Modern Synthesis Review

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...

Codon usage bias (CUB) is the phenomenon where certain synonymous codons are used more frequently than others to encode the same amino acid. While the genetic code is degenerate, meaning multiple codons can specify a single amino acid (e.g., both GCC and GCA code for alanine), this usage isn't random. A particular organism, or even specific genes within that organism, often shows a preference for a specific synonymous codon. This bias is a universal feature of all genomes, from bacteria to humans, and plays a critical role in gene expression.  Mutational bias refers to a preference for certain nucleotide changes. The presence of abundant tRNAs for a particular codon leads to faster and more accurate protein synthesis, which is especially important for highly expressed genes. Generally, mutational bias, which reflects the inherent biases in the DNA replication and repair machinery, is the primary driver of CUB in organisms with small effective population sizes and in ge...

Biased gene conversion (gBGC) (GC bias) is caused at meiosis or DNA repair above. In it A:T pairs tend to convert to G:C pairs. It accounts for 60% of mutations in organisms. It's caused by the fact that G:C pairs have three hydrogen bonds, not two like A:T pairs. They are more stable. This is a natural, non darwinian,  cellular mechanism. NeoDarwinism posits random, not biased, mutations due to DNA polymerase errors which make up less than 1% of mutations. The symphony of evolution plays out on the grand stage of genomes, with each substitution, insertion, and deletion composing a note in the intricate melody of change. Yet, deciphering this musical score often presents a thorny challenge: distinguishing the clear, resonant chords of positive selection from the subtle hums of background noise, most notably, biased gene conversion (BGC). This essay delves into this captivating scientific tango, advocating for a broadened null hypothesis in molecular evolutio...

Meiotic recombination is a fundamental biological process that shuffles genetic information, creating the genetic diversity essential for evolution. This process is not random; it occurs at "hot spots" and "cold spots" throughout the genome, and recent discoveries have revealed that this non-uniform distribution is heavily influenced by epigenetic. This understanding challenges the core tenets of the Modern Synthesis of evolutionary biology, a 20th-century framework that largely ignored the role of non-genetic inheritance and developmental processes. Meiotic Recombination Hot and Cold Spots Meiotic recombination begins with the formation of DNA double-strand breaks (DSBs), which are intentionally created by the cell's machinery. These breaks are the starting points for the exchange of genetic material between homologous chromosomes. However, the location and frequency of these breaks are not uniform across the genome. Recombination "hot spots...