Modern Synthesis Review

The discovery that epimutations spontaneous,heritable changes in DNA methylation act as a fast-ticking molecular clock in plants represents a profound shift in our understanding of evolutionary timescales and inheritance. This "epimutation-clock" provides an unprecedented tool for studying evolutionary divergence over remarkably short periods, a scale largely inaccessible to traditional genetic methods. The core finding is that stochastic changes in DNA methylation at certain cytosine sites, particularly in CG dinucleotides, accumulate at a rate orders of magnitude faster than genetic mutations, yet remain sufficiently stable and neutral to serve as a reliable temporal marker. How Epigenetics Affects the Molecular Clock Epigenetics refers to heritable changes in gene function that occur without a change in the DNA sequence itself. The key epigenetic mechanism in the plant clock is DNA methylation, the addition of a methyl group to a cytosine base. Specifically, th...

The discovery of extensive natural epigenetic variation at a de novo originated gene, specifically the Qua-Quine Starch (QQS) gene in the plant Arabidopsis thaliana, provides compelling evidence for the dynamic role of epigenetics in evolution. This finding challenges the established framework of the Modern Evolutionary Synthesis by demonstrating a source of heritable variation that is not directly tied to changes in the DNA sequence, suggesting a more complex and flexible evolutionary mechanism, particularly for young genes. How Epigenetic Variation Affects the De Novo Gene The study focuses on the QQS gene, which is involved in starch metabolism and is believed to have originated de novo meaning it evolved from previously non-coding DNA relatively recently in the Arabidopsis lineage. The research reveals that the expression of the QQS gene varies significantly across natural Arabidopsis populations. Crucially, this expression variation is negatively correlated with the l...

"How could all of these pieces fall into place through the random processes of mutation, recombination, and neutral drift—or at least enough of these pieces to produce a protogene that was sufficiently useful for selection to take hold? One can imagine a process by which short, simple genes periodically arise de novo, then gradually become more complex over time.” -Darwinian Alchemy De noo gene birth is the process where new genes arise from previously non-coding DNA sequences. These "newborn" genes can code for proteins or function as RNA genes. The exact mechanisms are unclear, but they may involve changes that create open reading frames (ORFs) or transcriptional activation. This process contributes to genetic novelty and can play a role in adaptation. Here are 10 ways in which de novo gene birth by Neo-Darwinism is improbable: De novo gene birth requires a large number of mutations to occur in a specific order. This is because a new gene must be created fr...

The journal article "Phylo-Epigenetics in Phylogeny Analyses and Evolution" delves into the critical, yet often overlooked, role of epigenetic inheritance in shaping evolutionary history and determining phylogenetic relationships. By focusing on a "phylo-epigenetic" approach, the research challenges the strictly gene-centric view of evolution championed by the Modern Synthesis, proposing that heritable non-genetic information significantly contributes to the diversity and evolutionary trajectories of species, particularly in mammals. The Involvement of Epigenetics Epigenetics refers to heritable changes in gene activity and expression that occur without altering the underlying DNA sequence.  These modifications act "on top of" the genetic code, determining which genes are active and which are silent, thereby shaping an organism's phenotype. The article specifically highlights the following mechanisms: DNA Methylation and CpG Dinucleotides ...

Phylogenetics, the study of evolutionary relationships among species, has long relied on comparing genetic sequences to construct evolutionary trees. The core assumption is that genetic mutations accumulate over time, and the more similar the DNA sequences are between two species, the more recently they shared a common ancestor. However, a new field called phyloepigenetics is emerging, which integrates epigenetic data into phylogenetic analysis, offering a more nuanced and potentially more accurate view of evolutionary history. This approach challenges some of the central tenets of the Modern Synthesis, the prevailing framework of evolutionary theory, by highlighting the role of non-genetic inheritance and environmental factors in shaping evolutionary trajectories. How Epigenetics Is Involved Epigenetics refers to heritable changes in gene expression that do not involve alterations to the underlying DNA sequence itself. The most studied epigenetic mechanism is DNA methylati...

The relationship between ontogeny (the development of an individual organism) and phylogeny (the evolutionary history of a species or group) has long been a central topic in biology. Epigenetics, the study of heritable changes in gene expression that don't involve alterations to the DNA sequence, offers a new perspective on this classic relationship. It suggests that environmental factors and an organism's developmental experiences can directly influence the course of development, challenging the core tenets of the Modern Synthesis. How Epigenetics is Involved in Ontogeny and Phylogeny Epigenetics provides a molecular mechanism through which environmental factors can influence an organism's development and, potentially, the development of its lineage. Epigenetics and Ontogeny During an organism's life, its cells, tissues, and organs differentiate from a single cell. This process, known as ontogeny, is meticulously regulated by the epigenome. The epigenome co...