Epigenetic speciation of Cichlids without Darwin

"Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish" and how it challenges neo darwinism.

Introduction

Neo Darwinism is the modern synthesis of Darwinian evolution and Mendelian genetics. It states that evolution is driven by natural selection acting on genetic variation. Genetic variation can arise through mutation, recombination, and gene flow. Natural selection can then act on this variation to favor individuals with traits that are better adapted to their environment.

In recent years, there has been growing evidence that epigenetic variation play a major role in evolution. Epigenetic variation is heritable change in gene expression that does not involve changes in the DNA sequence. It can be caused by environmental factors, such as diet, stress, and exposure to toxins.

One study that has investigated the role of epigenetic variation in speciation is the study of Astatotilapia calliptera, a cichlid fish that lives in crater Lake Masoko in southern Tanzania. This study found that there is extensive genome-wide methylome divergence between two lake ecomorphs of A. calliptera, which diverged approximately 1,000 years ago. The methylome is the pattern of DNA methylation in a cell or organism. DNA methylation is an epigenetic modification that can affect gene expression.

The study also found that the methylome divergence between the two lake ecomorphs is associated with altered transcriptional activity of ecologically relevant genes. For example, the benthic ecomorph, which lives in the deep, oxygen-poor waters of the lake, has reduced expression of genes involved in metabolism and energy production. This is likely an adaptation to the low-energy conditions of the benthic habitat.

Challenges to neodarwinism

The findings of this study challenge neodarwinism in several ways. First, they suggest that epigenetic variation can play a significant role in speciation. This is because epigenetic variation can lead to changes in gene expression that can be heritable, even in the absence of changes to the DNA sequence.

Second, the study suggests that epigenetic variation is different than natural selection variation. This is because the methylome divergence between the two lake ecomorphs is associated with altered transcriptional activity of ecologically relevant genes. This suggests that new epigenetic profiles are best adapted to their environment.

Third, the study suggests that the early stages of speciation can be driven by epigenetic variation. This is because the two lake ecomorphs of A. calliptera diverged only 1,000 years ago, which is a relatively short period of time. This suggests that epigenetic variation can accumulate and lead to speciation in a relatively short period of time.

Conclusion

The findings of this study suggest that epigenetic variation plays a significant role in speciation. This challenges the traditional view of speciation, which is based on the idea that speciation is driven by genetic variation alone. The study also suggests that the early stages of speciation can be driven by epigenetic variation.

This study is just one example of the growing body of evidence that suggests that epigenetic variation plays a role in evolution. As our understanding of epigenetics continues to grow, we are likely to learn more about how epigenetic variation can contribute to speciation and other evolutionary processes.

In addition to the study of A. calliptera, there are many other studies that have found evidence of epigenetic variation in other species. For example, one study found that epigenetic variation is associated with phenotypic differences between two populations of the guppy fish. Epigenetic studies showed how Darwin's finches adapted to new phenotypes.

These findings suggest that epigenetic variation is a widespread phenomenon that can have a significant impact on evolution. As our understanding of epigenetics continues to grow, we are likely to learn more about how epigenetic variation can shape the diversity of life on Earth.

Article Snippets

Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges

we assess the epigenetic basis of diversification during the early stages of speciation

Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago.

Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.

The genomic basis of adaptive phenotypic diversification and speciation has been extensively studied but many questions remain

Recent studies in plants and animals provided initial evidence for a contribution of heritable epigenetic divergence to functional phenotypic

We next examined the genomic localization of DMRs among populations and found promoter regions to be highly enriched in DMRs in all comparisons (greater than twofold enrichment), consistent with their cis-regulatory function

This suggests high methylome conservation between gene bodies of the most closely related populations.

We first noted that genes involved in transcription regulation were highly enriched in DMRs and then identified three further sets of biological processes for the genes enriched in methylome divergence

Notably, methylome divergence in developmental genes was shown previously to account for close to half of all species-specific epigenetic differences among three species part of the Lake Malawi cichlid radiation9

Additionally, regions showing benthic-specific methylome patterns and located in promoters, gene body and intergenic regions were significantly enriched for specific transcription factor binding motifs

This suggests cis-regulatory functions for such population-specific DMRs in development, hematopoiesis and metabolism, possibly correlated with acclimation to the benthic habitat. It is well established that differential methylation in promoter regions might impact the activity of methyl-sensitive transcription factors, therefore resulting in an altered transcriptional landscape21

suggesting an altered transcription factor activity landscape arising from population-specific methylome divergence, further work is needed to decipher the underlying mechanisms.

the role of epigenetics in facilitating rapid transcriptional divergence in the context of the early stages of speciation is currently unknown

methylation levels at promoter regions were significantly negatively correlated with transcriptional activity overall (

Critically, significant changes in transcriptional activity were strongly associated with methylome divergence at promoter regions (

these results suggest significant divergence in epigenetic and transcriptional landscapes affecting erythropoiesis and hemoglobin composition in benthic fish, which may facilitate occupation of anoxic conditions of the benthic habitat.

suggests that epigenetic divergence may have facilitated differences in dietary resource use patterns during colonization of Lake Masoko habitats.

