6/14/13 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

….the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

Facts:

Epigenetic modifications poster

DNA repair pathways poster

Epigenetic Dynamics in Stem Cells and Differentiation webinar

Epigenetic Editing: Permanently Modulate Gene Expression webinar

Histone modifications: a guide

Epigenetic Mechanisms in Early Mammalian Development webinar

DNA Methylation Changes During Cell Differentiation webinar

Chromatin: from nucleosomes to chromosomes

Epigenetics round-up of 2014

Changes in histone acetylation may aid memory reconsolidation in post-traumatic stress disorder

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Theme issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’ (2017)

Recombination rate variation in sexual organisms is energy-dependent and RNA-mediated. Variation is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. See: From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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.

A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.

Theories:

Review article: Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley, Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja
Phil. Trans. R. Soc. B December 19, 2017 372 20160455; doi:10.1098/rstb.2016.0455
http://rstb.royalsocietypublishing.org/content/372/1736/20160455

Review article: The impact of recombination on human mutation load and disease
Isabel Alves, Armande Ang Houle, Julie G. Hussin and Philip Awadalla
Phil. Trans. R. Soc. B December 19, 2017 372 20160465; doi:10.1098/rstb.2016.0465
http://rstb.royalsocietypublishing.org/content/372/1736/20160465

Opinion piece: Connecting theory and data to understand recombination rate evolution
Amy L. Dapper and Bret A. Payseur
Phil. Trans. R. Soc. B December 19, 2017 372 20160469; doi:10.1098/rstb.2016.0469
http://rstb.royalsocietypublishing.org/content/372/1736/20160469

Review article: Coevolution between transposable elements and recombination
Tyler V. Kent, Jasmina Uzunović and Stephen I. Wright
Phil. Trans. R. Soc. B December 19, 2017 372 20160458; doi:10.1098/rstb.2016.0458
http://rstb.royalsocietypublishing.org/content/372/1736/20160458

Review article: Evolution of recombination rates between sex chromosomes
Deborah Charlesworth
Phil. Trans. R. Soc. B December 19, 2017 372 20160456; doi:10.1098/rstb.2016.0456
http://rstb.royalsocietypublishing.org/content/372/1736/20160456

Research article: Low recombination rates in sexual species and sex–asex transitions
Christoph R. Haag, Loukas Theodosiou, Roula Zahab and Thomas Lenormand
Phil. Trans. R. Soc. B December 19, 2017 372 20160461; doi:10.1098/rstb.2016.0461
http://rstb.royalsocietypublishing.org/content/372/1736/20160461

(openaccess) Review article: The consequences of sequence erosion in the evolution of recombination hotspots
Irene Tiemann-Boege, Theresa Schwarz, Yasmin Striedner and Angelika Heissl
Phil. Trans. R. Soc. B December 19, 2017 372 20160462; doi:10.1098/rstb.2016.0462
http://rstb.royalsocietypublishing.org/content/372/1736/20160462

(openaccess) Research article: The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Thibault Latrille, Laurent Duret and Nicolas Lartillot
Phil. Trans. R. Soc. B December 19, 2017 372 20160463; doi:10.1098/rstb.2016.0463
http://rstb.royalsocietypublishing.org/content/372/1736/20160463

(openaccess) Research article: Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Josep M. Comeron
Phil. Trans. R. Soc. B December 19, 2017 372 20160471; doi:10.1098/rstb.2016.0471
http://rstb.royalsocietypublishing.org/content/372/1736/20160471

(openaccess) Review article: Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison, Stephen Sefick, Chase Rushton and Rita M. Graze
Phil. Trans. R. Soc. B December 19, 2017 372 20160459; doi:10.1098/rstb.2016.0459
http://rstb.royalsocietypublishing.org/content/372/1736/20160459

(openaccess) Review article: Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?
Christopher H. Morgan, Huakun Zhang and Kirsten Bomblies
Phil. Trans. R. Soc. B December 19, 2017 372 20160470; doi:10.1098/rstb.2016.0470
http://rstb.royalsocietypublishing.org/content/372/1736/20160470

Research article: What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling
Sviatoslav R. Rybnikov, Zeev M. Frenkel and Abraham B. Korol
Phil. Trans. R. Soc. B December 19, 2017 372 20160460; doi:10.1098/rstb.2016.0460
http://rstb.royalsocietypublishing.org/content/372/1736/20160460

Keep Reading