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Non-neutral synonymous mutations challenges decades of Neo-Darwinian Ka/Ks ratios

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The journal article "The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations" investigates the critical assumption of synonymous neutrality in evolutionary genetics, specifically concerning its impact on inferring the distribution of fitness effects (DFE) of nonsynonymous mutations. Traditional methods rely on synonymous variants as a neutral baseline to estimate demographic parameters, which are then used to model the DFE of nonsynonymous changes. However, evidence suggests that synonymous mutations are not always neutral , potentially affecting downstream analyses. The study employed simulations using SLiM and the DFE inference method Fit∂a∂i to test the robustness of DFE estimations when synonymous sites are under selection. The findings reveal that selection on synonymous mutations can lead to significant biases. Firstly, it results in the incorrect inference of recent population growth during demographic paramete...
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Epigenetics drives Neo-Darwinian Genetic Drift

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The journal article "The adaptive value of epigenetic mutation: Limited in large but high in small peripheral populations" delves into the significant role of epigenetic mutations in shaping adaptation, particularly within the context of peripheral populations. Its findings present a perspective that challenges traditional neo-Darwinian views, especially regarding the influence of genetic drift. Here's a breakdown of the key points and how they relate to the challenge of neo-Darwinian genetic drift: Core Findings: Epigenetic Mutation Rate: The study highlights the significantly higher rate of epigenetic mutations compared to genetic mutations. This rapid turnover offers a more immediate source of phenotypic variation. Peripheral Population Dynamics: It distinguishes between large and small peripheral populations, demonstrating that the impact of epimutations varies considerably between them. Large Peripheral Populations: In these populations,...
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Epigenetics: challenging Genetic Phylogenetics

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The field of genetic phylogenetics, which aims to reconstruct evolutionary relationships between organisms, has historically focused almost exclusively on changes in DNA sequences. However, a growing body of evidence indicates that epigenetic modifications, which alter gene expression without changing the underlying DNA sequence, can also play a significant role in evolution. This realization has led to a recent surge in interest in incorporating epigenetics into phylogenetic analyses. Here's a breakdown of how and why this shift is occurring: Traditional Phylogenetics and its Limitations: DNA-centric view: Traditional phylogenetics relies heavily on comparing DNA sequences to infer evolutionary relationships. The assumption is that changes in these sequences, through mutations, are the primary drivers of evolutionary divergence. This approach has been successful in reconstructing evolutionary trees for many groups of organisms. Neglecting Epigenetics: For a long time, ...
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Evolution By jumps - HGT and Epigenetics leaves Darwin Behind

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The concept of "saltational" changes in evolution, suggesting rapid, large-scale evolutionary shifts, has gained renewed attention with the increasing understanding of horizontal gene transfer (HGT) and epigenetics. Here's a breakdown of how these factors can contribute to evolutionary leaps beyond the gradual changes traditionally associated with evolution: Horizontal Gene Transfer (HGT): A Catalyst for Rapid Change Definition: HGT is the transfer of genetic material between organisms other than through traditional parent-offspring inheritance. This process is particularly prevalent in bacteria but also occurs in other organisms. Impact on adaptation: HGT can introduce entirely new genes and capabilities into an organism's genome in a single event. This can lead to dramatic phenotypic changes, such as antibiotic resistance in bacteria or the acquisition of new metabolic pathways. Such sudden acquisition of new traits can be considered saltatio...
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