Indeed, tissue-independent methylome divergence could reflect distinct core developmental processes between the populations, participating in early-life phenotypic differences, although methylome analysis of other somatic or embryonic tissues would be needed to further investigate their functions.

These results suggest that although methylome landscapes are highly environment-specific, showing high plasticity and significant association with altered transcriptional activity of functional genes, some methylome divergence has become fixed and may be inherited in populations of Lake Masoko (fixed DMRs

Our study lays the groundwork to investigate further the extent of the inheritance of epigenetic patterns in East African cichlids and assess any adaptive roles associated with methylome divergence

Our results provide direct and new evidence for functional and heritable methylome divergence associated with the early stages of speciation in the very young radiation (approximately 1,000 years ago) of Astatotilapia ecomorphs in Lake Masoko

In principle, therefore, epigenetic processes may provide the capacity for rapid occupation and competitive dominance in new ecological niches before fixation of epigenetic and genomic variation.

To our knowledge, our study demonstrates for the first time substantial methylome divergence, in part inherited, and associated with altered transcription in a very young vertebrate radiation at an unprecedented whole-genome resolution

Additionally, other epigenetic processes might be at play in parallel to DNA methylation in facilitating phenotypic diversification in teleost fish radiation, such as microRNAs1,1

A key challenge now is to determine the mechanisms and rates of fixation of heritable epigenetic variation within populations6,7,44, including epigenetic inheritance and reprograming, the extent of the adaptive advantage associated with methylome divergence, and how this associates with the genomic fixation observed during the later stages of speciation4,5,6,7,8




Comments

Post a Comment

Popular posts from this blog

Beyond the Sequence: The Epigenetic "Fingers" That Play the DNA Keyboard

Image
Imagine the keyboard itself is not a standard piano keyboard, but a modular synthesizer, capable of producing an almost infinite array of sounds. The DNA sequence, then, represents the fundamental building blocks of this synthesizer, the raw materials from which all sounds are generated. Epigenetics, our "fingers," manipulates these building blocks, adjusting parameters like volume, timbre, and rhythm, transforming the raw potential of the DNA sequence into a symphony of cellular functions. We can further refine the "fingers" analogy. Consider that each finger represents a distinct epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA.  DNA methylation, for instance, might be the "index finger," capable of precisely silencing specific genes, like muting individual keys on the synthesizer. Histone modifications, the "middle finger," could represent the ability to adjust the accessibility of the DN...
Read more

Why are Christian philosophers running towards Darwin while biologists are "running" away?

Image
As nature reveals the strength of epigenetics and the weakness of Neo-Darwinism, biologists are “running” away from the long-standing accepted theory. In The Federalist , April 2019, Benjamin Dierker reviews “Why one-third of biologists now question Darwinism”: "Current estimates are that approximately one-third of professional academic biologists who do not believe in intelligent design find Darwin’s Theory inadequate to describe all of the complexity in biology.” Dierker continues, “The important note is that these are not ideologues or religious zealots, nor do they propose a god or biblical solution.  Rather, they find problems in the lack of explanatory power of Darwin’s theory in light of modern understanding of mutation, variation, DNA sequencing and more. These expressions of doubt do not reject naturalism or evolution per se, but the rigor of the Neo-Darwinian model for explaining the development of life.” For 40 years, scientists calculated natural se...
Read more

Rewriting the Rules: Epigenomic Mutation Bias Challenges Randomness in Evolution

Image
This research challenges the long-held dogma that mutations occur randomly, irrespective of their consequences, by demonstrating a clear, epigenome-mediated mutation bias in Arabidopsis thaliana . The study meticulously unveils how mutation rates are not uniform across the genome but are significantly reduced in functionally constrained regions, particularly within gene bodies and essential genes. This discovery fundamentally alters our understanding of evolutionary processes, suggesting that mutation is not a purely directionless force. "Mutation bias reflects natural selection in Arabidopsis thaliana" This opening statement encapsulates the core finding: mutation rates are not random but reflect epigenetic pressures. The authors demonstrate that mutations are less frequent in crucial genomic regions, directly contradicting the prevailing theory of random mutation. This observation suggests an active mechanism that minimizes deleterious mutations in essentia...
Read more