Bridging the Genotype and the Phenotype: Towards An Epigenetic Landscape Approach to Evolutionary Systems Biology

  title={Bridging the Genotype and the Phenotype: Towards An Epigenetic Landscape Approach to Evolutionary Systems Biology},
  author={Jose Davila-Velderrain and E. R. Alvarez-Buylla},
Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great extent has been neglected in the study of evolution. What is the relevance of considering this generative process in the study of evolution? How can we study its evolutionary… 

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

A mechanistic understanding of why molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components and that also incorporate the restrictions underlying the genotype to phenotype mapping process.

Dynamic network and epigenetic landscape model of a regulatory core underlying spontaneous immortalization and epithelial carcinogenesis

Interestingly, epigenetic landscape analyses of the uncovered network shows that it recovers the generic time-ordered transitions documented during tumorigenic transformation in vitro of epithelial cells, which strongly correlate with the patterns observed during the progressive pathological description of epithel carcinogenesis in vivo.

Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

It is argued that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions, and the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models is criticized.

Annual Research Review: Anterior Modifiers in the Emergence of Neurodevelopmental Disorders (AMEND)—a systems neuroscience approach to common developmental disorders

The AMEND framework is presented, designed to reframe the field of prospective studies of neurodevelopmental disorders, and proposes conceptual, statistical and methodological approaches to separating markers of early-stage perturbations from later developmental modifiers.

Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs

The results show that Mexican maize phenotypic diversity can be classified in landraces using a small number of genomic markers, given the fact that landrace genomic diversity is influenced by environmental factors as well as artificial selection due to bio-cultural practices.

From 2D cell phenotypes to 3D live high-content imaging: new ways to windows

A possible model for studying "variability windows" and cell phenotype reprogramming using different somatic cell types as well as different cell culture systems - 2D monolayer, 3D single spheroids and microtissues accompanied with up-to-date live time-lapse microscopy analysis.



The inheritance of process: a dynamical systems approach.

It is argued that an explicit treatment of this genotype-phenotype map in terms of dynamical systems theory can provide an integrated understanding of evolution and development, and a conceptual framework is described, which demonstrates how development determines the probability of possible phenotypic transitions-and hence the evolvability of a biological system.

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology?

  • Sui Huang
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2012
The Neo‐Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern

From genes to phenotype: dynamical systems and evolvability

The mathematical properties of the genotype-phenotype mapping function are reviewed, its emerging properties are explored and they are related to the issue of opportunity and constraint in morphological evolution.

Mechanistic Explanations for Restricted Evolutionary Paths That Emerge from Gene Regulatory Networks

This study explores epistasis within GRNs capable of performing a common developmental function – converting a continuous morphogen input into discrete spatial domains and demonstrates that mechanistic constraints are common for GRNs that perform even a simple function.

Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease

Neo-Darwinian evolutionary theory is based on exquisite selection of phenotypes caused by small genetic variations, which is the basis of quantitative trait contribution to phenotype and disease.

Life's attractors : understanding developmental systems through reverse engineering and in silico evolution.

An approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary simulations is proposed, which allows us to characterize the regulatory structure and dynamical repertoire of evolving gene Regulatory networks with a reasonable amount of experimental and computational effort.

Evolutionary Systems Biology

  • O. Soyer
  • Biology
    Advances in Experimental Medicine and Biology
  • 2012
This book discusses how evolutionary systems biology will help understand adaptive landscapes and distributions of mutational effects and building synthetic systems to learn Nature's design principles.

Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape

This model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification and constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development.

Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways

  • Sui Huang
  • Biology
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • 2011
Three perspectives outside the realm of their familiar linear-deterministic view are discussed in qualitative terms: state space, high-dimensionality and heterogeneity, which jointly offer a new vista on stem cell regulation that naturally explains many novel, counterintuitive observations and their inherent inevitability, obviating the need for ad hoc explanations of their existence.