Near-neutrality, robustness, and epigenetics

Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution

The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces governing molecular evolution and their relative importance. The debate, initially focused on the amount of within-species polymorphism and constancy of the substitution rate, has spread, matured, and now underlies a wide range of topics and questions. The neutralist/selectionist controversy has structured the field and influences the way molecular evolutionary scientists conceive their research.

Adaptive evolvability through direct selection instead of indirect, second-order selection

Can evolvability itself be the product of adaptive evolution? To answer this question is challenging, because any DNA mutation that alters only evolvability is subject to indirect, "second order" selection on the future effects of this mutation. Such indirect selection is weaker than "first-order" selection on mutations that alter fitness, in the sense that it can operate only under restrictive conditions. Here I discuss a route to adaptive evolvability that overcomes this challenge. Specifically, a recent evolution experiment showed that some mutations can enhance both fitness and evolvability through a combination of direct and indirect selection. Unrelated evidence from gene duplication and the evolution of gene regulation suggests that mutations with such dual effects may not be rare. Through such mutations, evolvability may increase at least in part because it provides an adaptive advantage. These observations suggest a research program on the adaptive evolution of evolvability, which aims to identify such mutations and to disentangle their direct fitness effects from their indirect effects on evolvability. If evolvability is itself adaptive, Darwinian evolution may have created more than life's diversity. It may also have helped create the very conditions that made the success of Darwinian evolution possible.

Speciation and the developmental alarm clock

New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.

Formation of dominant mode by evolution in biological systems

A reduction in high-dimensional phenotypic states to a few degrees of freedom is essential to understand biological systems. Here, we show evolutionary robustness causes such reduction which restricts possible phenotypic changes in response to a variety of environmental conditions. First, global protein expression changes in Escherichia coli after various environmental perturbations were shown to be proportional across components, across different types of environmental conditions. To examine if such dimension reduction is a result of evolution, we analyzed a cell model-with a huge number of components, that reproduces itself via a catalytic reaction network-and confirmed that common proportionality in the concentrations of all components is shaped through evolutionary processes. We found that the changes in concentration across all components in response to environmental and evolutionary changes are constrained to the changes along a one-dimensional major axis, within a huge-dimensional state space. On the basis of these observations, we propose a theory in which such constraints in phenotypic changes are achieved both by evolutionary robustness and plasticity and formulate this proposition in terms of dynamical systems. Accordingly, broad experimental and numerical results on phenotypic changes caused by evolution and adaptation are coherently explained.

Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics

We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. First, linear approximation in intracellular reaction dynamics is used to demonstrate proportional changes in the expression of all cellular components in response to a given environmental stress, with the proportion coefficient determined by the change in growth rate as a consequence of the steady growth of cells. We further demonstrate that this relationship is supported through adaptation experiments of bacteria, perhaps too well as this proportionality is held even across cultures of different types of conditions. On the basis of simulations of cell models, we further show that this global proportionality is a consequence of evolution in which expression changes in response to environmental or genetic perturbations are constrained along a unique one-dimensional curve, which is a result of evolutionary robustness. It then follows that the expression changes induced by environmental changes are proportionally reduced across different components of a cell by evolution, which is akin to the Le Chatelier thermodynamics principle. Finally, with the aid of a fluctuation-response relationship, this proportionality is shown to hold between fluctuations caused by genetic changes and those caused by noise. Overall, these results and support from the theoretical and experimental literature suggest a formulation of cellular systems akin to thermodynamics, in which a macroscopic potential is given by the growth rate (or fitness) represented as a function of environmental and evolutionary changes.

Systematic Analyses and Prediction of Human Drug Side Effect Associated Proteins from the Perspective of Protein Evolution

Identification of various factors involved in adverse drug reactions in target proteins to develop therapeutic drugs with minimal/no side effect is very important. In this context, we have performed a comparative evolutionary rate analyses between the genes exhibiting drug side-effect(s) (SET) and genes showing no side effect (NSET) with an aim to increase the prediction accuracy of SET/NSET proteins using evolutionary rate determinants. We found that SET proteins are more conserved than the NSET proteins. The rates of evolution between SET and NSET protein primarily depend upon their noncomplex (protein complex association number = 0) forming nature, phylogenetic age, multifunctionality, membrane localization, and transmembrane helix content irrespective of their essentiality, total druggability (total number of drugs/target), m-RNA expression level, and tissue expression breadth. We also introduced two novel terms—killer druggability (number of drugs with killing side effect(s)/target), essential druggability (number of drugs targeting essential proteins/target) to explain the evolutionary rate variation between SET and NSET proteins. Interestingly, we noticed that SET proteins are younger than NSET proteins and multifunctional younger SET proteins are candidates of acquiring killing side effects. We provide evidence that higher killer druggability, multifunctionality, and transmembrane helices support the conservation of SET proteins over NSET proteins in spite of their recent origin. By employing all these entities, our Support Vector Machine model predicts human SET/NSET proteins to a high degree of accuracy (∼86%).

