Nutrient-dependent gene duplication in plants (but not animals?)

Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes

Excerpt 1) “A recent study demonstrated that the DNA methylation in promoter may play a significant role for functional divergence of duplicated genes in human [48].”
Excerpt 1 from the cited work [48]: “For 73% of gene pairs, one copy is always hypomethylated compared with the other. This refutes the idea that [RNA-directed] DNA methylation of genes is strictly determined in a tissue-by-tissue manner and indicates the presence of a common developmental programming underlying regulation of duplicate genes across divergent cell types.”
Excerpt 2) “In human, a exclusive relationship of gene body [RNA-directed] DNA methylation with evolutionary and expression divergence of paralogs could not be revealed [48].”
Excerpt 2 from the cited work [48]: “In summary, our study indicates that epigenetic modifications are important facilitators of duplicate gene evolution owing to their effect on functional divergence as well as potential dependence on genomic determinants. However, duplicate gene evolution provides an excellent system to investigate genetic and environmental factors of epigenetic divergence because we can study divergence of duplicate genes in the same genome, free from other confounding factors.”
My comment: RNA-directed DNA methylation and gene duplication are nutrient-dependent. That missing fact links the presence of common developmental programming, which underlies the epigenetic regulation of duplicate genes across divergent cell types, to another missing fact: Nutrient-dependent amino acid substitutions, which differentiate cell types in all individuals of species from microbes to man, are fixed in the organized genomes of mammals via the metabolism of nutrients to species-specific pheromones. Pheromones control the physiology of reproduction, and reproduction enables fixation of amino acid substitutions in populations.
The amino acid substitutions differentiate cell types in all individuals of all genera. However, these authors fail to link the conserved molecular mechanisms of cell type differentiation from plants to humans. Instead of following the lead provided in the cited work [48], enzymes automagically appear. After they have automagically appeared, the enzymes lead to DNA methylation, which is associated with mutations, natural selection, and the evolution of biodiversity in plants.
The enzymes, which automagically appear, are not associated with nutrient uptake or with nutrient-dependent RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions to cell type differentiation in plants and animals via biophysically-contrained protein folding.
Look closely at the authors’ claim: Excerpt 2) “In human, a exclusive relationship of gene body DNA methylation with evolutionary and expression divergence of paralogs could not be revealed [48].”
They appear to be claiming, as have many others, that mutations and natural selection might link the evolutionary divergence of human morphological and behavioral phenotypes. That claim is made because the exclusive relationship between the link from nutrient uptake and gene duplication “…could not be not revealed.” Biologically-based experimental evidence links ecological variation to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. But these authors leave us with the impression that the link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of plants and other animals may be different than the epigenetic link in humans because the direct link from nutrient uptake to ecological adaptation in humans “…could not be revealed.”
See also: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Excerpt 1) “…cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting.”
Excerpt 2) “This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control.”
My comment: The strong connection between quantum physics and structural biology means that light harvesting functions are not under genetic and evolutionary control. The connection from physics to biology links the epigenetic landscape to the physical landscape of DNA in the organized genomes of plants and animals via the conserved molecular mechanisms of amino acid substitutions and controlled protein folding that leads from ecological variation to ecological adaptations.
E.O. Wilson’s comment: “Humanity, I argue, arose entirely on its own through an accumulated series of events during evolution.”
Jordan et al., (2005) A universal trend of amino acid gain and loss in protein evolution. “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”
Wilson’s comments do not include information about any biologically-based evolutionary events, which others have described in the context of RNA-directed DNA methylation and RNA-mediated events that link nutrient-dependent pheromone-controlled biodiversity of morphological and behavioral phenotypes in species from microbes to man. I wonder if he knows anything at all about biologically-based cause and effect via the amino acid substitutions that differentiate all cell types in all individuals of all species.
RNA-directed DNA methylation From Fertilization to Adult Sexual Behavior
Excerpt:  Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
RNA-directed DNA methylation Establishing, maintaining and modifying DNA methylation patterns in plants and animals
RNA-directed DNA methylation Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana

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