective for analyzing mixed systems.
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