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution.

A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells

This report presents a study utilizing next-generation sequencing technology, combined with chromatin immunoprecipitation (ChIP-seq) technology to analyze histone modification induced by butyrate and to construct a high-definition map of the epigenomic landscape with normal histone H3 and H4 and their variants in bovine cells at the whole-genome scale. A total of 10 variants of histone H3 and H4 modifications were mapped at the whole-genome scale (acetyl-H3K18-ChIP-seq, trimethy-H3K9, histone H4 ChIP-seq, acetyl-H4K5 ChIP-seq, acetyl-H4K12 ChIP-seq, acetyl-H4K16 ChIP-seq, histone H3 ChIP-seq, acetyl H3H9 ChIP-seq, acetyl H3K27 ChIP-seq and tetra-acetyl H4 ChIP-seq). Integrated experiential data and an analysis of histone and histone modification at a single base resolution across the entire genome are presented. We analyzed the enriched binding regions in the proximal promoter (within 5 kb upstream or at the 5'-untranslated region from the transcriptional start site (TSS)), and the exon, intron and intergenic regions (defined by regions 25 kb upstream and 10 kb downstream from the TSS). A de novo search for the binding motif of the 10 ChIP-seq datasets discovered numerous motifs from each of the ChIP-seq datasets. These consensus sequences indicated that histone modification at different locations changes the histone H3 and H4 binding preferences. Nevertheless, a high degree of conservation in histone binding also was presented in these motifs. This first extensive epigenomic landscape mapping in bovine cells offers a new framework and a great resource for testing the role of epigenomes in cell function and transcriptomic regulation.

Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes

It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or “species” of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or “species” populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes.

Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells

Butyrate-induced histone acetylation plays an important role in the regulation of gene expression. However, the regulation mechanisms of histone modification remain largely unclear. To comprehensively analyze histone modification induced by butyrate, we utilized chromatin immunoprecipitation (ChIP) technology combined with next-generation sequencing technology (ChIP-seq) to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3 and acetylated histone H3K9 and H3K27 on a large scale. To determine the location of histone H3, acetyl-H3K9, and acetyl-H3K27 binding sites within the bovine genome, we analyzed the H3-, acetyl-H3K9-, and acetyl-H3K27-enriched binding regions in the proximal promoter within 5 kb upstream, or at the 5' untranslated region (UTR) from the transcriptional start site (TSS), exon, intron, and intergenic regions (defined as regions 25 kb upstream or 10 kb downstream from the TSS). Our analysis indicated that the distribution of histone H3, acetyl-H3K9, and acetyl-H3K27 correlated with transcription activity induced by butyrate. Using the GADEM algorithm, several motifs were generated for each of the ChIP-seq datasets. A de novo search for H3, acetyl-H3K9, and acetyl-H3K27 binding motifs indicated that histone modification (acetylation) at various locations changes the histone H3 binding preferences. Our results reveal that butyrate-induced acetylation in H3K9 and H3K27 changes the sequence-based binding preference of histone H3 and underlies the potential mechanisms of gene expression regulation induced by butyrate.

Phenotypic plasticity and robustness: evolutionary stability theory, gene expression dynamics model, and laboratory experiments

Plasticity and robustness, which are two basic concepts in the evolution of developmental dynamics, are characterized in terms of the variance of phenotype distribution. Plasticity concerns the response of a phenotype against environmental and genetic changes, whereas robustness is the degree of insensitivity against such changes. Note that the sensitivity increases with the variance, and the inverse of the variance works as a measure of the robustness. First, it is found that the response ratio is proportional to the phenotype variance, as described by extending the fluctuation-response relationship in statistical physics. Next, it is shown that through the course of robust evolution, the phenotype variance caused by genetic change decreases in proportion to that by noise during the developmental process. This evolution, resulting in increased robustness, is achieved only when the noise in the developmental process is sufficiently large; in other words, robustness to noise leads to robustness to mutation. For a system that achieves robustness in the phenotype, it is also found that the proportionality between the two variances also holds across different phenotypic traits. These general relationships for plasticity and robustness in terms of fluctuations are demonstrated using macroscopic phenomenological theory, simulations of gene-expression dynamics models with regulation networks, and laboratory selection experiments. It is also shown that an optimal noise level compatibility between robustness and plasticity is achieved to cope with a fluctuating environment.